cord-001274-vz0qvp01	2013	For this study, the L and P1 coding regions for eight FMDV A and nine FMDV O viruses isolated between 1975 and 2003 were successfully sequenced and analysed using phylogenetic analysis, examination of sequence variability, and identification of highly conserved genomic regions relating to previously identified FMDV functional and structural biological capabilities. The sub-Saharan African isolates included in this study belong to different topotypes of FMDV serotypes A and O as defined by 1D sequencing and represent a broad geographical distribution of viruses within East and West Africa. Characterising sequence variation in the VP1 capsid proteins of foot-and-mouth disease virus (serotype O) with the respect to virion structure Sequence analysis of monoclonal antibody resistant mutants of type O foot and mouth disease virus: evidence for the involvement of the three surface exposed capsid proteins in four antigenic sites
cord-003050-n25wnmq5	2018	The 4.2-kb plus-strand sequence of this virus encompasses four main open reading frames (ORFs), as expected for barnaviruses, including ORFs for a protease-containing polyprotein, an RNA-dependent RNA polymerase whose translation appears to rely on − 1 ribosomal frameshifting, and a capsid protein that is likely to be translated from a subgenomic RNA. Based on similar genome sizes, coding organizations, and P2-and P3-region sequence similarities, both MBV and RsBV1 appear to be most closely related to plant viruses in the unassigned genus Sobemovirus [12, 16] . As a result, the consensus sequence for the apparent new barnavirus reported here (GenBank MG686618) is 4206 nt long, appears to be coding complete for ORFs 1-4 ( Fig. 1) , and was newly assembled from a total of 821 individual reads (reads per position: mean, 19; range, 2-35).
cord-004672-0lf5j8lo	1987	In this communication, the structurM proteins of the wfld-ty]pe and mutant, viruses were compared by SDS-PAGE, peptide mapping, and twodimensional gel electrophoresis to determine which of the mutant structural proteins differed from that of wild-type and the extent of homology among analogous proteins. To determine whether the arrangement of the structural proteins on the surface of mutants 205 and 280 was similar to that of wild-type, purified virions were labeled with r25I and analyzed by SDS-PAGE (Fig. 2) . Eight virus-specified intracellular proteins were resolved in wild-type and mutant strain-infected cells: A (1-2 A), B (1), C (3), D (3 CD), 1 ABC, D 2 (1 CD), alpha (1 D), and gamma (1 C). To further examine these viruses for structural differences, surface labeling of intact wild-type and mutant virus particles was done to compare the arrangement of the structural proteins which form the xdral capsids.
cord-004673-c8qcjve9	1996	cDNAs encoding ORF 1a protein segments encompassing transmembrane segments 5 to 11 and its amphipathic C-terminal end as well as the N-terminal 80 amino acids of the downstream ORF 1b protein were transcribed and the transcripts in vitro translated in the absence and presence of microsomal membranes. Eisenberg hydrophobic moment analysis of the protein predicted the presence of eleven transmembrane segments in the C-terminal half of the molecule (amino acids 980-1852) that flank the serine protease domain, cDNAs encoding ORF la protein segments encompassing transmembrane segments 5 to 11 and its amphipathic C-terminal end as well as the N-terminal 80 amino acids of the downstream ORF lb protein were transcribed and the transcripts in vitro translated in the absence and presence of microsomal membranes. In the present study we provide strong evidence that the segment of LDV ORF la protein with transmembrane segments 5-11 (see Fig. 1 ) becomes intimately associated with endoplasmic reticulum (ER) membranes during synthesis and that none of its potential N-glycosylation sites becomes glycosylated.
cord-004680-u3cnsdl8	1991	Four isolates of infectious bronchitis viruses (IBV) from chickens with nephritis, were characterized by polymerase chain reaction (PCR) and restriction enzyme fragment length polymorphism (RFLP), and were found to be genetically different from the other twelve strains which we previously studied. HinfI digested pUC 19 DNA was used as the molecular size markers (3//), and their sizes are indicated in base pairs (bp) on the left In this study, essentially the same procedure was used in an attempt to characterize four IBV isolates F-88, Y-4, M-l, and NI-1 from chickens with nephritis in different endemic areas of Japan between 1988 and 1989. The results of the present study, indicate that the four recently obtained IBV isolates causing nephritis are, by our genetic criteria, similar to each other but different from previous isolates, hence are classified together into a new subtype (group VI). Serological comparisons of strains of infectious bronchitis virus using plaque-purified isolants
cord-004681-02wem2u3	1995	title: Ultrastructure and immuno-cytochemistry of BHK-21 cells infected with a modified Bucyrus strain of equine arteritis virus Morphogenesis of a modified Bucyrus strain of equine arteritis virus (EAV) in BHK-21 cells was studied. Bacillary tubules were first detected in the cytoplasm 8 h after infection, and mature virions 79 to 122 nm in diameter, 101 nm on average, were mostly observed in the cisternae of the rough endoplasmic reticulum (RER) at 12 h or later. Equine arteritis virus (EAV) has been classified into the Togaviridae family [22] on the basis of the virion size and morphology [23] . In the present study a mutant virus showing higher growth on BHK-21 cells than the parental Bucyrus strain of EAV [11] was examined for the fine structure, its morphogenesis and intracellular localization of viral antigen. Through cross-sections of the outer layer of the virion, a grape-like structure seemed to be subunits 13 to 20 nm in diameter around the core (Fig. 3c) .
cord-004685-qote5nx2	1994	The data indicate, among the mechanisms of resistance against the virus infection, a role of IFN gamma macrophage-activation and of antibodies against MHV3 which may delay the mean survival time in susceptible animals. The virus replication in target cells, the antiviral state induced by interferon (IFN) and the expression of a monokine with procoagulant activity (PCA) have been implicated in the resistance/susceptibility of the genetic homogeneous or heterogeneous mouse populations to the MHV3 infection [t, 2, 4, 7, 17, 18, 23, 243 . For the study of the individual correlation between in vivo resistance and in vitro inhibition of virus replication by IFN gamma, peritoneal macrophages from Hm, Lm and F 2 segregants were collected without sacrificing the animals, which were infected with MHV3 a week later. This brings further support to our previous suggestion that one of the main mechanisms involved in the resistance of mice to the MHV3 infection is based on the ability of their macrophages to restrict the virus replication upon IFN gamma activation [10 13, 153 .
cord-004690-q38ogrem	1992	Using a sensitive infant mouse bioassay to detect infectious virus, the pattern of mouse hepatitis virus (MHV) JHM dissemination in blood and other tissues was examined during the first 5 days following intranasal inoculation. Previous studies have shown that both of these mouse strains develop disseminated infections between days 3 and 5 after i.n. inoculation, but virus titers and disease are significantly greater in BALB mice compared to SJL mice [5] . The association of interferon-a/~ with viremia was explored initially by analyzing pooled samples of nasal turbinate, blood, liver, brain, or spleen obtained from 3 mice of each genotype on days 0 (controls), 1, 2, 3, and 4 after i.n. inoculation. In the current study, interferon was found in spleen and serum of MHV-JHM-infected BALB mice, but not nose, liver or brain and was not detectable in any tissue of SJL mice.
cord-004693-1xglujqk	1976	Late in infection large numbers of virus particles were present, mainly in cytoplasmic vacuoles, and the majority were released by cell lysis. Since this mechanism is the reverse of micropinocytosis it was important to establish in which direction the vesicles at the cell surface were moving in order to distinguish outgoing particles from already released progeny virus re-entering the monolayer in a secondary cycle of infection. Virus particles were seen in the process of budding from internal membranes but, unlike strain Beaudette, appeared to form predominantly within pre-existing cytoplasmic vacuoles (Fig. 8) . The method of release of virus particles by fusion of vacuoles with the cell plasma membranes seen in ''T'' strain infected cells appears similar to the process described for coronaviruscs from human respiratory infections (12) .
cord-004694-43yvs52a	2009	A total of 54 single HRV-positive specimens from children hospitalized with acute LRTIs were sequenced after performing RT-PCR based on the 5 0 NCR region. Recently, novel HRV species were identified and their members were reported to be associated with acute respiratory tract infections with febrile wheeze, asthmatic exacerbation, influenza-like illness, pneumonia and rhinitis [10, 13, 14, 17] . An association of members of novel HRV species with severe respiratory tract infections [19, 20] and a global distribution of members of novel species in respiratory specimens have Fig. 1 Phylogenetic tree of clinical viral isolates (n = 54) based on analysis of *285 bp from the 5 0 noncoding region (nt 178-462 of HRV16 L24917). In the present study, phylogenetic analysis of the 5 0 NCR region showed that QPM, HRV-C strain026 and HRV X1 were grouped into the HRV-C species, but 9 strains could not be identified.
cord-004713-gzts5h0y	1985	A pathogenetic study of pleural effusion disease (PED) in rabbits was made, using the virulent PED agent or virus (PEDV) and an avirulent derivate of this isolate. Support for this contention is the enhancement of virulence of PED virus (PEDV) observed in the "natural" disease and --after its isolation --by continued serial propagation in rabbits at intervals of 3---10 days (Fig. 1) . However, there is also evidence which might suggest that increasing time of persistence of virulent virus in the individual rabbit host may operate in the reverse direction by selecting a population of predominantly avirulent PEDV particles, which appear to be unable to cause disease unless undergoing new rabbit passages at short intervals (t, 6). After infection with the avirulent derivate, the isolates from serum obtained during the entire period of viraemia were demonstrable in serum dilution 10 -1 to 10 -a, but the primary rabbit inoculation of these dilutions never resulted in clinical signs of PED.
cord-004717-41ui4lqc	2011	Phylogenetic analysis of the 3 0 end of this strain suggests that a novel and possibly fifth lineage of AstV exists in swine and heightens concerns about the role of pigs as a potential source of emerging astrovirus infections. However, a group of four related sequences revealed only approximately 70% nucleotide identity to bat and human AstV sequences in the database, suggesting that these sequences were divergent from known PoAstV strains and possibly novel. Phylogenetic analysis of these sequences, in addition to prototypical animal AstV strains, confirmed their relatedness and grouped them in a unique lineage on a divergent branch distantly related to other known mamastroviruses (PoAstV 5 in Fig. 2a) . Phylogenetic analysis of the complete capsid coding region of PoAstV CC12 confirms that this strain forms a distinct lineage in the family Mamastroviridae, including previously identified porcine astroviruses from different continents (Fig. 2b ).
cord-004719-3stcx0dd	1993	In several groups of positive-strand RNA viruses, the movement function is provided by the proteins encoded by the so-called triple gene block including two putative small membrane-associated proteins and a putative RNA helicase. It is concluded that classification of movement proteins based on comparison of their amino acid sequences does not correlate with the type of genome nucleic acid or with grouping of viruses based on phylogenetic analysis of replicative proteins or with the virus host range. Limited sequence similarities were observed between i) movement proteins of dianthoviruses and the MIP family of cellular integral membrane proteins, and ii) between movement proteins of bromoviruses and cucumoviruses and M1 protein of influenza viruses which is involved in nuclear export of viral ribonucleoproteins. With representative sequences of plant virus genomes from many groups available, efforts were made to identify regions of similarity between known movement proteins and to predict movement functions for uncharacterized ORFs. Early observations made by this approach have been reviewed previously (e.g.
cord-004720-r6b34tjm	1987	Phosphonoacetic acid (PAA) and monensin were purchased from Sigma, Deisenhofen, Federal Republic of Germany, tunieamycin from Calbiochem, La Jolla, U.S.A. In a typicM experiment for the determination of infected cell DNA synthesis in the presence of monensin, parallel cultures of HFF (5 × 106 cells) were infected by HCMV (MOI of 1) and pulse labelled with att-thymidine (5 ~Ci/ml) during the late phase of the consecutive infectious cycle (28) . To examine whether pretreated cells support, viral replication, confluent serum-starved HFF were exposed to various concentrations of monensin prior to virus infection and subsequently pulse labelled with 3H-thymidine during the interval of expected viral DNA synthesis (28; Fig. 2 A) . This protocol again did not prevent subsequent recovery of viral DNA replication within 48-72 hours after removal, an observation which was based on the comparative anMysis by isopycnie centrifugation in CsC1 of DNA samples from untreated and drug-treated infected cultures labelled during corresponding pulse intervals (Fig. 2 B, w/o and monint) .
cord-004724-llex3yed	1991	Encephalomyocarditis (EMC) virus was isolated from aborted fetuses and lungs of suckling pigs from three Quebec pig farms that experienced outbreaks of reproductive failure in sows and respiratory problems in suckling and post-weaning piglets. Encephalomyocarditis (EMC) virus was isolated from aborted fetuses and lungs of suckling pigs from three Quebec pig farms that experienced outbreaks of reproductive failure in sows and respiratory problems in suckling and post-weaning piglets. Serological evidence of EMC virus infection was reported in Canadian swine herds and associated with sudden death in young piglets and reproductive problems [20, 21] . This report describes the isolation of EMC virus from the tissues of aborted fetuses and post-weaning piglets obtained from three different farms. Necropsied fetuses did not show typical gross and microscopic heart lesions previously reported from experimental and natural infection of newborn piglets with EMC virus [12] [13] [14] . An association between encephalomyocarditis virus infection and reproductive failure in pigs
cord-004727-9sniu39j	1981	
cord-004728-rjl35dpa	1979	After intranasal inoculation of suckling rats mouse hepatitis virus multiplied mostly in the nasal epithelium; though there were no symptoms, antibodies were produced. Bar represents 0.1 mm Two-, 4-, 6-and t0-week-old rats were also inoculated i.n. with t05 PFU of MHV-S and infectious viruses were assayed in the lung, brain, salivary glands and liver. So far only mice have been considered to be natural hosts of MHV and rat; has been excluded because highly virulent MHV inoculated by various routes did not cause any sy~lptomatic infection like that produced in the mouse (7, 13) . B~tATT and his eoworkers showed that SDAV multiplied in mice producing some histopathological changes in the respiratory system after i.n. inoculation (3) and we demonstrated in the w e s e n t paper that 3{HV infected rats of any ages. Pathogenicity of mouse hepatitis virus for mice depending upon host age and route of infection
cord-004729-nmkilkcx	1979	No clinical disease resulted but infectious virus was isolated from faeces for up to 22 days after infection and serum antibody was detected by neutralisation and immunofluorescence tests. No clinical disease resulted but infectious virus was isolated from faeces for up to 22 days after infection and serum antibody was detected by neutralisation and immunofluorescence tests. Control and infected animals were tested for TGEV excretion by attempted isolation of virus from faeces for up to 35 days after infection; occasionally rectal swabs were used to obtain fresh samples. The medium was changed after 24 hours and 4 days later any viral eytopathic effect was recorded, the medium was removed and passaged in fresh APT/2 cultures and the eoverslips were stained to demonstrate virM antigen by indirect immunofluorescence, using paired sera from a gnotobiotic piglet before and after TGEV infection, followed by FITCconjugated rabbit anti-swine globulin (Nordic Immunological Laboratories, London).
cord-004732-mgzmzeyr	1983	
cord-004733-i0a3igc7	1992	
cord-004738-vnz15x84	2006	To evaluate the trans-cleavage activity of RV protease on P200-derived substrates, a series of RV P200-related polypeptide expression plasmids that express protein with different N-terminal lengths from the cleavage site (72, 199, 309, and 475 residues) were constructed. To test whether replacement of P200-related sequences C-terminal to the cleavage site by non-rubella sequences affect RV protease trans-activity, the plasmid pRVS-GFP, which contains PCR-amplified RV protease substrate sequences representing polypeptide residues 827-1306 (residues 1302-1306 represent the C-terminal side of the cleavage site), fused at its C-terminus to GFP ORF in-frame, was created (Fig. 1B) . Similarly, to test whether a heterologous sequence on the N-terminal side of the cleavage site affects substrate recognition by the protease trans-activity, GFP ORF was fused in-frame at the N-terminus of the rubella sequence in the plasmid pRVS-1102-1548 to create pRVS-GFP-1102-1548 (Fig. 1B) . In this report, we have shown that RV protease trans-activity demonstrates substrate specificity by requiring an internal sequence within the region that is N-terminal to the cleavage site.
cord-004742-5movyeb4	1993	
cord-004743-ido065mh	1979	authors: Nagy, Éva; Lomniczi, B. title: Polypeptide patterns of infectious bronchitis virus serotypes fall into two categories Molecular weights of six major polypeptides of infectious bronchitis virus (IBV) are: 1. All IBV strains examined showed one of two protein patterns with polypeptides having apparent molecular weights in the range of 20,000 and 110,000 dalton (Fig. 1) . Pattern M (named after Massachusetts) includes strains from two serotypes, Massachusetts and Georgia (SE 17), and here the "broad" protein has an apparent molecular weight of 28,000 dalton. Pattern C (named after Connecticut) is characterized by a smaller "broad" protein of an apparent molecular weight of 24,000 dalton, and includes the five remaining serotypes studied: Connecticut, Delaware (Gray), Iowa 97, Iowa 609 and Australia T.
cord-004749-wyzb8v4a	1989	
cord-004754-5596p4ma	2014	title: Effects of origin and state of differentiation and activation of monocytes/macrophages on their susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) To evaluate the effect of maturation of monocytes/macrophages on their susceptibility to PRRSV, freshly isolated AMf, PMf and BMo from ®ve donors were seeded in 24-well tissue culture plates at a concentration of 10 6 cells/ml/well and further incubated in RPMI medium plus 5% of foetal bovine serum at 37 C with 5% CO 2 . The virus titres and percentage of viral antigen positive cells in freshly isolated porcine AMf at 24 and 48 h after inoculation were respectively 1 to 2 log 10 TCID 50 and 5 to 10 times lower than those of one day cultivated ones, which is signi®cantly different (P''0.01). Porcine reproductive and respiratory syndrome virus infection of alveolar macrophages can be blocked by monoclonal antibodies against cell surface surface antigens
cord-004755-rmnjs1t6	1988	Twelve hybridomas secreting monoclonal antibodies (MAbs) against Miller virulent strain of transmissible gastroenteritis virus (TGEV) were generated and characterized. Two E 2-specific MAbs had higher neutralizing antibody titers (782 to 34,117) and showed 4-to 13-fold differences in titers against the attenuated and virulent TGEV strains. Two E 2-specific MAbs had higher neutralizing antibody titers (782 to 34,117) and showed 4-to 13-fold differences in titers against the attenuated and virulent TGEV strains. In two previous studies, monoclonal antibodies (MAbs) to the structural proteins of the attenuated (Purdue) strain of TGEV were described [9, 12] . These MAbs were further characterized in various comparative assays including cell culture immunofluorescence, virus neutralization, and radioimmunoprecipitation for reactivity against the Miller virulent and Purdue attenuated strains of TGEV. Anti-E 1 MAbs prepared against a mixture of virulent Miller 3 and Purdue attenuated strains of TGEV had virus neutralizing antibody titers only in the presence of guinea pig, rabbit or swine complement [22] .
cord-004759-jozdnhgy	1979	Experimental infection of 2-day-old gnotobiotic lambs with lamb astrovirus produced mild diarrhoea after an incubation period of about 48 hours. Astrovirus was not observed in faeces from the lambs killed t4 and 23 hours p.i., but was first seen in the faeces of all other infected lambs between 38 and 48 hours p.i. At necropsy, astrovirus was detected in intestinal contents of all Iambs except that killed 14 hours p.i. The control lambs remained clinically normal, and passed firm brown faeces throughout the duration of the experiment. Specific immunofluorescent staining was detected only in scattered epithelial and subepithelial cells on small intestinal villi (Fig. 1) . Lactase levels in the 6 control lambs were ¢.5±0.5, 5.14-0.6, and 2.44-1.2 units/g tissue for the proximal, mid, and distal small intestinal sites respectively. In midgut of infected lambs, observations were consistently below those of the controls, fMling to a minimum of 1.2 units/g tissue at 23 hours p.i.
cord-004764-tmvebf23	1982	In addition to this disorder another CNS disease (subaeute selerosing panencephalitis --SSPE) has been associated with measles virus infection (1--3) . As the methods employed in these previous studies could only detect gross differences in virus-specific products, or examined one protein or ~ small p a r t thereof, we have chosen in this study to analyse the oligonncteotides from a T1 digest of the complete genome. purification scheme is hybridized to unlabelled messenger R N A from infected cells (Table 1) , it can be shown t h a t at, least 85 per cent, is protected from subsequent nuclease digestion and is thus assumed to be negative stranded. In order to compare the genomes of various measles isolates: unlabelled, single stranded, negative sense nueleocapsid I~NA was prepared from infected cell cytoplasm and purified in parallel with similar radio-labelled material as described in the previous section. 85 per cent measles-specific negative sense R N A b y hybridization to infected cell messenger I~NA.
cord-004765-7e4yu2do	1992	Maternally-derived antibody to enterotropic mouse hepatitis virus (MHV) strain Y was transferred to pups by both intrauterine (IgG) and lactogenic (IgA and IgG) routes. MHV-IgG, but not IgA or IgM, could be found in the serum of pups suckling immune dams. Stomach contents of pups suckling immune dams yielded constant IgG titers and gradually declining IgA titers up to the age of 14 days, but neither isotype of MHV antibody was detected at or beyond 21 days (Table 3 ). Pups from three consecutive litters born to immune and naive dams were exsanguated at 2, 4, 6, 8, and 10 weeks of age and sera were tested for MHV-specific IgG. Antibodies persisted for 4 weeks in pups born to dams with low MHV IgG serum titers and then declined to undetectable levels.
cord-004766-gvom0f13	1977	A remarkable increase in HA titers for weakly haemagglutinating Norwegian arbovirus strains, Uukuniemi and Runde viruses, was achieved by including treatment with the colloidal silica gel Aerosil in the antigen preparation scheme. Good antigens also were obtained from virus grown in BHK 21/c 13 cell cultures and concentrated by polyethylene glycol 6000/NaCl. Rubella virus HA antigen and HB(s)Ag were adsorbed to the gel, and excluded from a preparation by treatment with Aerosil. For production of arbovirus haemagglutinating (HA) antigens, the classical sucrose-aeeton extraction method (SA) (3) with infected suckling mouse brains has been almost undisputed, although methods based on infected cell culture fluids (2, 12) and infected mouse aseites fluids (8) have also been reported. Infected brain suspensions and PEG treated cell culture concentrates were titrated by intraeerebral inoculation in suckling mice after Aerosil absorption, incubation with shaking in waterbath at 45 ° C and untreated. Simple method for preparation of haemagglutinating arbo-A virus antigens from brains of suckling mice
cord-004769-hhge62sl	1992	title: Partial DNA cloning and sequencing of a canine parvovirus vaccine strain: application of nucleic acid hybridization to the diagnosis of canine parvovirus disease The cloning and sequencing of anEco RI-Pst I fragment derived from the replicative form of a canine parvovirus (CPV) vaccine strain are reported. In order to improve CPV diagnosis, radioactively labelled RNA or DNA and biotin labelled DNA obtained by random priming of the recombinant plasmid were used as probes mainly on gut or stool samples from naturally infected dogs. Results of filter hybridization correlated well with histopathological diagnosis of parvovirus infection and with hemagglutination tests performed on dog faeces. To elucidate whether the deletion observed was originally in the vaccine or was generated by cell culture passages in our laboratory, DNA sequence was determined on CPV-b 108 after PCR amplification of a 1000 bp fragment including the deleted region and the two H i n d I I I restriction sites (Fig. 1) .
cord-004774-fvf671jn	1985	Gut contents of nude and normal mice were examined by electron microscopy in association with an outbreak of diarrhea in a colony of nude mice. Gut contents of nude and normal mice were examined by electron microscopy in association with an outbreak of diarrhea in a colony of nude mice. Virus-like particles with a morphology consistent with previous descriptions of astroviruses of other species were demonstrated in a high percentage of the animals. Virus-like particles with a morphology consistent with previous descriptions of astroviruses of other species were demonstrated in a high percentage of the animals. In this note we report the detection of astrovirus-like partieles in gut contents from nude mice, with and without clinical signs of illness, and from normal symptomless mice in association with an outbreak of diarrhea. The morphology of the virus-like particles detected in gut contents of nude and normal mice corresponds to the previous description of astroviruses.
cord-004775-foaf3vyl	1987	A morphologically similar virus (Lyon 4 virus) detected in cattle in Lyon, France (6, 7) , was shown later to possess an antigenic relatedness to the Berne (BEV) and Breda (BRV) viruses. In thin sections through BEV infected cells (horse kidney, embryonic mule skin, equine dermal cells) densely staining spherical, elliptieM and elongated particles were detected (2, 9) . Thin sections through BRV infected intestinal cells of calves (10, 11, 12) showed elongated viral particles with rounded ends measuring 42 × 100.5 nm. The high molecular weight virion protein in the range of 75-100 kD of BEV is glycosylated, probably by N-linked oligosaccharides since tunicamycin, an antibiotic known to inhibit N-linked oligosaccharide synthesis, prevented the formation of infectious virus as well as appearance of the 75-100 kD band in PAGE of infected cells (20) . Evidence of a reaction of the particles in human feces with sera containing antibodies against BRV and BEV, respectively, were obtained in IEM (8), (Flewett personal communication).
cord-004778-xrv0qs6n	1986	The Smith strain of mouse cytomegalovirus (MCMV) was infectious for infant and mature DA strain laboratory rats as judged by development of neutralizing antibodies and specific spleen cell proliferation on stimulation with MCMV antigen. In the following report, we describe a transient, effect of MCMV infections on rat T lymphoc~ helper/suppressor cell ratios and on spleen cell proliferation following stimulation with mitogens and MCMY antigen. Seven days after MCMV infection, a consistently greater proliferation of spleen cells from MCMV infected rats as compared to control animMs was seen with M1 mitogens and also in unstimulated background cultures (Table 2 and Fig. 1 and 2 ). P. route for infants and adults of three strains of laboratory rats as judged by virus isolation, neutralizing antibody response and development of a high level of spleen cell reactivity to MCMV antigen.
cord-004781-ajf9zig0	2014	Primary cultures of murine, feline, and human microglia and astrocytes were infected with several different rabies viruses: two unpassaged street virus isolates, a cell culture-adapted strain, and a mouse brain-passaged strain. Primary cultures of murine, feline, and human microglia and astrocytes were infected with several different rabies viruses: two unpassaged street virus isolates, a cell culture-adapted strain, and a mouse brain-passaged strain. In addition, a number of studies have reported rabies viral antigens and virions in human [1, 13, 29] and murine astrocytes [10, 18, 23] , and in murine rami®ed microglial cells [27] , begging the question of the role of these cells in viral replication and persistence, as well as pathogenesis. In the present study, as an initial step toward evaluation of the potential involvement of these glial cells in rabies virus infections, we have directly examined the ability of different rabies virus strains and isolates to infect and replicate in primary cultures of microglia and astrocytes.
cord-004790-69lry0ys	1986	The source of these discrepancies is not immediately apparent; however, our results may explain why seroconversion to mouse adenovirus is not observed among mice thought to be infected with the virus. Finally, we provide serologic evidence that an outbreak of disease in a mouse breeding colony which sustained high infant mortality was associated with the introduction of a mouse adenovirus strain closely related to MAd-K 87. Sera from mice housed in two intramural, barrier-maintained facilities were Mso free of antibody to MAd. Only three mouse sera ofl61 which were tested reacted by IFA with MAd bivalent antigen. (19) for growth of MAd-FL in primary mouse kidney cultures, we have found that the majority of infectious progeny virions (between 90 and 99 percent) are released fl~om infected L 929 or CMT-93 cells. We have provided serologic evidence linking an outbreak of clinical disease in a breeding colony of mice to infection with MAd-K 87 or a very closely related virus.
cord-004793-6yh36r0w	1990	Previous studies have shown that replication in vitro of the porcine parvovirus (PPV) isolate, KBSH, was restricted at 39°C but not at 37°C. In this study, Kresse and KBSH isolates were passaged up to ten times in swine testicle (ST) cells at non-permissive temperatures, and at subsequent passage viral protein synthesis, viral DNA synthesis, and progeny virus were evaluated. Kresse and KBSH isolates were serially passaged at non-permissive temperatures in an attempt to evaluate the effect of in vitro passages on the pattern of virus replication. KBSH appeared to gain the ability to replicate in swine fetuses following serial cell culture passages at 39 °C evidenced by fetal death and virus detection in fetal tissues. Furthermore, KBSH isolate passaged at 39 °C for 10 times now showed the ability to replicate in swine fetuses, indicating that pathogenicity can be recovered by serial adaptation at the mean body temperature of pigs, 39 °C.
cord-004798-5budstbg	1976	Plaque assay in DBT cells with DEAE-dextran and trypsin presents a titration system for MHV3 as sensitive as the LD(50) assay in mice. In DBT cells overlaid with ME)/I containing 1 per cent Noble agar, 5 per cent CS, 10 per cent TPB, and 1 : 10,000 neutral red, MHV3-plaques of 0.6--1.4 mm (mean value = 0.9 ram) in diameter could be counted at 40 hours p.i. The plaques were clearly-defined and sometimes contained a deeply-stained area at their center. To ira.prove the sensitivity of the plaque assay we examined the effect of diethylaminoethyl-dextran (DEAE-D) on the plaque formation and plaque diameter of MHV3, as BRADBUllNE and TYRREL]5 had reported that DEAE-D added to overlay agar increased the plaque number of human coronavirus (2). 1%eplication and plaque formation of mouse hepatitis virus (MttV-2) in mouse cell line DBT culture
cord-004802-rhkrmftn	1982	Replication of the virus in cell culture was found to be less dependent upon trypsin than that of human, bovine and porcine rotaviruses. Reproducible, sharp-edged plaques of various sizes were produced by the canine rotavirus in an established cell line of fetal rhesus monkey kidney, MA104, under overlays of carboxymethyl cellulose or agarose. By plaque reduction neutralization assay, a two-way antigenic relationship was found between the canine (CU-1) and simian (rhesus MMU 18006 and SA-11) rotaviruses. Although canine rotavirus readily replicated and produced CPE in monolayer cultures of MA104 cells in the absence of trypsin, detectable plaques were not formed even 8 D P I under the overlays of CMC or agarose without trypsin. Since both IFT and CFT detect only group-specific antibodies, and rotaviruses from one species can infect another species (5, 8, 34, 36, 46, 50, 51, 52, 55) , it was not clear from these studies whether the antibodies in the dogs resulted from infection with distinctly canine rotavirus or with human or some other rotavirus.
cord-004808-6w9n03fy	1995	title: Detection of equine arteritis virus (EAV) by polymerase chain reaction (PCR) and differentiation of EAV strains by restriction enzyme analysis of PCR products A polymerase chain reaction (PCR) based assay capable of detecting and differentiating seven strains of equine arteritis virus (EAV) from around the world was developed. A potymerase chain reaction (PCR) based assay capable of detecting and differentiating seven strains of equine arteritis virus (EAV) from around the world was developed. Viral RNA from cell culture fluids infected with each of the seven EAV strains and RNA from the live vaccine, Arvac, was detected by PCR using four sets of primers. The objective of this study was to detect each of the EAV strains using PCR, and to differentiate the strains through restriction enzyme analysis of their PCR products, based on the M protein nucleotide sequence data of the strains, together with those of the Bucyrus [7] and modified Bucyrus strain [251.
cord-004810-g0y7ied0	2003	The S1 glycoprotein gene of IBV isolates were amplified by reverse transcriptase – polymerase chain reaction (RT-PCR) and analyzed by restriction fragment length polymorphism (RFLP) analysis. And these IBV isolates showed different patterns from each other and non-Korean IBV isolates in reverse transcriptase-polymerase chain reaction-restriction fragment length polymorphism (RT-PCR-RFLP) analysis [29] . Amplified S1 genes were first classified by RFLP analysis and then the representative strains were cloned, sequenced and compared to other non-Korean published IBV sequences. Phylogenetic trees were constructed from the nucleotide and deduced amino acid sequences of the S1 glycoprotein genes of Korean IBV isolates and non-Korean IBV strains (Fig. 3) . Korean IBV K281-01 and K210-02 isolates formed distinct clusters that were related to non-Korean IBV Ark99, Ark DPI, Gray and JMK strains although K281-01 and K210-02 isolates were classified into the Arkansas type by PCR-RFLP analysis.
cord-004812-ikco4h5k	1997	title: Identification of amino acids involved in a serotype and neutralization specific epitope with in the s1 subunit of avian infectious bronchitis virus We identified amino acids involved in a serotype specific, conformationally dependent epitope by analysis of the S1 gene of 13 monoclonal antibody-neutralization-resistant mutants. However, based on data obtained using monoclonal antibodies (Mab), there appears to be at least three to ®ve neutralizing, conformationally dependent epitopes on the S1 subunit in different IBV strains [13, 15, 20] . Mab-neutralization-resistant (NR) mutants have been used to identify amino acids (AA) involved in conformationally dependent epitopes in the spike protein of IBV [5, 12] . Based on AA substitutions in Mab-NR mutants, the S1 subunit was divided into three regions associated with neutralizing, conformationally dependent epitopes. In previous research, AA substitutions in IBV Mab-NR mutants were divided into three regions associated with neutralizing epitopes.
cord-004825-cdvnqfjz	1994	The entry mechanism of Junin virus (JV) into Vero cells was studied analyzing the effect of lysosomotropic compounds and acid pH on JV infection. Vero cells grown in coverslips were infected with JV (moi 1) and 15 mM ammonium chloride was added to the culture medium after adsorption. To reinforce that the membrane fusion activity of Junin virus is expressed at low pH, the formation of JV-induced syncytia in infected Vero cells incubated in medium at pH 5.5 or 7.5 was quantitated. In fact, a bypass of the ammonium chloride block of JV infection was achieved when the extracellular medium was at a pH below 6.1 (Fig. 5) , suggesting that the acidic conditions would probably trigger direct fusion of virus envelope with the cell membrane.
cord-004827-bnf3mvaf	2005	Phylogenetic relationships have been found useful for virus identification, work on origin, speed and mechanisms of evolution, taxonomy, and the elucidation of transmission pathways (e.g. the transmission of HIV from a source to a victim [16] ). In vitro, a single round of replication of HIV-1 in T lymphocytes generated on average 9 recombination events per virus [14] . Approximately 50% of sequence changes are consistent with evolution by point mutations; other changes are due to multiple recombination events. After an introduction in which basic genetic terms were defined (mutation and mutation rate, hypermutation, recombination, reassortment, segmentation etc), the quasispecies concept was presented according to which any sample of an RNA virus represents a ''swarm'' of closely related mutants. ''To maintain RNA structure, evolution selects against better alternatives elsewhere in the genome''. The aim of the talk was to show the significance of RNA structural considerations for the evolution of viruses. Plant RNA virus evolution
cord-004831-lu62noak	1987	title: A novel method for the detection of early events in cell-cell fusion of Semliki Forest virus infected cells growing in monolayer cultures Furthermore, it was shown that potassium cyanide, a potent inhibitor of polykaryon formation in the described system, inhibits an early step of membrane-membrane fusion of neighbouring cells. Furthermore, we show that potassium cyanide, a potent inhibitor of SFV induced polykaryon formation (4) acts at an early stage in the fusion process. The aim of this investigation was to clarify the early events in cell-cell fusion and the action of potassium cyanide an inhibitor of oxidative phosphorylation-which inhibits SFV-induced polykaryon formation [4] -on the fusion process. That this assumption holds true is depicted in Fig. 1A where a single, SFV infected cell was injected with Lucifer yellow 5 minutes after exposure to pH 6. Therefore, it can be concluded that potassium cyanide inhibits SFV-induced polykaryon formation at the level of membrane-membrane fusion.
cord-004838-cdas57cx	1995	title: Sequence analysis of open reading frames (ORFs) 2 to 4 of a U.S. isolate of porcine reproductive and respiratory syndrome virus The sequence of ORFs 2 to 4 of a U.S. isolate of porcine reproductive and respiratory syndrome virus (PRRSV), ATCC VR2385, was determined by analysis of a cDNA λ library. No overlap was found between ORFs 4 and 5, and instead there was a 10 bp sequence which separated these two ORFs. The nucleic acid homology with corresponding ORFs of the European PRRSV isolate Lelystad virus (LV) was 65% for ORF 2, 64% for ORF 3 and 66% for ORF 4. Cloning, expression, and sequence analysis of the ORF 4 gene of porcine reproductive and respiratory syndrome virus MN-lb Molecular cloning and nucleotide sequencing of the 3''-terminal genomic RNA of porcine reproductive and respiratory syndrome virus
cord-004840-4rbrzv5o	2013	title: Development of real-time RT-PCR for detection of human metapneumovirus and genetic analysis of circulating strains (2009-2011) in Pune, India This study describes the development of real time RT-PCR assay for the detection of all four HMPV lineages (A1, A2, B1, B2) in respiratory specimens and genotyping of circulating strains from July 2009 to August 2011 in Pune, western India. [24] designed two sets of primers and probes within the nucleoprotein gene to detect all known genetic lineages of HMPV in a one-step real-time RT-PCR. We have designed a primer-probe set using conserved regions of the nucleoprotein gene to detect all known genetic lineages of HMPV in a one-step real-time RT-PCR. Detection of human metapneumovirus RNA sequences in nasopharyngeal aspirates of young French children with acute bronchiolitis by real-time reverse transcriptase PCR and phylogenetic analysis
cord-004848-2cfphi88	1990	In this way these workers have identified three intracellular RNAs (4.8, 4.2, and 2.4 kb) as well as the genome (8.2 kb) and shown that these form a nested set of 3'' co-terminal molecules similar to that observed in coronavirus infected cells. We have used this to probe FCV-infected cells for the synthesis of virus specific RNA and confirm and extend the observations of Neill and Mengeling. Subcloning of the virus 3'' end into a single stranded vector has allowed us to examine the occurrence of positive and negative sense RNA separately. Finally this inference was confirmed by subcloning the terminal EcoRI/PstI fragment into M13 and determining its sequence (Fig. 3a) , This showed a poly A stretch preceded by a short run ofpoly C which is exactly that structure expected for cDNA clones derived by this method from an mRNA 3'' end. However, the negative strand-specific probe also showed hybridization to subgenomic messages 2-4, but this was not observed until later in infection than the detection of the positive forms of these molecules.
cord-004849-d64hnqkh	1989	The replication of four porcine parvovirus isolates, NADL-8, NADL-2, KBSH, and Kresse, in swine testes cells were compared at temperatures of 32, 37, and 39 °C. Similar patterns of cell associated virus were detected from both NADL-8 and NADL-2 infected ceils at the 3 temperatures (Fig. 2 a, b) , whereas marked differences were again observed for Kresse and KBSH-infected cells (Fig. 2 c, d) . Since marked differences in replication of Kresse and KBSH isolates were observed at 37 and 39°C evidenced by both intracellular and extracellular infectious virus and HA antigen, further characterization of viral polypeptide production was attempted. Temperature dependent differences in the number and quantity of viral polypeptides were observed in cells infected with Kresse and KBSH and propagated at either 32, 37 or 39 °C (Fig. 3 A) . To further examine the mechanism of temperature-dependent replication of PPV isolates, the synthesis of viral D N A was evaluated by nucleic acid hybridization of cell extracts (Fig. 4) .
cord-004851-h9ppa064	1991	The viral proteins have not been identified, but on the basis of the predicted amino acid sequences, hydrophobicity plots, location of potential glycosylation sites and similarities of these properties to those of pestiand flaviviruses, the following genome organization has been predicted. A recent study of stored blood samples from prospective studies of 15 U.S.A. patients with transfusion-associated chronic hepatitis documented by liver biopsies indicated that the time course of changes in plasma ALT activity and of the formation of anti-HepCV antibodies can vary considerably between patients [4] . The putative nucleocapsid protein sequence derived from PCR products of RNA extracted from healthy Japanese carrier plasma exhibited a 97.4% amino acid identity with the sequence determined for the original chimpanzee HepCV isolate (HepCV-1) but only a 90.5 % identity at the nucleotide level [45] [46] [47] .
cord-006106-u5npu6ng	2002	
cord-006459-9kizif98	2009	Clinical signs, pathological changes and viral replication in lungs, arterial blood gas, and cytokines in bronchoalveolar lavage fluid (BALF) were observed at different time points after infection. Our data show that H9N2 viral infection resulted in ARDS in mice, and this may facilitate studies of the pathogenesis of future potential H9N2 disease in humans. Arterial blood gas, white blood cell counts, tumor necrosis factor (TNF)-a and interleukin (IL)-6 levels in bronchoalveolar lavage fluid (BALF), and viral titers in the lungs were measured at different times. In H9N2-virus-infected mice, we observed that circulating leukocytes dramatically decreased in the blood and that a great number of inflammatory cells infiltrated the lungs. Acute respiratory distress syndrome induced by avian influenza A (H5N1) virus in mice
cord-006674-ywzpwlrb	1992	When the activity of xanthine oxidase (XO) in lung tissue homogenates was measured, the activity was found to significantly increase after intranasal infection with MCMV irrespective of CP administration and there was a good correlation between the elevation of XO activity and the degree of pathological changes in the lung. Furthermore, recent studies have shown that the enhanced production of superoxide radicals by xanthine oxidase (XO) plays a key role in the pathogenesis of influenza virus-induced pulmonary infection [1, 193. In this study, we have established a model of murine cytomegalovirus (MCMV) pneumonitis in ICR mice, measured XO activity in tung tissues, and evaluated the effect of superoxide dismutase (SOD) and allopurinol in this model. Although the precise role of superoxide radicals in the pathogenesis of MCMV pneumonitis is still unknown, such a process seems to be involved in the formation of pulmonary lesions in MCMV-infected mice.
cord-010900-2ie1v1wy	2020	
cord-011105-or9azf1g	2020	title: Full-genome sequences of GII.13[P21] recombinant norovirus strains from an outbreak in Changsha, China Further, we determined the full-genome sequences of two strains of GII.13[P21] recombinant noroviruses, which were 7434 nt long. Although those genotypes have not caused severe outbreaks, studying these strains has helped us to obtain more information on the genetic diversity and gene constellation of noroviruses. Hence, we determined the genome sequences of GII.13[P21] recombinant strains isolated in the city of Changsha, China. Although the sporadic norovirus genotypes do not cause serious epidemic worldwide, unlike GII.2[P16] and GII.4[P4], due to these special binding sites, human infections are associated with severe vomiting and diarrhea. Although only a few samples were collected in this outbreak, we obtained the full genome of GII.13[P21] recombinant strains that have rarely been reported in China. Full-genomic analysis of a human norovirus recombinant GII.12/13 novel strain isolated from South Korea Full-genome sequence analysis of an uncommon norovirus genotype, GII.21, from South Korea
cord-012032-zolowuhj	2020	To further examine the antiviral effects, another murine macrophage cell line, J774A.1, was used, and a similar inhibitory effect of 2''-FdC on MNV-1 replication was observed, with decreased viral RNA and NS1/2 protein expression ( Supplementary Fig. 1 ). As shown in Fig. 3D and E, the viral NS1/2 protein expression and viral titers were further decreased when the antivirals were used in combination, supporting the synergistic antiviral effects of 2''-FdC with MPA, ribavirin, or T705 against MNV replication. The combined effect of 2''-FdC and ribavirin on viral replication was analyzed using a qRT-PCR assay (n = 2-4) and mathematical modeling using MacSynergy. RAW264.7 cells were infected with MNV-1 at an MOI of 1 for 1 h and then left untreated or treated with 2''-FdC and MPA, ribavirin, or T705 at the indicated concentrations for 20 h, alone or in combination.
cord-026518-xv03vpji	2020	An additional 52 14-day-old SPF chickens were randomly divided into four equal groups (N = 13) to investigate the effect of chIL-12 used as an adjuvant to the F gene DNA vaccine. Two weeks after booster vaccination, the birds were challenged with NDV and mortality for 14 days was evaluated the two delivery methods might induce different immune responses in chickens. Oladele and colleagues constructed a DNA vaccine based on the HA gene of H5N1 avian influenza virus and found that EP delivery could enhance the antibody response, significantly reduce morbidity, and protect chickens from fatal NDV attack [25] . However, although all of the chickens in the pCAG-F/EP group survived, they did not all have detectable neutralizing antibodies, indicating that antibodies may not be essential for protection and that cell mediated immunity might play an important role in plasmid DNA-induced protection against NDV challenge.
cord-029775-mntcor5d	2020	For the initial reactivity test, double-stranded DNA fragments (gBlocks® Gene Fragments) including the sequence targeted by the PCR primers (approximately 1700 bp each) of the human sapovirus genotypes GI.1 (GenBank accession number X86560), GI.2 (AB614356), GI.3 (AB623037), GI.4 (AJ606693), GI.5 (DQ366345), GI.6 (AJ606694), GI.7 (AB522390), GII.1 (AJ249939), GII.2 (AY237420), GII.3 (AB630068), GII.4 (AB522397), GII.5 (LC190463), GII.6 (AY646855), GII.7 (AB630067), GII.8 (KX894315), GIV.1 (DQ058829), GV.1 (DQ366344), and GV.2 (AB775659) were synthesized (Integrated DNA Technologies, Coralville, IA), and 1.0 × 10 4 copies of these fragments were used. The target regions of HuSaV-F1, -F2, and -F3 recently designed as forward primers in a broadly reactive real-time PCR for human sapoviruses [11] are similar to those of SV-F13 and SV-F14 (Fig. 2) , and the sapovirus-specific sequence of M13R-HuSaV5498R (5′-CCCCANCCNGCVHACAT-3′) ( [11] are shown in parentheses. The assay including two primers (M13F-HuSaV-5159F and M13R-HuSaV-5498R) generated similar-sized PCR products (approximately 380 bp) for all of the sapovirus genotypes tested (Fig. 1A, right panel, and Fig. 1B) .
cord-032801-b2ncmkjg	2020	It was discovered that enriched GO terms (such as histone acetylation and positive regulation of phosphorylation) and pathways (such as glycosylphosphatidylinositol (GPI)-anchor biosynthesis and DNA replication) might be closely associated with the pathogenic mechanism of these two viruses, and key genes (such as TBCK and GPC) might be involved in the progression of HFMD. In the current study, we aimed to discover significant differentially expressed genes in EV-A71-and CV-A16-infected respiratory epithelial cells through transcriptome sequencing. For example, transcriptome analysis revealed differentially expressed genes, including SCARB2, miR-3605-5p, and enriched ECM-receptor interaction and circadian rhythm pathways involved in the pathogenesis of HFMD in CV-A16-infected HEK 293T cells [9] . These 111 common differentially expressed genes were used to perform hierarchical cluster analysis, and the heatmap result showed that these genes were mainly clustered into two categories-either significantly upregulated or significantly downregulated, suggesting that EV-A71 and CV-A16 infections result in largely similar transcriptome-level changes.
cord-048485-b8xb1f12	2008	RNA pools prepared from two infected piglets were used to compare whole mucosal gene expression at 12 and 18 hpi to expression in uninfected germ-free piglets (n = 3) using a porcine intestinal cDNA microarray. However, the fluorescence intensity was not higher than the background threshold for any of these probes, indicating that mRNA concentrations of these cytokines (including IFN-c) in infected and uninfected mucosal scrapings were too low to detect by microarray analysis, probably due to the relatively low percentage of cytokine-producing (immune) cells present in intestinal mucosa [6] . Using microarray analysis, we detected a set of genes that are differently expressed in rotavirus-infected jejunal mucosa compared to uninfected mucosa. Perhaps, enhanced expression of a PLA2-inh in our study may be a countermeasure of specific intestinal epithelial cells to normalize and/or inhibit PLA2 enzyme activity in response to extra-and intracellular changes in [Ca 2+ ] evoked by rotavirus replication, either to protect specific cells from extra-and intracellular membrane-damage or to negatively regulate A-acid production.
cord-252037-rj61mzqj	2005	In this study, we examined: i) the circulation rate of hMPV among the other respiratory viruses during 3 consecutive winter-spring seasons; ii) the relative circulation of the 2 types and the 4 subtypes of hMPV during the same 3-year period; iii) the relative impact of hMPV as compared to hRSV in determining admission to the hospital of infants with acute respiratory infections. The relative distribution of different respiratory viruses causing severe infections requiring admission to the hospital of infants and young children in three consecutive winter-spring seasons from 2001 through 2004 is reported in Table 2 Within the aliquot of patients found positive for some respiratory virus, no difference in the circulation rate was observed for respiratory virus infections caused by influenzavirus B, hPIVs, hAdVs, hCoVs, and coinfections along the three years studied.
cord-252232-vgq6gjpx	2010	Here, we extended our previous study to ACE2 molecules from seven additional bat species and tested their interactions with human SARS-CoV spike protein using both HIV-based pseudotype and live SARS-CoV infection assays. However, although the genetically related SARS-like coronavirus (SL-CoV) has been identified in horseshoe bats of the genus Rhinolophus [5, 8, 12, 18] , its spike protein was not able to use the human ACE2 (hACE2) protein as a receptor [13] . To this end, we have extended our studies to include ACE2 molecules from different bat species and examined their interaction with the human SARS-CoV spike protein. Our results show that there is great genetic diversity among bat ACE2 molecules, especially at the key residues known to be important for interacting with the viral spike protein, and that ACE2s of Myotis daubentoni and Rhinolophus sinicus from Hubei province can support viral entry.
cord-254405-yc1q20fz	2018	Furthermore, we cultured the virus and screened for attenuated PEDV strains by analyzing the genovariations that occurred during passaging -confirming the results in animal experiments. [27] analyzed a cell culture-adapted PEDV (passage 100) strain with a smaller ORF3 gene and found it to have lower virulence relative to the wild-type virus. Molecular characterization of the ORF3 and S1 genes of porcine epidemic diarrhea virus non S-INDEL strains in seven regions of China Comparative genomic analysis of classical and variant virulent parental/attenuated strains of porcine epidemic diarrhea virus Isolation and identification of porcine epidemic diarrhea virus strain HBMC2012 and its pathogenicity in piglet Cloning and further sequence analysis of the spike gene of attenuated porcine epidemic diarrhea virus DR13 Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China
cord-255653-0bj5eh5d	1981	A possible antigenic relationship between the porcine enteropathogenic coronavirus-like agent (CVLA) and 6 known coronaviruses was examined by immunoelectron microscopy (IEM) and by immunofluorescence (IF). CVLA did not show cross reactivity with infectious bronchitis virus, transmissible gastroenteritis virus (TGEV), canine coronavirus (CCV) hemagglutinating encephalomyelitis virus (HEV), neonatal calf diarrhea coronavirus (NCDCV) or feline infectious peritonitis virus (FIPV). The CVLA was shown by serologic cross protection studies to differ from the two knowm porcine coronaviruses, transmissible gastroenteritis virus (TGEV) and hemagglntinating encephalomyelitis virus (HEV) (4, 14) . The coronaviruses selected for the present study were TGEV, HEV, neonatal calf diarrhea coronavirus (NCDCV), canine coronavirus (CCV), avian infectious bronchitis virus (IBV) and feline infectious peritonitis virus (FIPV). This hyperimmune serum had a virus neutralizing titer of 1:2560 when tested against the cell culture adapted Purdue strain of TGEV. Antiserum to TGEV reacted with CCV, but did not show detectable antigenic cross-reactivity with FIPV.
cord-256859-7ixegm72	2006	Except for isolates in genotype V, which included the Mass-type strains, none of the Chinese IBV isolates examined in this study shared more than 83% amino acid similarity in the S1 protein with the H120 vaccine strain. Furthermore, almost all of the Chinese IBV isolates contained deletions and insertions except for those of the Mass-type IBV, which were included in genotype V in this study, and had amino acid sequences similar to those of the H120 strain ( Table 4 ). The low identities (<83%) of amino acid sequences between Chinese IBV isolates and H120, except for those of the Mass-type IBV, which were included in genotype V in this study, may account for the prevalence of the viruses during the past ten years in spite of the extensive use of Mass-type vaccines in the field in China.
cord-257859-9hmrt96h	2014	
cord-258374-qht98q0l	2009	title: Neutrophil survival factors (TNF-alpha, GM-CSF, and G-CSF) produced by macrophages in cats infected with feline infectious peritonitis virus contribute to the pathogenesis of granulomatous lesions Furthermore, it was investigated whether macrophages, one of the target cells of FIPV infection, produce neutrophil survival factors (TNF-alpha, GM-CSF, and G-CSF). The neutrophil survival rates were significantly increased in the presence of the culture supernatant of macrophages infected with the mixture of FIPV and MAb 6-4-2 compared to those in the presence of other supernatants (Fig. 5) . When SPF-cat-derived alveolar macrophages were infected with a mixture of FIPV and MAb 6-4-2, the intracellular TNF-alpha, GM-CSF, and G-CSF mRNA levels increased (Fig. 6 ). These cytokine mRNA levels were also elevated in macrophages infected with FIPV and MAb 6-4-2, clarifying the presence of neutrophil survival factors in the macrophage culture supernatant. It was suggested that: (1) FIPV-infected macrophages release TNF-alpha, GM-CSF, and G-CSF in response to virus replication, and (2) these cytokines act on neutrophils and prolong their survival.
cord-258768-bjjfkfgg	2010	Two hundred fifty samples were collected in total, Fig. 2 Phylogenetic tree based on partial S gene nucleotide sequences of CCoVs described in this study and reference strains. As a result of RNA recombination, insertions, deletions and a high susceptibility to frequent mutation, coronaviruses can mutate rapidly, leading to new genotypes (CCoV-I), biotypes (pantropic CCoV) and host variants (canine respiratory coronavirus), all of which may present possible difficulties regarding successful vaccination of dogs. As a result of this study, it can be concluded that although it appears that the viral evolution of CPV type 2 is not yet a significant problem for the canine population in Ireland, vaccine efficacy may need to be re-evaluated by the animal healthcare industry, as it is a possibility that the new CPV-2c strain will eventually emerge into the population as a result of importing dogs from other parts of the world.
cord-259193-ifdjyp5b	1984	
cord-260708-l9w5jhsw	2013	
cord-261036-zdhg4axx	2010	
cord-261749-lq1ah16x	2006	At EC36 there were extensive discussions of proposals to revise the statutes under which ICTV operates and to revise the International Code for Virus Classification and Nomenclature (ICVCN). In response to the proposal that ICTV should provide for each approved species a latinized binomial name to link its common name(s), the ''type'' description and the classification, the EC felt that there was little support in the virology community for using latinized names. The changes proposed further stipulated that ICTV should keep an official list of virus names that were used previously but are no longer in current taxonomy. It was pointed out that fixing these lists of criteria was an important task for individual SGs. It was proposed that the category "tentative species" be eliminated from taxonomic usage because a virus can either be a member of a species or it cannot.
cord-262505-1ufgwxxg	1983	Several mouse hepatitis viruses (MHV) with different pathogenicity were studied by oligonucleotide fingerprinting. The MHVs isolated from separate cloned neuroblastoma cell lines persistently infected with JHM strain were also found to have diverged more markedly than the corresponding virus maintained under the conditions of lytic infection. The viruses maintained under the latter conditions exhibit much more variability, suggesting that persistent infections may be a mechanism contributing to the genetic heterogeneity of the current MHV strains. To study the genetic relationship of different MHV strains causing various diseases in mice, we first examined the oligonucleotide fingerprints of two of the IKHVs isolated in Japan. To assess the genetic stability and variability of MItV and to study the possible mechanism of viral divergence observed as above, we examined the heterogeneity of viral genomic sequences in viruses isolated from persistently and latently infected cells.
cord-263193-paeosfiu	2020	Here, primary chicken embryo kidney (CEK) cells and specific-pathogen-free (SPF) chickens were infected with three pathogenic IBV strains, and it was observed that the TLR7-MYD88 pathway was inhibited but the TLR3-TIRF pathway was activated. To investigate the effect of innate immune molecules, agonists of TLR3, TLR7, and MDA5 and inhibitors of key molecules of the TLR3 pathway were added to CEK cells that had grown to 80-90% as instructed by the reagent manufacturer (InvivoGen, CA, USA) as follows: 5 μg of imiquimod (a TLR7 agonist) per mL for 12 h, 10 μg of low-molecular-weight (LMW) polyinosinic-polycytidylic acid (poly(I:C)) (a TLR3 agonist) per mL for 12 h, 0.5 μg of poly (I:C)-LMW/LyoVec (an MDA5 agonist) per mL for 12 h, 10 μM Pepinh-TRIF (a TRIF inhibitor) for 6 h, 5 μM celastrol (an NF-κB inhibitor) for 1 h, 50 μM chloroquine (an inhibitor of endosomal acidification) for 0.5 h, and 5 μM BX795 (a TBK1 inhibitor) for 6 h.
cord-264392-he1vekrt	2008	This study confirmed the classification of NarPV as a member of the subfamily Paramyxovirinae and established the close genome organization and sequence relationship between the two rodent paramyxoviruses isolated almost a decade apart and from two locations separated by more than 15,000 km. This was then followed by PCR to fill in the ''''gaps'''' using specific primers designed from NarPV Nariva virus genome 201 sequences obtained from the cDNA subtraction or degenerate primers designed using highly conserved consensus sequences of known paramyxoviruses in the subfamily Paramyxovirinae. Overall comparison of deduced sizes and amino acid sequences of all proteins indicated that NarPV is most closely related to MosPV (Table 1) genome is significantly larger (16,650 nt) than that of NarPV due to the longer untranslated regions (UTRs) located at the 3 0 end of most genes ( Fig. 1b and Table 1 ).
cord-265201-ab67pnct	1980	The hemagglutination (HA) and receptor destroying enzyme (RDE) activities of a newly isolated mouse enteric coronavirus (designated as DVIM) are described. H e madsorbed s y n e y t i u m which were i n c u b a t e d at 37 ° C to release I~BCs for 60 minutes, were exposed to freshly p r e p a r e d RBCs a n d p h o t o g r a p h e d Above results strongly suggest that DVIM possesses an enzymatic activity which reacts with surface components of RBCs. However, this enzymatic action appears to differ from the bacterial neuraminidase and that of Influenza-A virions. A densitometer scan of a stained polyacrylamide gel of the polypeptides of virus particles treated with bromelain (1.0 mg/ml at 37°C for 15 minutes) is shown in Fig. 4 .
cord-265631-b0kg6qpo	2017	title: Retrospective investigation and evolutionary analysis of a novel porcine deltacoronavirus strain detected in Thailand from 2008 to 2015 We performed a retrospective investigation of the presence of PDCoV in intestinal samples collected from piglets with diarrhea in Thailand from 2008 to 2015 using RT-PCR. Positive samples were subjected to full-length genome characterization followed by genetic analyses to compare Thai strains of PDCoV to those from other countries and to investigate the genetic similarity and the evolutionary relationships among them. To investigate its evolutionary relationships to foreign PDCoV strains and estimate the divergence time of PDCoV in Thailand, phylogenetic analysis of the full-length nucleotide sequence of the PDCoV isolate collected in this study, together with 21 other PDCoV isolate sequences (Supplementary Table 1 ), was performed using the Bayesian Markov chain Monte Carlo (BMCMC) method implemented in the program BEAST v1.8.3 [2, 3] .
cord-265768-hwki5lk2	2020	title: An emerging novel bovine coronavirus with a 4-amino-acid insertion in the receptor-binding domain of the hemagglutinin-esterase gene We previously reported a novel recombinant bovine coronavirus (BCoV) strain that was circulating in dairy cattle in China, but this virus was not successfully isolated, and the genetic characteristics of BCoV are still largely unknown. A 3D model constructed based on the crystal structure of bovine coronavirus hemagglutinin-esterase (SMTL ID: 3cl4.1) using the online software SWISSMODEL (https ://www.swiss model .expas y.org/inter activ e) showed that the position of the 4-aa insertion in the R3-loop between F 211 and F 212 in HE in the recombinant BCoV strains would alter the spatial conformation of the receptor-binding site relative to that in the HE recombinant strains and prototype strains lacking this insertion ( Fig. 2B and C) .
cord-266716-pghnl980	2018	title: Isobavachalcone inhibits post-entry stages of the porcine reproductive and respiratory syndrome virus life cycle Since the first report of a porcine reproductive and respiratory syndrome (PRRS) outbreak, tremendous efforts to control this disease, including various national policies and plans incorporating the use of multiple modified live-virus vaccines, have been made. Western blot analysis revealed that PRRSV N protein levels decreased markedly, indicating that increasing concentrations of IBC significantly inhibited PRRSV replication (Fig. 1F) . The in vitro study established that IBC efficiently inhibited the replication of both HP-PRRSV and the current Chinese epidemic NADC30-like strains without significant drug toxicity. Role of phosphatidylinositol 3-kinase (PI3K) and Akt1 kinase in porcine reproductive and respiratory syndrome virus (PRRSV) replication Pathogenicity and antigenicity of a novel NADC30-like strain of porcine reproductive and respiratory syndrome virus emerged in China NADC30-like strain of porcine reproductive and respiratory syndrome virus
cord-267155-3rhdxzj3	1980	
cord-267446-rpv19oy6	2011	The addition of trypsin was shown to induce fusion of the infected Vero cells, resulting in the formation of multiple syncytia, and produced a significant increase in virus titer after several passages. For example, infection by severe acute respiratory syndrome coronavirus (SARS-CoV) and murine hepatitis virus strain 2 (MHV-2) requires proteolytic cleavage in their target cells, which is mediated by trypsin-like proteases [24, 29, 32] . To investigate the effects of proteolytic cleavage of the surface protein of Vero cells and free virions by trypsin, Vero cells or KPEDV-9 were pre-treated with trypsin prior to infection. These results are consistent with the suggestion that trypsin is not absolutely essential for Vero-cell-adapted PEDV infection, as reported for other group 1 coronaviruses, but the titer increases during infection with trypsin-treated virus.
cord-269948-zfbu9646	2011	
cord-270473-5tok4mqk	2003	
cord-271831-vekok62k	2005	Feline infectious peritonitis virus (FIPV) (Coronaviridae) causes the most lethal viral infection in cats: FIP. In this study, infection kinetics (titres and antigen expression) of FIPV 79-1146, and FECV 79-1683, were determined in peripheral blood monocytes from 3 donor cats and compared to those in Crandell feline kidney (CrFK) cells. Two coronaviruses are described in cats: feline infectious peritonitis virus (FIPV) and feline enteric coronavirus (FECV). Within this population of 19 cats, the monocytes isolated from 9 cats showed a continuous increase in viral antigen positive cells during a 24 hour time span after inoculation with FIPV. Monocytes from 9 cats did not sustain both FIPV and FECV infection since the number of viral antigen positive cells dropped after 6 or 12 hpi (third pattern). In an infection kinetics study where another cell type, feline peritoneal macrophages, was used, different results in the antigen expression kinetics were obtained [29] .
cord-271884-86yl9ren	1977	In search for a suitable method for sero-ecological screenings for arboviruses in Norway, efforts were undertaken to make the immunoelectroosmophoresis technique more sensitive than here to fare in detection of antibodies. The isolation of Uukuniemi (UUK) group viruses and a new coronavirus-like agent, Runde virus, from Norwegian Ixodes ticks (19, 21, 22, 23) , were intended to be followed up promptly by sero-ecological surveys by a standard haemagglutination inhibition test (HAI). B y using a gel composed of 0.4 per cent agar and 0.6 per cent agarose, and concentrated B H K antigens, results comparable to the H A I titers were obtained for the reference sera with all the viruses tested. Provided the opportunity to concentrate the antigen, the modifications used in this work to obtain a sensitive I E O P for antibody detection might prove valuable also with other viruses.
cord-272955-kkkrkgg1	2009	title: Molecular characterization of adenoviral infections in Cuba: report of an unusual association of species D adenoviruses with different clinical syndromes The objectives of this study were to identify and characterize members of different adenovirus species at the molecular level and to describe the correlation between viruses and clinical syndromes during a period of 4 years. Four isolates from clinical materials obtained from patients with encephalitis, acute flaccid paralysis and meningoencephalitis were identified as belonging to the species Human adenovirus D. In the present report, the nested PCR method used was able to detect different HAdVs in clinical samples and supernatant culture with a sensitive internal control system to assure the quality of reaction conditions in each individual tube. Human adenovirus DNA was detected in the supernatant of a cell culture infected with viruses obtained from fecal specimens taken from a patient with acute flaccid paralysis (AFP), as well as in two cases of meningoencephalitis.
cord-272973-kzaowysv	2018	PEDV NA, IgG and IgA were detected in the serum of piglets born to immunized gilts, demonstrating the transfer of antibodies through colostrum and milk. In the present study, we investigated the immunogenicity of ORFV-PEDV-S recombinant virus in pregnant gilts and its ability to induce passive immunity and protection in piglets born to immunized animals. Animals in G1 seroconverted to PEDV, presenting detectable levels of IgG, IgA and NA a week after challenge of the piglets (day 7 post-birth; Fig. 1 ). Notably, passive transfer of antibodies from gilts to piglets was observed in both G2 and G3, as PEDV-specific IgG, IgA and NAs were detected in serum of piglets born to immunized gilts following ingestion of colostrum and milk. Additionally, passive transfer of antibodies from gilts to piglets was observed, as PEDV-specific IgG, IgA and NAs were detected in serum of piglets born to immunized gilts following ingestion of colostrum and milk.
cord-274780-fmnro0kw	1981	Astroviruses were detected by electron microscopy in the feces from a 4 month old kitten with diarrhea. Astroviruses were detected by electron microscopy in the feces from a 4 month old kitten with diarrhea. The clinical disease manifested by the cat and the observed morphology of the viral particles are consistent with previous reports on astroviruses of other species. The clinical disease manifested by the cat and the observed morphology of the viral particles are consistent with previous reports on astroviruses of other species. Viral antigen was detected by indirect immunofluorescent staining within the cytoplasm of cultured cells infected with fecal material of human (10, 11) and bovine (23) astroviruses. Studies on the pathogenesis of astrovirus infection in lambs have shown the site of virus multiplication to be the mature villous epithelial cells of the small intestine (21, 22) .
cord-276617-chgjpg0v	2008	The present study shows that: (1) the ratio of peripheral blood sIg(+) CD21(−) B-cells was higher in cats with FIP than in SPF cats, (2) the albumin-to-globulin ratio has negative correlation with the ratio of peripheral blood sIg(+) CD21(−) B-cell, (3) cells strongly expressing mRNA of the plasma cell master gene, B-lymphocyte-induced maturation protein 1 (Blimp-1), were increased in peripheral blood in cats with FIP, (4) mRNA expression of B-cell differentiation/survival factors, IL-6, CD40 ligand, and B-cell-activating factor belonging to the tumor necrosis factor family (BAFF), was enhanced in macrophages in cats with FIP, and (5) mRNAs of these B-cell differentiation/survival factors were overexpressed in antibody-dependent enhancement (ADE)-induced macrophages. We also collected macrophages from FIP cats and measured the expression levels of the viral RNA and mRNA of B-cell differentiation/survival factors: IL-6, CD40 ligand (CD40L), and Bcell-activating factor belonging to the tumor necrosis factor family (BAFF).
cord-276630-qci7khki	2020	Due to the evidence of the anti-SARS-CoV-2 activity of various clinically available agents, drug repositioning stands out as a promising strategy for a short-term response in the fight against the novel coronavirus. Only seven drugs (chloroquine, tetrandrine, umifenovir (arbidol), carrimycin, Table 1 Clinical evidence of potential candidates for drug repositioning against COVID-19 (SARS-CoV-2) *Lopinavir (400 mg) + ritonavir (100 mg), q12h, orally; associated with umifenovir (200 mg), q12h, orally. [14] reported that the use of arbidol in combination with lopinavir/ritonavir inhibits the aggravation of pneumonia caused by SARS-CoV-2 and promotes a virus-negative conversion in patients from China. Of these, only six drugs (lopinavir/ritonavir, umifenovir (arbidol), remdesivir, chloroquine, and hydroxychloroquine) have shown promising results in preclinical trials and have clinically lessened the symptoms of COVID-19. Although lopinavir/ ritonavir had low anti-SARS-CoV-2 activity, arbidol, remdesivir, and chloroquine/hydroxychloroquine showed promising effects against this coronavirus.
cord-277847-vgf9lz76	2014	
cord-278388-lzvtgwox	2014	
cord-279676-sk9xyd1r	2020	In situ hybridization (ISH) and immunohistochemistry (IHC) are essential tools to characterize SARS-CoV-2 infection and tropism in naturally and experimentally infected animals and also for diagnostic purposes. In situ hybridization (ISH) and immunohistochemistry (IHC) techniques allow visualization of viral nucleic acid and protein antigens, respectively, within tissues and cells. For this purpose, the development of SARS-CoV-2-specific ISH and IHC are both critical for the assessment of viral distribution, cell tropism, and cytopathology within tissues, complementing classical histopathology, various molecular tools, and serological assays. Thus, the objective of this study was to develop RNAscope ® ISH and IHC methods for the detection of SARS-CoV-2-specific antigen and RNA in infected cells that can be utilized for both research (e.g., studies involving experimentally and naturally infected animals) and diagnostic purposes. Furthermore, the development of IHC and ISH tools is of utmost significance for understanding the pathogenesis of SARS-CoV-2 by characterizing the viral tissue distribution/cellular tropism in animal models and humans.
cord-280781-u3wd27rn	1978	title: Stability of neurotropic mouse hepatitis virus (JHM strain) during chronic infection of neuroblastoma cells A line of mouse neuroblastoma cells which was chronically infected with the neurotropic strain (JHM) of MHV, a member of the coronavirus group, was established. The addition of low concentration antiviral antibody modulated the infection to a carrier culture with viral antigen in the cytoplasm of the cells, but no infectious virus was produced, and the cells lacked both surface viral antigen and CPE. Following incubation at room temperature for 30 minutes in the presence of anti-JHM hyperimmune aseitie fluid (50 per cent plaque reduction neutralization titer = 1/1~00), serial dilutions were plated on the indicator monolayers and fixed with 0.5 ml of DMEM plus 5 per cent FBS containing 0.6 per cent agarose. Figure 3 shows that following the initial passage in the presence of antibody, there was an increase in both the supernatant and cell associated virus titer, which rapidly declined until after 4 serial passages no infectious virus was detectable.
cord-280865-shwxhak9	2018	
cord-280905-g2vcy9ea	2009	
cord-281410-y558a5jf	1981	title: Propagation of the Kakegawa strain of bovine coronavirus in suckling mice, rats and hamsters Infected animals died with nervous symptoms, and serial passage was readily accomplished by intracerebral inoculation with brain emulsions. Infected animals died with nervous symptoms, and serial passage was readily accomplished by intraeerebral inoculation with brain emulsions. The present paper describes briefly our recent observation that the Kakegawa strain of BCV readily propagates in suckling mice, rats and hamsters. Four-day-old mouse 3 days after intraeerebral inoculation with the 3rd mouse brain passaged Kakegawa strain (left) and an uninoeulated 4-day-old mouse (right) Four litters (10 to 12/litter) of suckling mice were inoculated intracerebrally with infected tissue culture fluid containing 106-5 TCID50/ml. These findings showed that the viruses recovered from the brains of affected animals were antigenieally the same as the cell culture passaged virus and could be clearly differentiated from the MttV strain 2.
cord-282062-h9smg0w9	2018	We detected a novel feline stool-associated circular DNA virus (FeSCV) in fecal samples from cats with diarrhea using consensus primers matching those of circovirus and cyclovirus. Feline cyclovirus was identified by next-generation sequencing analysis in which the viral gene was detected in a pooled fecal sample collected from 4-5 healthy cats. In this study, we performed nested PCR using Circoviridae family consensus primers and detected novel CRESS DNA viruses in several cats with diarrhea symptoms. However, we concluded that FeSCV is a circular DNA virus based on the following: 1) No Giardia intestinalis was detected in the fecal test, and 2) the complete genome of FeSCV was amplified using the rolling-circle amplification and inverse PCR assays. We detected a novel CRESS DNA virus, FeSCV, in fecal samples from cats. Although it was detected using consensus primers of circovirus and cyclovirus, FeSCV was phylogenetically positioned in a clade different from that of these viruses.
cord-283178-4wefykbi	2018	
cord-283525-kvcqayl4	2009	This study investigated the inhibitory effect and mechanism of nitric oxide (NO) on porcine parvovirus (PPV) replication in PK-15 cells. The results showed that two NO-generating compounds, S-nitroso-l-acetylpenicillamine (SNAP) and l-arginine (LA), at a noncytotoxic concentration could reduce PPV replication in a dose-dependent manner and that this anti-PPV effect could be reversed by the NO synthase (NOS) inhibitor N-nitro-l-arginine methyl ester (l-NAME). As shown in Fig. 1a , SNAP and LA have the ability to inhibit PPV replication in PK-15 cells, and there is a dose-dependent relationship between the inhibitory effect and the SNAP (or LA) concentration. As shown in Fig. 2 , the PFU value increased with later addition of SNAP (or LA), and adding SNAP (or LA) 6 or 3 h prior to viral infection resulted in the highest level of inhibition. Our results demonstrate that NO specially inhibits the PPV replication cycle during the step of viral protein synthesis (Fig. 3b) .
cord-283710-55m16q7c	2014	Multivariate analysis showed that single infections with HAdV-7 were associated with a higher prevalence of severe pneumonia. There is therefore a need for continuous surveillance, with extensive molecular characterization, to determine the prevalence and genetic characteristics of the circulating HAdVs. The current study was performed to identify the predominant HAdV types associated with pediatric pneumonia and to trace the new genetic variants that might be derived from recombination of different types. However, HAdV infection was associated with more-severe pneumonia and more frequent transfer to the intensive care unit in comparison with HAdV-negative patients (P \ 0.001 and P = 0.027, respectively) ( Table 1) . These findings have the clinical implication that in patients with severe pneumonia, the contribution of HAdV, especially HAdV-7, should be considered with high priority, regardless of whether another respiratory pathogen has been detected. Identification and typing of adenovirus from acute respiratory infections in pediatric patients in Beijing from
cord-283804-dje7qbps	1977	The polypeptides of the different density virus particles from the three IBV strains were analysed on polyacrylamide gels. Other studies on the polypeptide composition of eoronaviruses have shown 6 polypeptides in the virus particles of human coronavirus (HCV) strain OC43 (7) a n d t r a n s m i s s i b l e g a s t r o e n t e r i t i s v i r u s ( T G E V ) (5), a n d 7 p o l y p e p t i d e s in t h e v i r u s p a r t i c l e s of H C V s t r a i n 229 E (8) Virus Polypeptide Analysis Figure 2 shows the polsTeptides of the purified major virus species of the IBV strains Beaudette, Connecticut and Massachusetts, on polyaerylamide gels.
cord-284087-g2jfnxja	2013	In this study, we investigated the molecular evolution of influenza virus A(H1N1)pdm09 in the 2010/11 influenza season in southern Germany by sequence analysis of the influenza virus hemagglutinin gene from 25 patients with mild, moderate, and severe disease. The H275Y mutation in the influenza virus neuraminidase gene, known to confer resistance to the neuraminidase inhibitor oseltamivir, was detected in one patient. Aim of this study was to investigate the molecular evolution of A(H1N1)pdm09 in the 2010/11 influenza season in southern Germany by sequence analysis of the HA gene of mild, moderate, and severe influenza cases. In order to detect molecular changes in the HA gene of influenza virus, 33 A(H1N1)pdm09 HA sequences representing 25 individual patients were analysed. e., C 2 weeks) of influenza virus in the respiratory tract was observed in 6 of the 25 patients (24 %; 3 with severe, 2 with moderate, and 1 with mild disease).
cord-285329-62yafd2d	1995	The antigenic and biological properties of 6 strains of bovine coronavirus (BCV) derived from neonatal calf diarrhea (CD) and 8 strains of BCV from winter dysentery (WD) of adult cattle, propagated in HRT-18 cells, were compared to determine if CD and WD strains belong to distinct serotypes or subtypes of BCV. However, in virus neutralization tests, antisera to 1 CD and 2 WD strains had 16-fold or lower antibody titers against 3 WD and 1 CD strains than against the homologous strains, and this variation reflected low antigenic relatedness values (R=13–25%), suggesting the presence of different subtypes among BCV. Receptor-destroying enzyme activity with mouse erythrocytes was not UExpressed as the reciprocal of the highest dilution of virus causing complete disappearance of HA patterns at 4 °C after 2 h incubation at 37 °C ° CD Calf diarrhea, WD winter dysentery of adult cattle dM/C Ratio of HA titer with mouse erythrocytes to HA titer with chicken erythrocytes detected for any strain of BCV.
cord-285429-vmnj25b5	2014	A total of 332 fecal specimens collected during January-December 2008 from adult patients with diarrhea were screened for group A and C rotaviruses, noroviruses GI and GII, sapovirus, Aichi virus, human parechovirus, enterovirus, adenovirus and astrovirus by RT-multiplex PCR. This study provides epidemiological data for a wide variety of diarrheal viruses circulating in adult patients with diarrhea in Chiang Mai, Thailand. Then, the specimens were tested for the presence of SaV, AiV, group A rotavirus (RVA), group C rotavirus (RVC), HPeV, NoV GI and GII, EV, AdV, and AstV by RT-multiplex PCR using the protocol described previously by Khamrin et al. In addition, this study clearly demonstrates that HPeV is an unusual cause of acute gastroenteritis in adults compared to other viruses. The relatively low rate of diarrheal virus detection in adults with diarrhea in this study suggests that acute gastroenteritis in adults in this area may be caused by other pathogens.
cord-285547-7m3dh8hu	2011	In the present study, a surveillance of avian influenza was carried out in Vietnam in domestic ducks and wild birds in 2009 and 2010, and the isolates were antigenically and phylogenetically analyzed and their pathogenicity in birds and mammals was assessed. One hundred tracheal and cloacal swab samples that were viral gene positive from 600 domestic ducks and 207 wild birds (night heron, Nycticorax nycticorax; grey heron, Ardea cinerea; purple heron, Ardea purpurea; chinese pond heron, Ardeola bacchus; chinese egret, Egretta eulophotes; little egret, Egretta garzetta; intermediate egret, Egretta intermedia; cormorant, Phalacrocorax carbo; little cormorant, Microcarbo niger; Japanese bush warbler, Cettia diphone; black-browed reed warbler, Acrocephalus bistrigiceps; olive bulbul, Iole virescens; black capped kingfisher, Halcyon pileata; collared kingfisher, Halcyon chloris; racket tailed treepie, Crypsirina temia; oriental magpie robin, Copsychus saularis; tiger shrike, Lanius tigrinus; yellow bittern, Ixobrychus sinensis; indian cuckoo, Cuculus micropterus; common koel, Eudynamys scolopacea; and black collared starling, Sturnus nigricollis) in April 2009 and March 2010 in southern Vietnam were inoculated into the allantoic cavities of 10-day-old embryonated chicken eggs.
cord-285892-tp6mlqtw	2012	In this study, RNA corresponding to bovine enterovirus (BEV) was detected in 24.6 % of faecal samples (17/69) from diarrheic and healthy cattle in six different areas in China by an RT-PCR screening method. These viruses were characterized molecularly through sequence analysis of complete genomes, and the BHM26 and BJ50 isolates were therefore classified into genotype 2 of the BEV-B cluster. A total of 69 bovine diarrheic and healthy faecal specimens from six different areas were examined by RT-PCR using the primer pair 6424U24 and 7450L24, which cover the highly conserved partial 3D gene and 3 0 UTR of BEVs. The results showed that virus-specific RNA could be detected directly in faecal material in 17 of 69 samples (24.6 %). The results showed that the 3D/3 0 UTR (1026 nt) of BHM26 and BJ50 shared 86 % and 88 % nucleotide sequence identity, respectively, to that of BEV strain Jena38/02 (GenBank accession number: DQ092789), indicating that the two isolates are bovine enterovirus.
cord-286794-adbxzgvs	2019	title: Identification and complete genome characterization of human enterovirus 117 from a child with pneumonia in China In this study, human enterovirus C117 (EV-C117) was detected in a 3-month-old boy diagnosed with pneumonia in China. Here, we report the identification and complete genomic sequence of EV-117 in a child with pneumonia in China, which may provide more information for understanding EV-C117 infection. Using multiple primers (Table 1) , we determined the full-length viral genome sequence of the strain detected in patient CQ6747 (GenBank accession no. Conversely, all genome regions of CQ6747 showed less similarity to other EV-C strains (including EV-C104, EV-C105, EV-C109, and EV-C118) ( Table 2) . Complete genomic sequencing shows that polioviruses and members of human enterovirus species C are closely related in the noncapsid coding region Complete genome sequence of a novel human enterovirus C (HEV-C117) identified in a child with communityacquired pneumonia Respiratory infection with enterovirus genotype C117, China and Mongolia
cord-287275-vwyny1vt	2018	In this study, a Chinese PDCoV strain, designated CHN-HG-2017, was isolated from feces of a suckling piglet with severe watery diarrhea on a farm located in central China. Tissues of small intestines from CHN-HG-2017-infected piglets at 4 DPI displayed significant macroscopic and microscopic lesions with clear viral antigen expression. In addition, it has been reported that newborn piglets inoculated with two recent Chinese PDCoV isolates, named CHN-HN-2014 and CHN-GD-2016, developed clear clinical signs, including severe diarrhea, vomiting, and dehydration [21, 22] . Analysis of the genomic sequence suggested that CHN-HG-2017 is a potential recombinant virus derived from Chinese and Vietnam PDCoV strains. To confirm that virus propagation had occurred, the infectivity of the plaque-purified CHN-HG-2017 strain in LLC-PK1 cells was tested by IFA and western blot with an mAb against the PDCoV N protein. Isolation, genomic characterization, and pathogenicity of a Chinese porcine deltacoronavirus strain CHN-HN-2014
cord-288948-89cdfhi0	2020	This study reports the characterization of four divergent MVC strains detected between 2012 and 2018, three of which were from dogs illegally imported into Italy, most probably from Eastern Europe, that cluster together phylogenetically but share low genetic similarity with the fourth MVC from an autochthonous dog and other available MVC sequences. In detail: the complete ORF1, encoding the NS1 protein, of three of the four MVC isolates (Italy/4033/2012, BIO-CRIME/2018 and Italy/59116/2017, which had a gap of 17 nt) was sequenced and was 2325 bases in length, corresponding to 774 aa (Fig. 1a) . The phylogenetic tree based on the ORF2 nt sequences encoding the VP1/VP2 proteins (Fig. 2c) , was constructed using all 124 MVC sequences available in the GenBank database and included the only Italian MVC sequence available, Italy/285_11/2011 (JQ612703_Canine_ minute_virus_strain_285_11_Italy_2011), for which only the partial VP1/VP2 sequence is present [9] .
cord-289926-y1rjgbui	2014	Using sequence analysis methods we have discovered significant sequence similarity between this central domain of HDAg and the HMG (High Mobility Group) box of the SRY gene [40] , whose product binds to DNA and is essential for sex determination. The sequence similarity between the central domain of HDAg and the HMG (High Mobility Group) box of the SRY gene suggests that SRY may be a cellular cognate of HDAg. Another candidate for the ''captured'' cellular RNA was recently proposed: a 202 residue cellular protein referred to as DIPA (delta interacting protein A) was identified by co-immunoprecipitation with HDAg and by its in vivo ability to inhibit viral replication [5] . Statistically significant sequence similarities are limited to the functionally essential regions of both genes: in the SRY gene the similarity is confined to the HMG (High Mobility Group) box, a DNA binding motif found in the HMG protein superfamily [24, 31] , in HDAg the similarity is limited to RNA-binding domain.
cord-290546-zu5ns4yq	1983	The size and heat sensitivity of Pleural effusion disease (PED) agent or virus (PEDV) propagated in rabbits were examined. PEDV and the Stockholm agent appeared identical concerning pathogenic and immunogenic properties by infection experiments and protection tests in rabbits. The third isolate, obtained from the laboratory, which several years previously had supplied material for demonstration of the Stockholm agent, differed from PEDV in pathogenic and immunogenic properties. Stock PEDV consisted of pooled rabbit sera obtained 48 hours after subcutaneous inoculation with pleural fluid or infectious serum. Stocks of the Stockholm agent and the three isolates were from the first or second rabbit passage, prepared in the same manner as for PEDV. HCV229E and CV Paris were used as antigens in E L I S A to detect antibody rises to coronaviruses in paired sere from 20 rabbits infected with the 5 isolates.
cord-290695-ubrqy2zf	1988	Polykaryon formation in bovine fetal spleen (BFS) cells infected with bovine coronavirus L9 occurred only in media supplemented with trypsin. Cell fusion and polykaryon formation in cultures infected with bovine coronavirus (BCV) occur late in the virus replication cycle. We analyzed the trypsin-dependent cell fusion of BCV-infected BFS cells and found that the range of pH 7.5 to 8.0 was optimal for polykaryon formation. The cells were inoculated with BCV at a multiplicity of 2 PFU per cell, incubated in MEM containing trypsin (0.4 ug per ml; Sigma Chemical Company) treated with L-l-tosylamide-2-phenylethyl chloromethyl ketone, an inhibitor of chymotrypsin activity. The ability of anti-BCV IgG to affect polykaryon formation at 37 °C was tested by two procedures: (i) Infected cell monolayers were incubated for 6 h in trypsin-free MEM then exposed to MEM that contained antibody freshly diluted with trypsin containing medium. Trypsin treatments of BCV-infected BFS cells during the time of maximal fusion enhancement were effective only with media of pH levels 7.5 to 8.0.
cord-290819-zhywlf6r	2020	title: The antiviral protein viperin interacts with the viral N protein to inhibit proliferation of porcine epidemic diarrhea virus In the early stage of virus infection, the pattern recognition receptor (PRR) signaling pathway of the host cell is activated to induce interferon production, activating interferon-stimulated genes (ISGs) that encode antiviral proteins that exert antiviral effects. Increased expression of interferon and viperin and decreased replication of PEDV with a clear reduction in the viral load were observed in PEDV-infected IPEC-J2 cells. After virus infection, pattern recognition receptors recognize released viral nucleic acids and activate downstream signaling pathways to promote the production of specific transcription factors and type I interferons [25] . These results indicate that PEDV infection upregulates the expression of interferon and viperin in IPEC-J2 cells. This study showed that the expression of type I interferon increases and that of viperin is also upregulated in IPEC-J2 cells infected with PEDV.
cord-291530-ffex7dw9	2007	Field canine coronaviruses (CCVs) identified during a series of outbreaks of gastroenteritis in Swedish dogs were subjected to genetic analysis involving the open reading frame 1b (ORF1b) and the membrane (M) and spike (S) protein genes. Four field viruses originating from the Stockholm region presented identical sequences and segregated separately from other CCVs characterized so far and from GOT/05, the variant recovered in Western Sweden. In the alignment based on 3 0 S gene sequences, the Swedish field viruses displayed higher ranges of nucleotide and amino acid identity with both CCVs and FCoVs of type II (Table 2 ). Comparable or even higher percentages of nucleotide variation were observed between GOT=05 and the same reference strains, thus suggesting that GOT=05 also constitutes a genetically distinct variant among CCVs. In addition, 5 0 S gene sequences related to CCV type I were identified among the SWE1 viruses and UPPS2=04.
cord-291707-dzmvjh7j	1987	FIPV grows to higher titer, forms larger plaques and switches off host cell protein synthesis more effectively than FECV. It was reported that both virus strains produce relatively large plaques in cell culture and grew to fairly high titers (1) . This indicated the differences were consistent and were not due to maturation artitSct. There was a cell protein band just above the nucleoprotein of the FECV 79-1683 of the radiolabelled virus. The FIPV strains produced larger plaques in CrFK cells and half a log higher titer of virus than the FECV strain. Host cell protein synthesis was also shut offby infection with murine coronavirus and different strains vary in the extent to which they do it, (25) . In this study, all 3 st, ruetural polypeptides appeared synchronously in cells infected with FIPV or FECV strains. Viral protein synthesis in mouse hepatitis virus strain A 59-infected cells: effect oftunieamyein
cord-291718-cz1bi0ym	2017	Furthermore, the IBV replicase-encoded PLP, including the downstream transmembrane (TM) domain, is a DUB enzyme and dramatically reduced the level of Ub-conjugated proteins, while processing both K48and K63-linked polyubiquitin chains. Overall, these results demonstrate that the IBV-encoded PLP-TM functions as a DUB enzyme and suggest that IBV may interfere with the activation of host antiviral signaling pathway by degrading polyubiquitin-associated proteins. Further experiments indicated that the proteinase PLP-TM plays an important role in IBV DUB activity and can process both K48-and K63-linked polyubiquitin chains. Overall, the results of our study show that IBV has DUB activity and confirm that PLP-TM is not only a classic papain-like protease encoded by IBV but is also a multifunctional protein that plays important roles in the regulation of interactions between IBV and host antiviral innate immune response proteins. IBV PLP-TM may prevent the activation of host antiviral signaling pathways by degrading polyubiquitin chains associated with ubiquitin proteins.
cord-292286-ygomb3oi	2017	Flavonoids are widely distributed as secondary metabolites produced by plants and play important roles in plant physiology, having a variety of potential biological benefits such as antioxidant, anti-inflammatory, anticancer, antibacterial, antifungal and antiviral activity. The antiviral activity of flavones is known from the 1990s, when it was showed that the simultaneous application of apigenin with acyclovir resulted in an enhanced antiviral effect on herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) in cell culture [92] . Besides these DNA viruses, apigenin was found to exert antiviral effect against African swine fever virus (ASFV), by suppressing the viral protein synthesis and reducing the ASFV yield by 3 log [46]. Besides these viruses, EGCG has been found to exert antiviral activity against HCV by preventing the attachment of the virus to the cell surface and suppressing RNA replication steps [8, 15] . Antiviral activity of baicalin against influenza A (H1N1/ H3N2) virus in cell culture and in mice and its inhibition of neuraminidase
cord-293945-gyb9mjb5	2012	Virus yield reduction assay ST cell monolayers were infected with TGEV with or without probiotic bacteria treatment according to the experimental design. faecium (1.00E?07 CFU/ml) when the probiotic was added to the cells together with the virus during the infection period (competition assay). faecium inactivates TGEV particles by direct physical interaction with virus, a cell-free preincubation assay was performed. faecium together with the virus significantly increases mRNA expression levels of the pro-inflammatory cytokines interleukin 6 (IL-6) and IL-8 (an approximately 3-and 13-fold increase, respectively) when compared with TGEV-infected ST cells that had not been exposed to the probiotic (Fig. 6) . faecium (pretreatment), the viability of TGEV-infected cells was protected, and virus yields were reduced (Figs. In this study, the competition assay in which virus and probiotic bacteria are present in the culture medium side by side, exhibited the most pronounced antiviral activity in terms of cell survival (Figs.
cord-294138-h7sfd1wa	2020	Both countries were involved in the United States Agency for International Development''s (USAID) Emerging Pandemic Threats PREDICT program, and surveillance of bats in wildlife markets in rural areas in Laos using family-level PCR assays revealed the presence of CoV RNA in 41 animals [5] . Considering the significant interactions of wildlife and especially rodents with humans in Laos, we were interested in investigating the presence of CoVs in these animals, which can be primary or intermediate hosts for CoVs with zoonotic potential. Since there are abundant contact opportunities for wildlife pathogens and humans in Laos, and considering that coronavirus-zoonotic events can involve intermediate hosts, as in the cases of SARS and MERS, we focused our screening on non-bat species potentially capable of playing that role. It is worth noting that we targeted rodents most likely to be in contact with humans and transmit virus and found fewer CoV-RNA-positive animals than in other studies of rodents in the region or elsewhere.
cord-294218-v4gjabp3	1989	Pulse labeling of cells with [(35)S]methionine or [(3)H]glucosamine at different times after infection, followed by SDS-PAGE and Western immunoblotting analysis using rabbit anti-TCV hyperimmune serum, was used to resolve and identify TCV-induced intracellular proteins. In the present study, we have investigated the intracellular synthesis and post-translational modifications of virus-coded polypeptides in cultures of HRT-18 infected with TCV in the presence or the absence of glycosylation inhibitors. Radioim-munoprecipitation experiments using the anti-TCV hyperimmune serum, after [35S]methionine and [3H]glucosamine labeling, confirmed the absence of the peplomeric glycoproteins from TM-treated cells, whereas the relative amount of the unglycosylated high mol.wt, polypeptide species increased (Fig. 4A, lanes 5 and 7) . In this paper, we described the identification of virus-induced intracellular polypeptides in TCV-infected HRT-18 cells, the kinetic of their synthesis, their post-translational processing in the presence of glycosylation inhibitors and their significance with respect to the production of mature virions.
cord-294323-mryiqmsw	2018	The wide range of hosts provides influenza A viruses greater chances of genetic re-assortment, leading to the emergence of zoonotic strains and occasional pandemics that have a severe impact on human life. Here, we primarily discuss the pathogenesis of influenza virus type A, its epidemiology, pandemic potential, current status of antiviral drugs and vaccines, and ways to effectively manage the disease during a crisis. A genetic shift occurs when two or more different influenza virus strains infect the same cell in a host, leading to recombination of genetic materials, an event that occasionally generates a new strain with a novel combination of hemagglutinin and neuraminidase. The antiviral drugs currently available against influenza viruses are adamantane derivatives (amantadine and rimantadine) and neuraminidase (NA) inhibitors (zanamivir, oseltamivir and peramivir). Due to the increasing burden of vaccine formulations and cases of antiviral-drug-resistant influenza virus isolates turning up every year, it has become necessary to search for alternatives to the current treatment and prevention strategies.
cord-294467-kq5wmavt	2014	title: Characterization of haemagglutinin-esterase protein (HE) of murine corona virus DVIM by monoclonal antibodies We analyzed the characteristics of seven monoclonal antibodies (mAbs) raised against purified HE (hemagglutinin-esterase) glycoprotein of the murine coronavirus DVIM (diarrhea virus of infant mice). Neutralizing activity was shown in group A mAbs exclusively, suggesting that the ratio of HA and/or AE activities may play important roles in the cell fusion activity of DVIM-infected cells. As described in a previous report [8] , by treatment of DVIM with the non-ionic detergent NP-40 we isolated the HE protein, which carries the functional sites for both acetylesterase (AE) and the haemagglutination (HA) activities. We examined the cytopathic effect of mAbs with respect to the formation of syncytia in DVIM-infected cells. The antibodies that had low titers to both activities did not delay the fusion of infected cells.
cord-294947-g4ntyddb	2016	title: Establishment of a nanoparticle-assisted RT-PCR assay to distinguish field strains and attenuated strains of porcine epidemic diarrhea virus In this study, a nanoparticle-assisted polymerase chain reaction (nanoparticle-assisted RT-PCR) assay targeting the ORF3 of PEDV was developed to distinguish PEDV field strains from attenuated strains by using a specific pair of primers. The nanoparticle-assisted RT-PCR assay we describe here can be used to distinguish field strains from vaccine strains of PEDV, and it shows promise for reducing economic loss due to PEDV infection. The results showed that the nanoparticle-assisted RT-PCR assay could distinguish PEDV field strains from the attenuated strain in samples from infected pigs. The present study demonstrated that an effective nanoparticle-assisted RT-PCR assay targeting the ORF3 gene of PEDV was able to distinguish field strains from attenuated vaccine strains. Development of a nanoparticle-assisted PCR assay for detection of porcine epidemic diarrhea virus
cord-295308-ruwxm4fd	2008	title: Identification of a recombinant dengue virus type 1 with 3 recombination regions in natural populations in Guangdong province, China Using recombination analysis, we identified a recombinant dengue virus type 1 strain, namely, GD23/95, with three recombination regions, located within the sequences of the prM/E junction, NS1, and NS3, respectively. This appears to be the first study to confirm the existence of three recombination regions in a single dengue virus isolate and to report recombination between parent virus strains isolated from the same geographic area (Guangdong province, China). Recombination events have been proven to occur in RNA viruses such as polioviruses [3] , feline calicivirus [4] , Western equine encephalitis virus [6] , severe acute respiratory syndrome coronavirus (SARS-CoV) [20, 21, 25] , and hepatitis C virus (HCV) [2, 9, 10, 12, 17] .
cord-295409-7l0pglef	1989	The ability to propagate SDAV to high titers in the widely available L-2 cell line should promote the study of this virus and facilitate its comparison with other murine coronaviruses. In LBC cells inoculated with strain #681 of SDAV, CPE was first detected in infected cultures 48 hours pi, and syncytia were observed by 72 hours pi [11] . Viral antigen and TCIDs0 titers of 107/0.2ml could be detected in inoculated culture fluid at 24 hours pi by the tenth passage of SDAV in LBC cells [11] . Submandibular and parotid salivary glands from animals infected with the eighth pass of SDAV were homogenized to make a 10% (w/v) suspension in PBS, then 0.5 ml was inoculated onto L-2 or L-929 cells, incubated at 37 °C, and observed for evidence of viral antigen and CPE. Following 5-6 serial passages of supernatant fluid from infected cell cultures, viral antigen, infectious virus, and CPE could be readily demonstrated.
cord-296167-np0b9a7o	2010	In the present study, the 3′ terminal 7.2 kb of the genome of a recently isolated variant of IBV (N1/03) was sequenced and compared with the sequences of classical and novel strains of IBV, the two main groups of these viruses in Australia. The 3 0 -terminal 7.2 kb of the genomes of the representative classical and novel Australian IBV strains were aligned with the sequences from the same region of the N1/03 isolate, and the multiple alignment results were introduced into SimPlot version 3.5.1 to identify likely recombination sites [19] . It would be appropriate to sequence and analyse the polymerase genes of classical, novel and new variant strains of IBV to obtain further information about the relationships between the different Australian IBVs. Isolation and characterization of new infectious bronchitis virus variants in Hungary
cord-298883-uiwg482s	2001	Post-weaning multisystemic wasting syndrome (PMWS) is a recently identified disease of pigs linked to the emergence of a new porcine circovirus (PCV2). We report here the characterization of immunorelevant linear B-cell epitopes of the Open Reading Frame 2-encoded protein (Orf2) from PCV2 by an enzyme-linked immunosorbent assay (ELISA) using experimental antisera collected from pigs inoculated with a PCV2 isolate. Antibodies to the 117 to 131 epitope (B-133) were detected in 22% and 100% of specific pathogen-free (SPF) pig sera 6 and 11 weeks post inoculation, respectively. Here, we describe the characterization of an Orf2 peptide as an immunorelevant PCV2 specific linear B-cell epitope by ELISA, using sera from pigs experimentally inoculated with a PCV2 isolate, and its potential use as a serological marker to detect PCV2 antibodies following natural infection in swine herds.
cord-299342-l8ugjou9	1988	Using gut sections from pigs infected with porcine epidemic diarrhea virus (strain CV 777) and ascitic fluid from cats which had succumbed to feline infectious peritonitis (FIP), a weak cross reaction was found by immunofluorescence. No reaction was found at the nucleocapsid protein position when blots of a mock infected N L F K cell lysate had been incubated with anti-CV 777 antibodies. As shown in figure 3 , results of the RIP confirmed the cross-reaction between pig anti-CV 777 sera and the 43,000 protein of FIPV found in Western blots; the homologous reaction reveals the typical pattern of FIPV structural polypeptides with Mr of 210,000 (peplomer), 45,000 (nucleocapsid) and 25,000 to 32,000 (envelope). We have confirmed the finding of cross reactions within one group, namely between transmissible gastroenteritis virus (TGEV) of swine, FIPV and canine enteric coronavirus, and showed that common determinants are present on all three structural polypeptides [7] .
cord-299345-2i48ld8d	2019	Pairwise identity analysis of the whole genome sequences revealed that PEDV/Belgorod/dom/2008 is an intermediate between PEDV and transmissible gastroenteritis virus (TGEV) strains. Based on the phylogenetic analysis of the M gene, the PEDV/Belgorod/ dom/2008 isolate belongs to the same clade as other virulent Russian PEDV strains, indicating a high degree of sequence homogeneity in the M gene (Fig. 3a) isolate is genetically distinct and does not belong to any group (Fig. 3b ). The identification of recombinant regions in PEDV/Belgorod/dom/2008 can be useful for further analysis of evolutionary variability, epidemiology, and development of a new diagnostic gene-based assay for porcine epidemic diarrhea virus. Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China
cord-299428-gon6bzat	2012	To better understand the molecular epidemiology of infectious bronchitis virus (IBV) in the United States following the introduction of commercial IBV vaccines, we sequenced the S1 and N structural protein genes of thirteen IBV field isolates collected in the 1960s. Analysis of the S1 sequence showed that seven isolates were of the Massachusetts (Mass) genotype, five were SE17, and one was of the Connecticut (Conn) genotype, suggesting that these three IBVs were circulating in commercial poultry raised in different regions in the United States during the 1960s. In addition, the Mass-type isolates had high levels of sequence identity in the S1 gene compared with widely used modified live vaccines (Mass41, Ma5 and H120) and modern field strains from the USA and other countries, suggesting a common ancestor.
cord-299763-ttb7o8lv	2016	Necropsy performed on the dog revealed that the surgeries were not the cause of death; however, degenerative viral hepatitis, showing intranuclear inclusion bodies in hepatic cells, was observed in histopathologic examination. On analyzing the in situ hybridization images, hepatic cells surrounding the damaged regions and intranuclear inclusion bodies were found positive for MVC nucleic acid (Fig. 1) . However, the NP1 region of the 15D009 strain showed greater nucleotide and amino acid sequence similarity to that of the HM-6 strain (AB158475), which was isolated from a Korean dog in 2004 (99.1 % and 99.4 %, respectively), compared to those of the other MVC strains (mean similarities of 90.9-91.4 % and 93.0 %, respectively) ( Table 1 ). A minute virus of canines (MVC: canine bocavirus) isolated from an elderly dog with severe gastroenteritis, and phylogenetic analysis of MVC strains
cord-302063-ct5rvqtd	2016	RNA was extracted and tested by reverse transcription polymerase chain reaction (RT-PCR) for the presence of rotavirus, norovirus, astrovirus, torovirus, coronavirus and bovine viral diarrhea virus. Bovine rotavirus and bovine coronavirus (BRV and BCV) are the leading causes of viral diarrhea [2] , although bovine viral diarrhea virus (BVDV), bovine norovirus (BNoV), bovine astrovirus (BAstV) and bovine torovirus (BToV) have also been implicated. The phylogenetic analysis of the BRV-VP7 coding sequences revealed that they clustered with the G6 and G10 genotypes of group A rotaviruses (http://rotac.regatools.be/) [19] (Fig. 2) . One of the study sequences (BNoV-4) grouped differently from the remaining sequences, with 87.5 % and 96.7 % nt and aa identity, respectively, and showed maximum identity to isolates from Italy (BEC195), the UK (Aberystwyth24) and Belgium (Florennes-B242). BNoV was molecularly detected (24 %) either alone or as a co-infection with other enteric viruses (BRV and BAstV).
cord-302323-vvo8a4hp	2015	To determine whether these mutations lead to changes in antigenicity, as suggested by the failure of PEDV vaccines in China, we first optimized the codons of typical S genes of the CV777 vaccine strain (G1 subtype) and LNCT2 strain (G2 subtype) and expressed the recombinant full-length sequence of the S protein in a eukaryotic expression system. The findings of this study confirmed that the recombinant S protein was highly immunogenic in Cross serum neutralization (SN) between the S proteins of the two PEDV subtypes and anti-S PAbs. Reciprocals of PEDV neutralizing antibody titers were expressed as the dilution inhibiting PEDV infection by 50 %, which was calculated as follows: Log50 % neutralizing titer = L-d (s-0.5), where L is the log of the lowest dilution factor, d is the difference between the dilution factors, and s is the sum of the ratios of positive wells Variation between porcine epidemic diarrhea virus subtypes 545 mice and could effectively induce production of antibodies, especially neutralizing antibodies.
cord-302798-q0mbngqy	2018	In this study, the role of circoviruses (CVs) in mink acute gastroenteritis was investigated, and the MiCV genome was molecularly characterized through sequence analysis. MiCVs and previously characterized CVs shared genome organizational features, including the presence of (i) a potential stem-loop/nonanucleotide motif that is considered to be the origin of virus DNA replication; (ii) two major inversely arranged open reading frames encoding putative replication-associated proteins (Rep) and a capsid protein; (iii) direct and inverse repeated sequences within the putative 5ʹ region; and (iv) motifs in Rep. Pairwise comparisons showed that the capsid proteins of MiCV shared the highest amino acid sequence identity with those of porcine CV (PCV) 2 (45.4%) and bat CV (BatCV) 1 (45.4%). In our study, sequence analysis confirmed that MiCV genomes displayed the characteristics of members of the genus Circovirus, and the common features included their genome organization, the presence of a potential stem-loop and conserved nonanucleotide motif postulated to be the origin of viral DNA replication, and major ORFs and repeats [26, 27] .
cord-302871-x3mjov5l	2016	This study presents the pathological, immunohistochemical, and molecular findings associated with the extra-intestinal detection of canine kobuvirus (CaKV) in a 5-month-old Chihuahua puppy, that had a clinical history of bloody-tinged feces. There are few descriptions of coinfection due to CaKV and other viral agents: a recent study identified CaKV in association with a several agents including canine herpesvirus type 1 (CaHV-1), canine distemper virus (CDV), canine parvovirus (CPV), and canine adenovirus A types 1 (CAdV-1) and 2 (CAdV-2) in diarrheic and non-diarrheic dogs from Korea [19] . Furthermore, widespread viral dissemination was demonstrated in multiple tissues as CaKV nucleic acids were detected in the liver, lung, brain, and tonsils of this Fig. 2 Phylogenetic analysis of a partial nucleotide sequence (nt 201) of the RdRp gene (a) and partial region of the VP1 protein (nt 303) of canine kobuvirus (CaKV) (b).
cord-304109-yirs7kjg	2009	The polyomaviruses KI (KIPyV) and WU (WUPyV) have recently been discovered in specimens from patients with respiratory tract infections. Nasopharyngeal aspirates or bronchoalveolar lavage specimens of 229 children with acute respiratory tract infection were screened for KIPyV and WUPyV using polymerase chain reaction-based methods. Since 2001, an increasing number of ''''new'''' respiratory viruses have been detected in children with respiratory tract infection (RTI), including the human metapneumovirus (hMPV) and the human bocavirus (hBoV) [4, 15] . The authors amplified and cloned the genome of WU Polyomavirus (WUPyV) from NPA of a 3-year-old patient with pneumonia without detection of other respiratory pathogens. The very low prevalence of polyomavirus KI and WU DNA in NPA specimens of 3 out of 229 pediatric patients with acute RTI in this series does not confirm or exclude a pathogenic role of these newly described viruses. Presence of the newly discovered human polyomaviruses KI and WU in Australian patients with acute respiratory tract infection
cord-305859-vt8vwo3y	2017	Fecal virus shedding, seroconversion and histopathology were evaluated in 3-7-year-old gnotobiotic calves orally inoculated with porcine deltacoronavirus (PDCoV) (9.0-9.6 log(10) genomic equivalents [GE] of OH-FD22-P5; n=4) or porcine epidemic diarrhea virus (PEDV) (10.2-12.5 log(10) GE of PC21A; n=3). In PDCoV-inoculated calves, an acute but persisting fecal viral RNA shedding and PDCoV-specific serum IgG antibody responses were observed, but without lesions or clinical disease. Our study demonstrated that Gn calves orally inoculated with the PDCoV strain OH-FD22 (ICs of cell-culture grown PDCoV from infected Gn pigs) develop an acute infection with persistent fecal PDCoV RNA shedding and PDCoVspecific serum IgG antibody responses, but show no signs of significant intestinal lesions or clinical disease [8] . In our study, there were no detectable fecal viral RNA shedding, virus-specific serum IgG antibody responses, histological lesions, and clinical disease in Gn calves orally inoculated with the PEDV strain PC21A (ICs of wild-type PEDV-infected Gn pigs) [6] .
cord-306380-msk9p1yy	2000	Phylogenetic analysis of selected regions of the genome of the DE072 serotype field isolates further support those results and indicate that isolates within the same serotype may have different amounts of nucleotide sequence similarity with each other in individual genes other than the S gene. Further, we conducted sequence analysis of six isolates of the DE072 serotype in order to determine if recombination is frequently occurring in this region in field isolates of IBV. We conducted phylogenetic analysis by dividing 3.8 kb of the 3 end of the genome among five IBV strains at the IG sequences. However, these 6 isolates had a much different level of nucleotide sequence similarity with each other in gene 3 and gene 4, and clustered randomly with other serotypes of IBV (Fig. 3) . Sequence analysis of gene 3, gene 4 and gene 5 of avian infectious bronchitis virus strain CU-T2 Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus
cord-306725-0vam15pt	2020	Sequence analysis showed that the two isolates shared 10 identical amino acid mutations in the S protein compared to the complete S sequences of BToV available in the GenBank database. A phylogenetic analysis based on the complete amino acid sequence of the S protein showed that the BToVs could be separated into four groups (Fig. 2) , designated tentatively as group 1 to group 4. The bovine torovirus strains BToV/SC-1/China and BToV /SC-2/China investigated in this study are indicated by black triangles Fig. 2 Phylogenetic tree based on the deduced 1586-aa sequence of the complete S gene. Moreover, the two Chinese strains shared identical unique amino acid changes in the S and HE genes when compared to the other strains with sequences available in the GenBank database, indicating the unique evolution in Chinese BToV strains. Moreover, two complete BToV genome sequences were obtained from the clinical samples, and these two BToV isolates had unique amino acid changes in the S and HE proteins.
cord-307098-oq7zrnuv	2014	Co-cultivation of MHV-nonpermissive hamster BHK cells devoid of mouse Bgp with mouse DBT cells infected with MHV-A59 or JHMV induces syncytia formation on BHK cells (Bgp-independent fusion). Under a phase contrast microscopy, JHMV (cl-2, sp-4) induced the Bgp-independent syncytia on BHK cells similar to those observed on DBT cells, while such syncytia were not seen with the infection of other MHV strains (MHV-1, MHV-3, MHV-A59, MHV-S, srr7, srr11 and srr18). Interestingly, no syncytia formation was demonstrated on BHK cells with other strains or srr mutants under the phase contrast microscopy, though all of them produced syncytia on Bgp-positive DBT cells [10] . The cl-2 S protein could have a very strong Bgp-independent fusion activity, but its replication in BHK cells could be less efficient than the other MHV strains. Present study showed that JHMV (cl-2 and sp-4) could induce syncytia on BHK cells detectable by microscopy, whereas the other MHVs and srr mutants failed.
cord-307378-cx1jz7wf	2020	Since the first official report of the spread of SARS-CoV-2 infections in the city of Qom in mid-February, Iran has become the country most affected by the COVID-19 epidemic in the Middle East. The aim of the present study was to evaluate whether the distance from the epicenter of the infection (Qom) or demographic factors such as population density and the ratio of the elderly population are associated with the incidence of COVID-19 in different Iranian provinces. Through regression analysis, this study aimed to evaluate whether the distance of different Iranian provinces from the epicenter of the infection (Qom) was associated with the incidence of COVID-19 at the early stages of the epidemic in Iran. COVID-19 has spread to all 31 Iranian provinces, and the city of Tehran, the densely populated capital with over 13 million people located 150 km northeast of Qom, leads the country in COVID-19 cases ( Table 1) .
cord-307408-6wfx0wey	2013	title: Phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in central China based on the ORF3 gene and the main neutralization epitopes In this study, we aimed to investigate the molecular epidemiology and antigenic variability of PEDV field strains based on analysis of ORF3 and a portion of the S gene encoding three neutralizing epitopes (aa 499-638, 748-755, and 764-771) of the S protein. To further investigate the molecular epidemiology of this virus, we chose the ORF3 gene and a partial S gene encoding a region including three neutralization epitopes for studying the evolutionary characteristic and antigenic variation of PEDV. Based on the sequence analysis of ORF3 and partial S genes of PEDV, molecular epidemiology was conducted using 14 field strains from central China. Sequence and phylogenetic analysis of nucleocapsid genes of porcine epidemic diarrhea virus (PEDV) strains in China
cord-308950-bl83r4v3	2002	Our objective was to determine if fAPN can serve as a receptor for infectious bronchitis virus (IBV). Feline kidney cells that express fAPN and hamster kidney fibroblasts that do not express fAPN were inoculated with IBV and monitored for replication by indirect fluorescent assay and confocal microscopy and in chicken embryonated eggs. To evaluate the permissiveness of cells to IBV, monolayers of transfected (pBK-fAPN and pBK-CMV) BHK-21, non-transfected BHK-21 and FEK on coverslips were infected with a 10 3.2 EID 50 of Ark/IBV virus. To test the hypothesis that the feline APN had a role in permissiveness of FEK cells to Ark/IBV, BHK-21 cells were transfected with pBK-CMV plasmid or pBK-fAPN. The BHK-21 cells transfected with pBK-fAPN were shown to express the fAPN receptor on the cell surface (Fig. 3) , and were permissive to Ark/IBV (Figs.
cord-309145-6aqc074e	1994	The interferon induction system, in which attachment of virus glycoprotein to the cellular receptor on the cell surface triggers interferon induction in lymphoid cells, is similar to a system in which plant lectins such as concanavalin A (Con-A) and phytohemagglutinin (PHA) stimulate lymphocytes and consequently induce interferon. For example, sialyl-oligosaccharides are receptors for parainfluenza and influenza viruses [62] , human membrane cofactor protein (CD46) for measles virus [13, 58] , MHC class I for Semliki Forest virus (SFV) [24] , MHC class II for lactose dehydrogenase virus (LDH virus) [26] , phosphatidylserine and phosphatidylinositol for vesicular stomatitis virus (VSV) [51] , the CD4 for human immunodeficiency virus (HIV) [11, 43] , the C3d receptor CR2 for Epstein-Barr virus [15, 59, 69] , acetylcholin receptor for rabies virus [47] , the intercellular adhesion molecule-1 (ICAM-1) for the major subgroup of human rhinoviruses [23, 67, 69] , another member of the immunoglobulin superfamily for poliovirus [45, 54-1, a basic amino acid transporter for gibbon ape leukemia virus and feline leukemia virus [1, 40, 68, 70, 71] , aminopeptidase N [13, 75-1 or a member of the carcinoembryonic antigen family of proteins for the coronavirus virus [14] , a high-affinity laminin receptor for sindbis virus [72] , ~2 subunit of human VLA-2 for echoviruses 1 and 8 [5] , erythrocyte P antigen for B19 Parvovirus Viral glycoproteins and interferon induction 193 [6] , and CD13 (human aminopeptidase N) for cytomegalovirus [66] .
cord-310669-6hwq5jfv	2005	Two training centres for working dogs were monitored for one year to determine the presence of viruses and viral antibodies and their association with canine infectious respiratory disease (CIRD). Canine herpesvirus (CHV) has been detected in dogs with CIRD [3] the importance of this infection in the pathogenesis of the disease however has not yet been determined. From dogs that were not on the study but showed clinical symptoms of CIRD, both a blood sample and a swab were taken at the time of disease as well as four weeks after. In total twelve out of 54 serum samples (22.2%) obtained from dogs on the day they entered Kennel A were positive for antibodies to CRCoV. None of the samples obtained from dogs at Kennel B tested by PCR for CRCoV (n = 28), CPIV (n = 18), CAV (n = 9) or CHV (n = 26) were found positive.
cord-311773-r9c7sx6r	1991	Cell lines of rodent origin were tested for susceptibility to infection with rat coronavirus (RCV), including sialodacryoadenitis virus (SDAV) and Parker''s rat coronavirus (PRCV). In a single attempt to isolate SDAV-681 from the lung of an experimentally infected rat, syncytia and viral antigen were first seen after 6 passages in untreated L2 (Percy) cells. Based on this finding, a small study was initiated to ascertain the sensitivity of trypsin-treated L2 (Percy) cells for primary isolation of RCVs. Virus isolations were attempted using tissue homogenates previously tested for SDAV-681 by infant mouse inoculation (Table 4 ). Of the cell lines and treatments tested, L2 (Percy) cells treated with trypsin supported maximal growth of RCVs as evidenced by syncytium formation and viral antigen. RCV growth in L2 (Percy) cells was not enhanced by trypsin treatment of later passages when the enzyme was added at the time of virus inoculation.
cord-312338-r6jqmes3	2012	This study aimed to identify the most common viral strains responsible for respiratory tract infections in asthma/COPD patients (without exacerbations) in Qatar during the winter season (2008) (2009) . This study aimed to identify the most common viral strains responsible for respiratory tract infections in asthma/COPD patients (without exacerbations) in Qatar during the winter season (2008) (2009) . carried out a study in the UK to investigate the role of viral infections in acute exacerbations of asthma in schoolchildren, and they reported that the most commonly identified virus type in this population was rhinovirus [3] . During October 2008-March 2009, adults with COPD or asthma, seeking care at the Chest clinic of the Hamad Medical Corporation, Qatar, with symptoms of upper respiratory tract infection were eligible for participation. Our study is the first in Qatar to analyse the clinical aetiology of respiratory tract viral infections in adult patients from all age groups with asthma or COPD.
cord-312787-j7ye7ed5	1996	coli-expressed ORFs 5 to 7 gene products, suggested that antibodies directed against the envelope E protein appear by day 7 p.i., whereas antibodies directed against the nucleocapsid N and membrane M proteins can only be detected by the end of the second week p.i. No correlation could be demonstrated between VN and IIF antibody titers, viremia, and viral protein specificities of circulating antibodies at various times p.i. Summary. coli-expressed ORFs 5 to 7 gene products, suggested that antibodies directed against the envelope E protein appear by day 7 p.i., whereas antibodies directed against the nucleocapsid N and membrane M proteins can only be detected by the end of the second week p.i. No correlation could be demonstrated between VN and IIF antibody titers, viremia, and viral protein specificities of circulating antibodies at various times p.i. The porcine reproductive and respiratory syndrome virus (PRRSV) is an enveloped RNA virus which has been found to be responsible for reproductive failure in sows of any parities (late-term abortions, increased numbers of stillborn, mummified and weakborn pigs) and respiratory problems affecting pigs of all ages [8, 20] .
cord-314069-8dxzf2ip	2016	authors: Dongliu, Yuan; Guoliang, Yang; Haocheng, Xu; Shuaijia, Qing; Li, Bing; Yanglei, Jia This study reports an outbreak of acute febrile respiratory illness caused by human adenovirus B [P14H11F14] in a military training center in China between May and June 2014. A HAdV-B [P14H11F14] virus was confirmed as the etiological pathogen of this acute outbreak of febrile respiratory illness based on clinical manifestations, epidemiological characteristics, specific molecular detection results, phylogenetic analysis, and serological assays. In conclusion, the regional CDC officials concluded that a type-55-like human adenovirus B human/CHN/SD77001/ 2014/[P14H11F14] virus was the etiological pathogen responsible for this acute FRI outbreak based on the clinical manifestations in the patients, the epidemiological characteristics of the outbreak, the HAdV-DNA-specific PCR results, isolation of the virus, sequencing and alignment of the PCR amplicons, homology and phylogenetic analyses based on the complete E1A, penton base, hexon, and fiber gene sequences, and serological assays specific for HAdV IgA/IgG.
cord-314751-i9rxesrg	2014	In this study, a codon-optimized PEDV S1 gene containing amino acid residues 25–738 was synthesized based on a multiple alignment of the S amino acid sequences of PEDV field isolates and used to establish a stable porcine cell line constitutively expressing the PEDV S1 protein. In the present study, therefore, we first synthesized a full-length, codon-optimized PEDV S1 gene and then generated a stable porcine-origin cell line constitutively expressing the recombinant S1 protein. These results were coincident with the rabbit study described above, since the rabbit antisera generated by immunization with the recombinant S1 protein also contained low levels of neutralizing antibodies to the heterologous PEDV vaccine strain. In the present study, the first aim was to stably express the full-length, codon-optimized S1 gene of PEDV in porcine-origin cells and to evaluate the immunogenicity and efficacy of the recombinant S1 protein.
cord-315811-wpeac0lk	2016	The aims of our current study were to investigate i) the pathogenicity of the tissue-culture-grown PDCoV (TC-PDCoV) strain OH-FD22 at passage 5 (P5), P20, and P40 on LLC-PK cells in 14-day-old Gn pigs compared with that of the wild-type parent virus [12] ; ii) Fecal PDCoV shedding, viremia, and pathology tested at post-inoculation day (PID) 1 to 23-24 or PID 28; iii) possible attenuation of TC-PDCoV OH-FD22 P40, the highest passage in cell culture among the passages tested; iv) serum-PDCoV-specific IgG and IgA and virus neutralization (VN) antibody titers and any differences in the titers among OH-FD22 P5, P20, and P40-inoculated pigs; and v) the genetic stability of TC-and Gn-pig-passaged PDCoV OH-FD22 P5, P20, and P40 by analysis of the complete spike (S) and nucleocapsid (N) gene sequences. Regardless of the cell culture passage number of the virus strains used, serum virus neutralization (VN) antibodies were first detected in all of the original and TC-PDCoV OH-FD22-inoculated pigs at PID 7 (64-256), and thereafter, the titers increased gradually and peaked at PID 23/24.
cord-316153-wet0go35	1995	An antigenic variant of avian infectious bronchitis virus (IBV), a coronavirus, was isolated and characterized. Therefore, several recently reported diagnostic and serotyping methods of IBV which are based on dot-blot hybridization, restriction fragment length polymorphism (RFLP), and polymerase chain reaction (PCR), may not reveal the true antigenic and/or genetic nature of IBV isolates, and may in fact yield misleading information. More recently, two American field isolates were found to contain fragments of Mass-like sequences in the S1 gene, which were 94% to 95% homologous to IBV strain Mass41 [38] . Sequence data were obtained from cDNA clones, except for the first 1100 bases of the S gene, the last 200 bases of the N gene, the 3'' end non-coding region of CU-T2, and the partial Gene3 of Ark99 and Ho1152, which were obtained from direct sequencing of IBV genomic RNA. Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus
cord-316525-uadfehr6	2004	Surprisingly, we found that 7 putative recombination regions, located in Replicase 1ab and Spike protein, exist between SARS-CoV and other 6 coronaviruses: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), human coronavirus 229E (HCoV), murine hepatitis virus (MHV), and avian infectious bronchitis virus (IBV). After potential recombination events were identified by at least 3 methods above, separate neighbor joining trees were constructed for each putative recombination region to better evaluate the evidence for conflicting evolutionary histories of different sequence regions. Two regions (13151-13299 and 16051-16449, position in alignment) are identified as putative recombination regions and all 6 coronaviruses are potential parents with SARS-CoV as potential daughter. In this study, seven recombination detection methods and phylogenetic analyses were performed on SARS-CoV and the six coronaviruses identified by BLAST (IBV, BCoV, HCoV, MHV, PEDV and TGEV).
cord-316797-sf2lu45f	1985	Rat coronavirus readily propagated and induced marked cytopathic effect in a rat cell line, LBC cell culture, which provided a sensitive, practical assay system for viral infectivity and neutralizing antibody, and a satisfactory source of the virus. The growth of RCV has been reported on a primary rat kidney cell culture but not on any established cell lines. This brief communication recommends a rat cell line, LBC, providing propagation of RCV and useful tool for infectivity assay. The culture fluid sampled at ¢8 hours p.i. was assayed for infectivity by inoculating into LBC cells prepared in 13 × 100 mm test tubes, showing an infectivity titer of i07.5 50 per cent tissue culture infective doses (TCIDs0)/0.2 ml. The LBC cell culture might be a much more useful tool for RCV propagation and assay. The LBC cells can also support growth of siModaeryoadenitis virus of rat, strain 681 (1), but not of MHV strains (unpublished observation).
cord-317009-8tqnt1l9	2011	However, other viruses, including bovine torovirus (BToV), are also suspected to be etiologic agents of diarrhea [14, 15, 21] , although the epidemiological situation of infections caused by these viruses in adult cattle remains unclear. In the present study, we report the epidemiological features of three outbreaks of epidemic diarrhea in adult cows between May 2007 and February 2008 at three dairy farms in Niigata Prefecture, Japan, in which BToV was detected as the only pathogen. Further, we describe the isolation of a cytopathogenic BToV strain from diarrheic feces using HRT-18 cells, as well as the molecular characterization of the detected BToVs. Three epidemic outbreaks of adult cattle diarrhea occurred between May 2007 and February 2008 in Niigata Prefecture, Japan. Here, we examined the etiological agents and conducted detailed serological tests with samples from three outbreaks of adult cattle diarrhea in Niigata, Japan, and found that BToV was the only causative pathogen.
cord-317617-snrumw3x	1981	Recently, a new viral agent (DVIM) was isolated from an infant mouse with diarrhea, by the utilization of cultured cells. It has also been shown by complement fixation tests that this new isolate is antigenically related to known coronaviruses, avian infectious bronchitis virus (IBV) and mouse hepatitis virus strain-2 (MHV-2). A virus isolated from t h e intestine of a n i n f a n t mouse w i t h clinical signs of diarrhea, d e s i g n a t e d DVIM, was generously p r o v i d e d b y Dr. K o z a b u r o Sato (Central L a b o r a t o r y of Shionogi P h a r m . Mouse hepatitis virus (MHV), a member of coronaviruses, has been described as a common cause of enteric infection in baby mice (8, 21) . Lethal enteritis in infant mice caused by mouse hepatitis virus New strain of mouse hepatitis virus as the cause of lethal enteritis in infant mice
cord-318731-vlszl0i8	2019	title: Molecular characterization of HLJ-073, a recombinant canine coronavirus strain from China with an ORF3abc deletion Interestingly, sequence analysis suggested that HLJ-073 contained a 350-nt deletion in ORF3abc compared with reference CCoV isolates, resulting in the loss of portions of ORF3a and ORF3c and the complete loss of ORF3b. This is the first report of the isolation of strain HLJ-073 in China, and this virus has biological characteristics that are different from those of other reported CCoVs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-019-04296-9) contains supplementary material, which is available to authorized users. In the present study, we report the emergence and molecular characterization of an, FCoV-like recombinant CCoV-HLJ-073, which was isolated from a fecal sample from a dead dog that exhibited enteritis. We isolated a canine coronavirus with a deletion in the ORF3abc region from a dead dog in China.
cord-321195-cndq6aqb	2014	In this study, we have developed a chimeric virus-like particle (VLP) vaccine candidate for porcine reproductive and respiratory syndrome virus (PRRSV) and H3N2 influenza virus and investigated its immunogenicity in mice. The HA and M1 proteins from the H3N2 influenza virus and the PRRSV GP5 protein fused to the cytoplasmic and transmembrane domains of the NA protein were both incorporated into the chimeric VLPs. Analysis of the immune responses showed that the chimeric VLPs elicited serum antibodies specific for both PRRSV GP5 and the H3N2 HA protein, and they stimulated cellular immune responses compared to the responses to equivalent amounts of inactivated viruses. Serum samples were collected on the 14th, 28th, and 42nd day after primary immunization of mice (8 per group) vaccinated with chimeric VLPs, inactivated H3N2 virus, or PBS. A trivalent virus-like particle vaccine elicits protective immune responses against seasonal influenza strains in mice and ferrets
cord-321471-gev5xq3a	2013	The activation of PI3K-Akt pathway promotes cell survival by the phosphorylation of numerous substrates such as glycogen synthase kinase-3 (GSK-3), FoxO1, Bad and mTOR [5, 11, 24, 36, 38] . Previous studies have shown that during PRRSV infection of porcine monocyte-derived dendritic cells (Mo-DCs), the PI3K/Akt pathway is activated at 90 min and 4 h postinfection (h p.i.), and it is inhibited at 12 h p.i. A number of studies have shown that the PI3K/Akt signaling pathway is functionally dependent on downstream substrates of Akt such as FoxO1, Bad and mTOR for regulation of cell survival [3, 11, 15, 25] . Since increased phosphorylation of Akt induced by HP-PRRSV was observed at 5 min and 15 min postinfection in virus-infected MARC-145 cells, and at 5, 15 and 30 min postinfection in PAMs, we hypothesized that the virus entry process accounted for this early-stage activation.
cord-322593-bgm6smuo	2016	In this present study, we assessed the antiviral properties of recombinant porcine SP-A (RpSP-A) on PRRSV infection in Marc 145 cells and revealed its antiviral mechanism using a plaque assay, real-time qPCR, western blotting analysis and an attachment and penetration assay. Our results showed that RpSP-A could inhibit the infectivity of PRRSV in Marc 145 cells and could reduce the total RNA and protein level. Notably, porcine ficolin is also a collagenous lectin that was established to reduce PRRSV infection in Marc-145 cells in neutralization assays and to inhibit the replication of infectious viral particles in a GlcNAc-dependent manner [30] . Porcine reproductive and respiratory syndrome virus-infected alveolar macrophages contain no detectable levels of viral proteins in their plasma membrane and are protected against antibody-dependent, complement-mediated cell lysis Recombinant porcine lung surfactant protein A inhibits porcine reproductive and respiratory syndrome virus infection into host cells in vitro
cord-322760-tsxniu3j	2016	Thus, older age, pre-existing concurrent diseases, and delayed confirmation increase the odds of a fatal outcome in nosocomial MERS-CoV outbreaks in the Middle East and South Korea. Information on all laboratory-confirmed MERS cases was obtained from various publicly available sources, including WHO Global Alert and Response updates, documents officially released by the local health bureau, news releases from Middle Eastern and South Korean authorities, the Weekly Epidemiological Record, ProMed posts, and literature published from 1 April 2012 to 29 June 2016 (http:// www.who.int/csr/don/archive/disease/coronavirus_infections/ en/). In this study, we compared the mortality risk factors in two different nosocomial outbreaks, based on 51 nosocomial outbreaks of MERS-CoV infection in the Middle East and one large outbreak identified in South Korea. The severity of nosocomial outbreaks and the risk of fatal infection in HCP were significantly lower than the overall rate in the Middle East and South Korea. Middle East respiratory syndrome coronavirus (MERS-CoV) nosocomial outbreak in South Korea: insights from modeling
cord-324377-br2uorg8	2015	We determined the antiviral effect of Lithium Chloride on canine parvovirus type 2 in feline kidney cells. These results indicated that lithium chloride could be a potential antiviral drug for curing dogs with canine parvovirus infection. The specific steps of canine parvovirus entry into cells that are affected by lithium chloride and its antiviral effect in vivo should be explored in future studies. As a control, cells infected with the same dose of CPV were not treated with LiCl. Subsequently, the antiviral efficacy was evaluated by analysis of viral RNA levels, protein expression level and CPE. These results indicate that treatment of F81 cells with LiCl inhibits CPV infection and reduces the cytopathic effect in a dose-dependent manner. No significant differences in the relative levels of viral VP2 gene DNA or viral titers were observed between drug-treated and mocktreated cells, indicating that LiCl had no effect on CPV attachment and replication in F81 cells ( Fig. 4A and B) .
cord-324495-0pee1i3o	2015	
cord-325827-492xi3ee	1988	Subsequent observations based upon seroepidemiological surveys and electron microscopy of fecal material verified that cheetahs were indeed capable of being infected by coronaviruses, which were antigenically related to coronaviruses affecting domestic cats, i.e. feline infectious peritonitis virus/feline enteric coronavirus. The purpose of this review is to present desciptions of the various forms of coronaviral infections in the cheetah relying upon studies of both natural infections, as well as experimental infections in other species with coronaviruses, such as mouse hepatitis virus (MHV), canine coronavirus (CCV), transmissible gastroenteritis virus (TGEV) of swine, and bovine coronavirus (BCV) of neonatal calves [28, 36, 39, 49, 57, 60, 61, 75, 79, 92] . The occurrence of coronaviral infections of the cheetah have now been documented based on serology, electron microscopy of fecal contents, and the occurrence of fatal forms of infectious peritonitis compatible with the clinicopathologic signs observed in domestic cats with FIP [7, 10, 26, 29, 38, 43, 56, 72] .
cord-327855-txryqil7	2003	Analysis of total cellular RNA from HM175/18f infected FrhK4 cells by denaturing agarose gel electrophoresis and Northern blot hybridization revealed extensive degradation of both the 28S and 18S ribosomal RNA (rRNA) molecules. In this study, we report that infection of FrhK4 cells with the HAV cp strain HM175/18f results in the degradation of ribosomal RNA (rRNA) and the reduction of several cellular mRNAs including β-actin and GAPDH. Degradation of rRNA is a feature of virus infection in interferon (IFN) treated cells and is believed to be due to the availability of double stranded RNA (dsRNA) during replication or transcription of the viral genome, resulting in the activation of the RNase L pathway [58, 59] . While the role of a viral protein in the activation of 2-5A/RNase L pathway in 18f or CBV1 infected FrhK4 cells cannot be ruled out, previous reports with EMC virus and the studies involving dsRNA clearly suggests a similar mechanism of rRNA degradation reported here.
cord-328381-bfvdhai8	2005	In all susceptible cell lines mRNA of the Angiotensin-converting enzyme 2 (ACE2), the functional receptor for SARS-CoV infection, could be detected by RT-PCR. In contrast, 50% of the Huh-7 cells were positive for viral antigen not until 31 h after infection ( The quantification of SARS-CoV RNA by quantitative real-time PCR revealed a significant increase of intracellular viral RNA in Vero E6, Huh-7, POEK, (Fig. 1/I A-C) and PS cells (data not shown). An increase of SARS-CoV RNA was detected in the supernatant of infected Vero E6, Huh-7, POEK ( Fig. 1/I A-C) and PS cells (data not shown). As expected, the investigation of all SARS-CoV susceptible cell lines (Vero E6, Huh-7, POEK and PS) for mRNA of ACE2 was positive in all cases though we failed to detect ACE2 expression by IFA, Western Blot and FACS analysis using commercially available monoclonal and polyclonal antibodies (ALPHA DIAGNOSTICS, San Antonio, USA) against human ACE2 (data not shown).
cord-329145-424vv8a8	2012	Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). Unfortunately, most ICTV Study Groups or other expert groups have not provided clear guidelines in the past, accepting strain and genetic variant names as they were suggested by different researchers in their publications rather than creating consistent nomenclature schemes that apply at least to all viruses of one family. To differentiate uncultured or passage 0 filoviruses for which near-complete genomic data are available from those that exist in culture, we propose to follow the suggestions of the Rotavirus Classification Working Group and to add the suffix ''''-wt'''' (for ''''wild-type'''') to their genetic variant names as outlined above.
cord-330035-0d6w8xyd	2017	
cord-330825-apfcql4m	2016	title: Phylogenetic tracking of current porcine epidemic diarrhea virus (PEDV) strains in the Philippines Since the receptor-binding sites and majority of the neutralization epitopes are located in the S1 portion, this region has been subjected to sequencing and molecular analysis to determine the genetic relatedness of different PEDV viruses [1] [2] [3] . Using data from swine farms in these provinces and diagnosis data from the College of Veterinary Science and Medicine in Central Luzon State University, the incidence is 67 % in Pampanga, 79 % in Tarlac, 61 % in Batangas, and 90 to 100 % in Agusan. This is the first report of PEDV S1 gene sequences from the provincial PEDV hotspots of the Philippines, which include Batangas, Pampanga, Tarlac and Agusan. Phylogenetic analysis of the spike (S) gene of the new variants of porcine epidemic diarrhoea virus in Taiwan Molecular characterization of the spike and ORF3 genes of porcine epidemic diarrhea virus in the Philippines
cord-332811-kjgah8ts	2015	title: Immunoprophylactic effect of chicken egg yolk antibody (IgY) against a recombinant S1 domain of the porcine epidemic diarrhea virus spike protein in piglets A codon-optimized PEDV S1 gene consisting of amino acid residues 25–749 was synthesized and used to establish a stable porcine cell line constitutively expressing a recombinant PEDV S1 protein containing the chicken immunoglobulin Fc fragment at its C-terminus. Moreover, oral passive immunization using chicken IgY raised against the PEDV S1 protein was found to control and prevent PED post-challenge in suckling piglets. All neonatal piglets except for animals in the control group were inoculated orally with 1 ml of the small-intestine homogenate containing 10 4 TCID 50 /ml PEDV field virus determined using real-time RT-PCR as described previously [10] . Immunoprophylactic effect of chicken egg yolk immunoglobulin (IgY) against porcine epidemic diarrhea virus (PEDV) in piglets
cord-333043-fe24ezt6	1977	uriae collected in the seabird colonies at Runde, Norway, two identical virus strains demonstrating no antigenic relationships to major arbovirus groups were isolated. Until then., no arbovirus isolates had been reported from this country, although ecological and cli-nicaI/epidemiological considerations (3, 24, 26) and a limited serological survey on bovine sera (28) indicated the existence of Central-European tick-borne encephalitis virus fool. uriae ticks collected at Runde in late September 1973, three virus strains have been isolated. Cells were washed with saline, virus was diluted ~enfold from 10 -1 to t0 -6 in the medium, A volume of 0.2 ml of each dilution was inoculated into three tubes and allowed to adsorb for 1 hour at room temperature before washing with saline and addition, of new medium, Culture tubes were incubated for 8 days at 37 ° C and inspected daily for a Cytopathie effect (CPE). Virus from mouse brains and cell culture demonstrated total i d e n t i t y b y these methods.
cord-333331-ddcz7zck	2011	An improved, sensitive, specific, and rapid one-step reverse transcription loop-mediated isothermal amplification (LAMP) assay targeting the 5′ untranslated region (UTR) was developed to detect hepatitis C virus (HCV) infection. A variety of molecular diagnostic assays, such as reverse transcriptase PCR [12] , nucleic-acid-sequence-based amplification [13] , transcription-mediated amplification [29] , branched-chain DNA assay [26] , and in-house realtime PCR [8] , have been developed for the detection of HCV RNA. Confirmed cases of HCV infection were verified by a positive result in an enzyme-linked immunosorbent assay (Kehua Bio-engineering, Shanghai, China) for antibodies against HCV or a quantitative real-time PCR for HCV RNA. Given that the sensitivity of the AP-LAMP assay for detecting HCV is higher than that of the pre-LAMP method, the pathway of AP-based amplification was investigated. Reverse transcription-loop-mediated isothermal amplification assay for rapid detection of hepatitis E virus
cord-333403-imx3990a	1989	The characteristics of a temperature sensitive feline infectious peritonitis virus (TS-FIPV) were examined. Viral structural proteins and RNA were synthesized at 39 °C but some undefined maturational defect prevented the formation of infectious TS-FIPV at its nonpermissive temperature. TS-FIPV proteins in supernatants from cells infected at 31 °C and 39 °C were examined by Western blot. Immune sera from both TS-FIPV vaccinated cats and WT-FIPV challenged cats showed the same differences in the envelope protein of the two viruses as did the monoclonal antibody (data not shown). The culture supernatant from TS-FIPV infected cells was monitored for the appearance of structural proteins at both the permissive and nonpermissive temperatures. All three structural proteins of TS-FIPV were detected in the cells by IFA at both the permissive and nonpermissive temperatures ( Table 2 ). Surface expression of TS-FIPV and WT-FIPV peplomer and envelope proteins but not nucleocapsid at the optimal temperature for each virus resembles the situation in FIPV-infected macrophage-like cells [8] .
cord-333636-h2sg6shp	2003	
cord-334090-66d8c75g	2016	Thus, the spread of viral respiratory diseases has become the most commonly reported condition in commercial broiler flocks in Iraq; however, there have been no studies on the detection and genotyping of these viruses using molecular techniques and sequencing. Phylogenetic analysis of the 32 strains (Fig. 2) revealed that Iraqi IBV strains could be classified into four genetic groups or genotypes: group I, variant 2 IS/1494-like viruses, including 15 field isolates (46.87 %); group II, 793/Blike viruses, including 13 field strains (40.62 %); group III, QX-like viruses, including three field strains (9.37); and caused by bacteria and mycoplasmas have already been detected on broiler farms located in the central and southern parts of Iraq. Our result were in line with those of Mahmood et al., who conducted the first study of identification and genotyping of IBV isolates and indicated that the 4/91-like virus is circulating on vaccinated broiler farms of the Kurdistan region of Iraq [21] .
cord-334810-hw1aijwf	2009	In August 2007, European bat lyssavirus type 2 (EBLV-2) was isolated from a Daubenton''s bat found at Stokesay Castle. However, studies with EBLV-1 infection in the natural host, Eptesicus serotinus, showed no substantial pattern of virus distribution in different non-neuronal organs in bats that developed disease [7] . Whilst this is widely documented for larger species, low levels of viable virus or viral RNA detected in saliva swabs tested during experimental studies with different bat lyssaviruses highlight the difficulty in determining the importance of this route of transmission for virus dissemination within a roost [5, 11, 14] . Detection of high levels of European bat lyssavirus type-1 viral RNA in the thyroid gland of experimentally infected Eptesicus fuscus bats Experimental infection of Serotine bats (Eptesicus serotinus) with European bat lyssavirus type 1a (EBLV-1a) Experimental study of European bat lyssavirus type-2 infection in Daubenton''s bats (Myotis daubentonii)
cord-335690-66t5fjld	1996	For this study we exploited the use of glutathione-S-transferase (GST)-core fusion proteins attached to an insoluble matrix (Glutathione Sepharose 4B) for rapid RNAprotein binding assays, and extended some of these results by mobility shift assays [17] which were possible because of the relatively small size of the RNA probes, KUN UTR probes bound strongly to fusion proteins incorporating full length or mature C, and to the isolated amino-terminal or carboxy-terminal domains of mature C. In attempts to define which regions of the mature form of C were binding to RNA, three regions enriched in basic amino acids were chosen arbitrarily for All these deleted fusion proteins bound to 3'' UTR and 5'' core probes on beads as efficiently as C107 (Fig. 3a) .
cord-338607-22f04uqe	1991	title: Genomic relationship between turkey and bovine enteric coronaviruses identified by hybridization with BCV or TCV specific cDNA probes Genomic relationships between turkey and bovine coronavirus (TCV and BCV), which are currently placed in distinct antigenic groups, were demonstrated by hybridization using specific cDNA probes. BCV-specific recombinant plasmids p 52, p 27, and p 247, which served previously for the optimization of hybridization conditions for BCV-RNA detection [33] , and probes pN 17 and pN 9, holding respectively the BCV N and M gene ( Fig. 1) , were used in the detection of several coronaviruses in order to establish the presence of potential genomic homologies. Clinical diagnosis of TCV was assayed with a pool of six 32p-labelled BCV specific recombinant plasmids (pBCV-pool), holding non-overlapping eDNA sequences, in order to amplify the detection signal. Detection signals were absent when testing spotted supernatant fluids of non-infected HRT-18 cells (Fig. 2) and when probing identical blots with 32p-labelled pUC-DNA (not shown), confirming the specificity of the hybridization signals obtained.
cord-338641-s006a7m0	2006	title: Reverse transcriptase-polymerase chain reaction for the detection equine rhinitis B viruses and cell culture isolation of the virus The RT-PCR was used to detect viral RNA in six of 17 nasopharyngeal swab samples from horses that had clinical signs of acute febrile respiratory disease but from which ERBV was not initially isolated in cell culture. Virus isolation in cell culture had been attempted for all 17 nasopharyngeal swab samples, but no CPE was visible during three passages on RK13, Vero and EFK cells. The conclusive determination of ERBV as the cause of equine respiratory disease by detection of virus in nasopharyngeal samples by nested RT-PCR is, however, also made difficult by the long-term persistent infection of horses with these viruses without causing apparent disease, as reported after the repeated isolation of ERBV1 over 2 years after two yearling colts were experimentally infected [3] .
cord-338916-fqxjzavm	2015	
cord-339178-d6f6a5ds	1978	Coronavirus-like particles were detected by electron microscopy in the intestinal contents of pigs during a diarrheal outbreak on 4 swine breeding farms. Coronavirus-like particles were detected by electron microscopy in the intestinal contents of pigs during a diarrheal outbreak on 4 swine breeding farms. Diarrhea was reproduced in experimental pigs with one of the isolates, designated CV777, which was found to be distinct from the 2 known porcine coronaviruses, transmissible gastroenteritis virus and hemagglutinating encephalomyelitis virus. Diarrhea was reproduced in experimental pigs with one of the isolates, designated CV777, which was found to be distinct from the 2 known porcine coronaviruses, transmissible gastroenteritis virus and hemagglutinating encephalomyelitis virus. In a search for rotaviruses on Belgian swine breeding farms with diarrheal problems, a new coronavirus-like particle was detected b y electron microscopic examination of intestinal or fecal samples from sick pigs.
cord-339991-k8z6v2vx	2003	UV-inactivated, infectious, and other forms of herpes simplex virus 1 (HSV-1) induced interferon (IFN) production by different routes in myeloid origin mononuclear cells (MOMC) (consisting predominantly of monocytes). Comparison of the activities of different strains of infectious HSV, UV-inactivated HSV, and a mutant HSV incapable of penetration (K T) [9] and results of treatment with a mannose receptor antagonist indicate that there are more than one mechanism for HSV induction of interferon in the MOMC origin cell populations. The greater response to UV-inactivated virus suggests that non-infectious virions and possibly HSV infected cell debris are the more potent activators of IFN α production and that replicating virus can limit the induction of interferon production as a means of escaping host protection. Interferons and the colony-stimulating factors IL-3 and GM-CSF enhance the ifn-alpha response in human blood leucocytes induced by herpes simplex virus
cord-340065-f4ffvkr9	1981	
cord-340422-8f5xe4zc	2001	
cord-340905-8nyew5i5	2015	The objective of the present study was to elucidate the relationship between the genotypes and geographic distribution of TCoV isolates from turkey farms in multiple states in the United States by using sequence analysis and comparing the full-length S gene. Three genetic groups, referred to as groups I, II, and III, were observed in North American TCoV isolates ( Fig. 2A) Because of the high degree of variation, most phylogenetic groupings based on the S1a deduced amino acid sequences did not have a bootstrap value over 50 % (Fig. 2B) . Nevertheless, the Texas TCoV isolates of group II and all three TCoV isolates of group III shown in the phylogenetic tree based on the full-length S nucleotide sequences still clustered according to their S1a amino acid sequences containing their HVR. In the present study, similar to previous findings with IBV strains, most of the variations in the S protein sequences among TCoV isolates were observed in the amino-terminal half.
cord-341278-klv9jdm8	1991	Infection of BALB/c mice with mouse hepatitis virus, strain JHM (MHV-JHM), at any of several intervals relative to ovalbumin (OVA) administration resulted in elevated OVA-specific IgG 2 a titers. Serum IFN-γ was not detected, but treatment of MHV-JHM-infected mice with monoclonal anti-IFN-γ antibody resulted in high mortality with decreased survival times, enhanced virus titers in liver and spleen, and more severe virus-associated pathology, compared to mock-treated, infected mice. Sera from mice infected with MHV-JHM one day prior to OVA administration contained substantially elevated levels of antigen-specific IgG2 a on day 7 (Table 1 ) with geometric mean titers that were 17 times control (OVA only) values at that interval. The elevated IgG 2 a OVA-specific response of most groups of MHV-infected mice and the preferential production of this isotype by mice infected one day prior to antigen administration suggested that these mice were producing IFNy. However, using the WEHI 279 B cell lymphoma bioassay [24] , attempts to detect the cytokine in sera of infected mice failed, as had earlier attempts to 27] .
cord-341342-kyavg4vu	1992	The RNase sensitivity of the ability of N protein to migrate into nondenaturing gels was not due to possible contaminating protease activity in the RNase preparations, since the same RNase-treated samples of translated N 148 P.S. Masters protein showed no degradation when analyzed by SDS-PAGE (Fig. 3, lanes an, lower) . Since the N mRNAs synthesized from the transcription vectors shown in Fig. 1 contained this portion of the leader sequence, it seemed possible that the N-RNA complex observed in nondenaturing PAGE was that of translated N protein binding to its own mRNA. That the observed complex was not due to translated N protein binding to the leader portion of its own mRNA was also supported by the observation that full-length N protein translated from a construct in which the MHV leader sequence was entirely deleted was also able to migrate into nondenaturing gels (data not shown).
cord-341383-e2jrhycj	2016	In this study, we investigated the prevalence and clinical characteristics of children with virus-related ARTIs and determined the spectrum of respiratory viruses and their correlation with meteorological variables in Jiading District, Shanghai, China. Investigations of the prevalence of ARTIs and its correlation with viral pathogens are critical for improving the prevention and treatment of ARTIs. There are more than 200 respiratory viruses that can cause ARTIs. Respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (HMPV), human parainfluenza virus (PIV), human enterovirus (EV), influenza virus (IFV), human coronavirus (CoV), adenovirus (ADV), and human bocavirus (BoV) are the most common viral agents associated with ARTIs, accounting for around 70 % of ARTIs [3, 4] . Seventeen respiratory viruses, including IFV (IFV-A/B/C), PIV 1-4, EV, RSV, CoV (229E, HKU1, OC43, NL63), ADV, HMPV, BoV, and HRV were detected among 691 of 2819 children with ARTIs in Nanxiang District of Shanghai (Table 3) .
cord-341469-7guojyay	2011	Especially, ORF3 gene analysis can be used for discrimination between vaccine and wild-type PEDVs. Sequence and phylogenetic analysis showed that recent, prevalent Korean PEDV field isolates have close relationships to Chinese field strains and differ genetically from European strains and vaccine strains used in Korea. Sequence analysis of the complete ORF3 genes showed that all PEDVs, including the Korean field isolates, fell into three groups, and group 3 had two subgroups (3-1 and 3-2), as can be seen in the phylogenetic tree (Fig. 2) . Genetic analysis based on complete M and ORF3 genes showed that each PEDV group had several unique characteristics, and these results indicated that specific groups of PEDVs may be differentiated from other PEDVs, including Korean field isolates, by specific nucleotide differences, but more PEDVs need to be analyzed for more accurate analysis.
cord-342568-3sj235rm	2017	In this study a new method for plant virus diagnosis is described using the Luminex xTAG technology to test for tospoviruses in general and for the four species TSWV, WSMoV, INSV and CaCV. Infected, dried plant material of 12 tospoviral isolates from eight different species was obtained from the DSMZ including single isolates of alstroemeria necrotic streak virus (ANSV), CaCV, GRSV, IYSV, TCSV and WSMoV as well as three isolates each of INSV and TSWV. The generic tospovirus primers Tospo_GENs/as (without tags) allowed the detection of all eight tospoviruses and of all three isolates of INSV and TSWV tested in RT-PCR experiments. A molecular assay for the detection of tospoviruses in general and for viruses from the four species belonging to this genus (TSWV, INSV, CaCV and WSMoV), using the Luminex xTAG technology, was successfully developed.
cord-343131-tu6g977q	2013	Using metagenomics and molecular cloning methods, we characterized five novel small, circular viral genomes from pig feces that are distantly related to chimpanzee and porcine stool-associated circular viruses, (ChiSCV and PoSCV1). This new clade of viruses, provisionally named porcine stool-associated circular virus 2 and 3 (PoSCV2 and PoSCV3), encodes a stem–loop structure (presumably the origin of DNA replication) in the small intergenic region and a replication initiator protein commonly found in other biological systems that replicate their genomes via the rolling–circle mechanism. The viral genomes can be divided into four regions: two large ORFs with deduced amino acid sequences exhibiting homology to the Rep and Cap of ChiSCV, a LIR that encodes multiple overlapping ORFs, and an SIR that contains a palindromic sequence capable of forming a stem-loop structure.
cord-343256-n593kh7u	1991	title: A comparison of the sensitivity and specificity of sialodacryoadenitis virus, Parker''s rat coronavirus, and mouse hepatitis virus-infected cells as a source of antigen for the detection of antibody to rat coronaviruses Using SDAVand PRC-infected L-2 cells as the source of antigen, and sera from rats collected post inoculation with either of these viral strains, the indirect fluorescent antibody (IFA) procedure was used to determine whether antibody titers could be used to differentiate infections from the homologous and heterologous virus. However, using MHV or SDAV-infected cells as the source of antigen, there was a significant difference in antibody titers to the homologous virus detected using the immunoenzyme technique. Using the I F A procedure and MHV-, SDAV-, or PRC-infected cells as a source of antigen and sera from rats exposed to S D A virus, antibody titers to all three antigens were similar (Table 1 ).
cord-343349-ftzjdvfj	1977	Virus was recovered from the nasopharynx and trachea after twenty-four hours and from the lung by day three but was not detected in respiratory tract after seven days. Viral antigen was detected by indirect immunofluorescence in the mucosal epithelium of upper respiratory tract and in pulmonary alveolar septae from day two to six postinoculation. Dacryoadenitis did not occur, sialoadenitis was detected in only three rats and virus was recovered from only one submaxillary salivary gland. Coronavirus infection is common in laboratory rats and two antigenically related viruses, sialodacryoadenitis virus (SDAV) and Parker''s rat coronavirus (PRCV), have been isolated from naturally-infected rats (2, 7) . Virus in lungs, tracheas, nasal washings, salivary glands and lacrimal glands was quantitated for individual rats. Virus was not detected in nasopharynx, trachea and lung a~ter day six and in other tissues after day seven except in ~he submaxillary salivary gland of one rat.
cord-343780-084lq92r	2018	title: Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan To investigate if PDCoV is also present in Taiwan, three swine coronaviruses—PDCoV, porcine epidemic diarrhea virus (PEDV), and transmissible gastroenteritis coronavirus (TGEV)—were tested using real-time reverse transcription polymerase chain reaction (rRT-PCR) in 172 rectal swab samples from piglets exhibiting diarrhea between January 2016 and May 2017 on 68 pig farms in Taiwan. Currently, there are at least three members of the family Coronaviridae that can cause diarrhea in pigs: transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), and porcine deltacoronavirus (PDCoV) [8] . Based on the real-time RT-PCR (rRT-PCR) detection results, the percentage of pig farms that were positive for at least of one of the coronaviruses was 25% for PDCoV (17/68), 22.1% for PEDV (15/68), and 2.9% for TGEV (2/68). Phylogeny analysis of PDCoV-N genes showed that PDCoVs found in Taiwan were highly similar in their nucleotide sequences to isolates from the United States, mainland China, and other countries (Fig. 1) .
cord-344464-if6js43s	2002	title: The complete genome sequence of gill-associated virus of Penaeus monodon prawns indicates a gene organisation unique among nidoviruses(*): Brief Report We report here a 5596 nt sequence comprising the 3′-end of the (+) ssRNA genome of gill-associated virus (GAV), an invertebrate nidovirus of Penaeus monodon prawns. The sequence extends from a subgenomic RNA start site 35 nt upstream of the 4923 nt ORF3 gene to a 3′-poly(A) tail of the 26235 nt genome of GAV. Completion of the genome sequence of GAV has revealed a gene organisation unique among nidoviruses in there is no discrete membrane protein gene and that the putative ORF3 spike glycoprotein gene resides downstream of a gene (ORF2) encoding a structural protein associated with nucleocapsids. A contig of a 5596 nt sequence from the GAV genomic 3 -poly(A) tail to an intergenic 5 -sgRNA start site 35 nt upstream of the ORF3 start codon [10] was deduced from overlapping cDNA clones (Figs.
cord-345552-h6fwi0qn	1997	The strength of the surface charge accumulated on the hydrophilic and hydrophobic regions correlated to the tissue tropism of the different adenovirus types. The sequence of the predicted protein, consisting of 937 amino acids, was obtained with the LaserGene software program EditSeq. The hydropathy data of hexon proteins from human adenovirus types 2, 3, 4, 5, 7, 12, 16, 40, 41, and 48, bovine adenovirus type 3, murine adenovirus type 1, and avian adenovirus types 1 and 10 were derived using the prediction method of Kyte-Doolittle in the LaserGene computer program Protean. The nucleotide and amino acid sequence pair distances and the phylogenetic tree of 14 hexon proteins showed serotypes of subgenera B, D and E to be closely related (Table 3 and Fig. 2) . DNA sequence of the adenovirus type 41 hexon gene and predicted structure of the protein
cord-345856-ckm0ol20	2009	Arbidol not only prevented the cytopathic effect (CPE) of CVB(5), as demonstrated in an MTT colorimetric assay, when added during or after viral infection, with a 50% inhibitory concentration (IC(50)) from 2.66 to 6.62 μg/ml, but it also decreased the CVB(5)-RNA level in infected host cells, as shown in semi-quantitative RT-PCR. Orally administered Arbidol at 50 mg/kg body weight/day (once a day) significantly reduced mean virus yields in the lungs and heart as well as mortality after infection for 6 days. In our previous study, Arbidol showed broad-spectrum antiviral activity against a number of respiratory viruses, including FLU-A, RSV, HRV 14, and CVB 3 in vitro [20] . The virus titers of lung and heart were significantly lower in mice receiving oral administration of Arbidol daily for 6 days than in the viral control group. We also cocultured HEp-2 cells with different doses of Arbidol after infection to study whether it still had an antiviral effect after virus entry into the host cell.
cord-345940-adg264vb	2018	In this study, we constructed scIAV-S, a single-cycle influenza A virus pseudotyped with the spike protein of porcine epidemic diarrhea virus (PEDV), and demonstrated that this virus could infect cultured cells and trigger massive syncytium formation. It should also be noted that control supernatants from HEK293T cells transfected with pCAGGS expressing S AVCT12 alone did not yield detectable syncytium formation in VeroE6-APN cells, suggesting that the detected syncytia were not due to PEDV-S expressed from residual plasmids (data not shown). To further test whether the mCherry expression in infected cells required active influenza A virus polymerase activity, we attempted to construct scIAV-S AVCT12 by omitting the plasmid encoding the PB2 polymerase and examined its infectivity in VeroE6-APN cells. Likewise, VeroE6-APN cells treated with NH 4 Cl (50 mM for 2 h) to neutralize the intracellular pH also displayed strong mCherry expression and extensive syncytium formation when infected with scIAV-S AVCT12 (Fig. 3A) .
cord-345957-wuk2arf9	2018	When compared to the only recorded BKoV genome sequence (BKoV/U-1/AB084788), the studied strain showed 94 amino acid (aa) substitutions through its entire polyprotein (2463 aa), one nucleotide (nt) insertion and one nt deletion in the 2B gene and 4-nt deletions in the UTRs (2 each). Initially, kobuviruses included Aichivirus (AiV), bovine kobuvirus (BKoV), and porcine kobuvirus (PKoV) based on the hosts infected e.g. humans, cattle, 1 3 and swine, respectively. In this study, we report BKoV infections among cattle populations of Egypt, the full-length genome of one Egyptian strain (BKoV/ Egy-1/ KY407744) as well as the phylogenetic analysis of BKoV strains from Cairo and Sharkia provinces. The RNA samples (n = 36) were subjected to RT-PCR for the detection of BKoV using degenerate primers (Univ-Kobu-F and Univ-Kobu-R), which amplify a conserved region in the 3D (RdRp) gene of all kobuviruses [12] ( Table 1 ).
cord-346321-drhiqch0	1994	title: The role of IgG subclass of mouse monoclonal antibodies in antibody-dependent enhancement of feline infectious peritonitis virus infection of feline macrophages Antibody-dependent enhancement (ADE) of feline infectious peritonitis virus (FIPV) infection was studied in feline alveolar macrophages and human monocyte cell line U937 using mouse neutralizing monoclonal antibodies (MAbs) directed to the spike protein of FIPV. It is especially important for development of vaccines to understand the relationship between FIPV neutralizing activity and ADE activity of anti FIPV MAbs. In this study, we determined the relationship between immunoglobulin subclass and ADE activity of FIPV-neutralizing MAbs, and attempted to explore mechanisms of ADE of FIPV infection in in vitro system using mouse MAbs and feline alveolar macrophages or human monocytes. The present study, however, explored ADE of FIPV infection by in vitro experiments in which xenogeneic combination of virus targets and anti-FIPV antibody, i.e., feline alveolar macrophages or human monocyte U937 cells and mouse anti-FIPV S protein MAbs, was used.
cord-346629-770qyee8	2004	title: Phylogenetic analysis of avian infectious bronchitis virus strains isolated in Japan To define the origin and evolution of recent avian infectious bronchitis virus (IBV) in Japan, a genetic analysis was performed. By phylogenetic analysis based on the S1 gene including the sequence of the hypervariable regions, IBV isolates in Japan were classified into five genetic groups, which included two already-known groups (Mass and Gray). In this study, to define the origin and evolution of recent IBV in Japan, we determined the nucleotide sequences of IBV isolated in Japan using the reverse transcriptase-polymerase chain reaction (RT-PCR) method coupled with direct sequencing, and analyzed the sequences phylogenetically with viruses isolated in other countries. By phylogenetic analysis, the IBV isolates in Japan used in this study were divided into five genetic groups (Fig. 1 ). Typing of field isolates of infectious bronchitis virus based on the sequence of the hypervariable region in the S1 gene
cord-346928-g1dqiki6	2003	Porcine respiratory coronavirus (PRCV), a spike (S) gene deletion mutant of Transmissible gastroenteritis virus (TGEV), causes mild or subclinical respiratory infections in pigs. In preliminary studies, inoculation of gnotobiotic pigs with each plaque-purified pair of the nasal and fecal PRCV isolates, revealed no clinical disease but different tropisms. Fecal and nasal swabs from the field cases (sentinel pigs), cell culture isolates and fecal and nasal swabs from gnotobiotic pigs were tested by nested-RT-PCR to detect and to differentiate TGEV and PRCV viral RNA as previously described by Kim et al. Fecal and nasal swab supernatant fluids from the sentinel field cases or the cell culture passaged PRCV isolates and nasal and fecal swabs from gnotobiotic pigs were diluted in minimum essential medium (MEM-E) and tested by CCIF to detect infectious virus using previously described procedures [23] .
cord-347443-0evqo01m	2013	Seasonality has been reported for many viruses, including influenza virus, respiratory syncytial virus (RSV), and the recently described human metapneumovirus (hMPV). Major causes of bronchiolitis and lower respiratory tract illnesses in children include respiratory syncytial virus (RSV), parainfluenza viruses, influenza virus, and human metapneumovirus (hMPV). The organism/viruses detected by the FilmArray included adenovirus, influenza A virus (FluA), influenza B virus (FluB), parainfluenza virus 1 (Para 1), parainfluenza virus 2 (Para 2), parainfluenza virus 3 (Para 3), parainfluenza virus 4 (Para 4), respiratory syncytial virus (RSV), coronavirus 229E (CoronaV 229E), CoronaV NL63, CoronaV HKU1, CoronaV OC43, human metapneumovirus (hMPV), Bordetella pertussis, Chlamydophila pneumoniae and Mycoplasma pneumoniae. In our study, 939 specimens were analyzed over the course of a year using a respiratory pathogen multiplex PCR that yielded a positivity rate of 65 % with multiple analytes detected in 12 % of specimens, especially in children. RSV and hMPV PCR-positive cases were statistically much more likely than Rhino/Entero PCR-positive infections to initially present with pneumonia or bronchiolitis in our study.
cord-348147-leni23pa	2007	Sequence analysis of the full-length and partial genomes obtained from naturally infected mice yielded valuable data on genetic diversity of murine noroviruses. These specimens were obtained from 28 different mouse lines, including immunocompetent mice, lines with muta(4), b-TCR À=À (2), RAG2=gChain À=À (5), B6 Casp À=À (2), CD36=SRA À=À (2), CCL3 À=À (2), LFA À=À (2), LyZ À=À (2), PSEN tg (2), Bl6 wt (4) a GE genome equivalents; for more than one positive sample the mean was calculated b Includes partial sequences of the ORFs (underlined isolates; ORF1, RNA polymerase gene; ORF2, capsid gene) Ã Contains both regions tions in a number of immune effector molecules, and transgenic mouse lines (Table 1) . Like human noroviruses, the present sequence data indicate that murine norovirus strains are also genetically diverse and can, therefore, be subdivided in genetic clusters.
cord-348163-9q1rt8i7	2015	Integrins are a family of receptor molecules that serve as entry receptors for a variety of different viruses, including foot-and-mouth disease virus (FMDV) [97] , Kaposi''s sarcoma-associated herpesvirus (KSHV) [5], herpes simplex virus-2 (HSV-2) [31], adenovirus [168] , human papillomavirus-16 (HPV-16) [3] , reovirus [40] , and others. On the other hand, interactions of viruses with cellular integrins induce conformational changes in the viral surface proteins, helping to expose the essential domains required for virus entry into a host cell [107] . Similarly, several human herpesviruses, including HSV [147] , KSHV [4], and CMV [93] , make their initial contact with cells by binding to cellsurface HSPGs. In general, binding of viruses to carbohydrate moieties on the surface of cells is the key step that induces conformational changes in the viral structure that are critical for interactions with entry-promoting receptors such as integrins.
cord-348179-i8w7huke	2012	Moreover, schizophrenia patients with increased CD4(+)/CD8(+) T-cell ratios (>2.03) had higher anti-HEV IgG detection rates than those with normal ratios (1.05-2.03). Epidemiological studies have already shown that the rates of hepatitis B and hepatitis C virus infection in patients with schizophrenia were five and 11 times higher, respectively, than the estimated general population rates [26] . In the current study, we found that the detection rates for HEV antibodies in schizophrenia patients were much higher than those in healthy controls. In the present study, the detection rate of anti-HEV IgG in schizophrenia patients with increased CD4 ? T-cell levels and the increased risk of HEV infection in schizophrenia patients. Moreover, significant differences of the serum IL-4, IL-10 and IL-12 levels were observed among schizophrenia patients with and without HEV IgG antibodies. Taken together, schizophrenia patients exhibited higher risk of HEV infection than controls in the present study.
cord-348867-c0xpzd4d	2017	In this study, a PIV5 variant (named ZJQ-221) was isolated from a lesser panda with respiratory disease in Guangzhou zoo in Guangdong province, southern China. Sequence alignment and genetic analysis revealed that ZJQ-221 shared a close relationship with a PIV5 strain of canine-origin (1168-1) from South Korea. In this study, a novel variant of PIV5 (designated as ZJQ-221) was isolated from a lesser panda with respiratory disease in Guangzhou zoo in Guangdong province, southern China. Fourteen samples were tested for the possible presence of three respiratory-related pathogens (including PIV5, canine distemper virus, and coronavirus) by RT-PCR according to previous studies [27, 28] . In summary, we have identified a novel PIV5 isolate in lesser panda and performed whole genome sequencing, indicating that this mammal may act as a possible natural reservoir for this virus. The complete genome sequencing and analysis of canine parainfluenza virus strain CC-14
cord-349800-s9w2yr08	1991	Seven monoclonal antibodies (MAbs) with neutralizing activity against feline infectious peritonitis virus (FIPV) strain 79-1149 (type II) were prepared. The reactivity of these MAbs with 6 viruses classified as FIPV type I (UCD-1, UCD-2, UCD-3, UCD-4, NW-1, and Black), feline enteric coronavirus (FECV) type II strain 79-1683, canine coronavirus (CCV) strain 1-71, and transmissible gastroenteritis virus (TGEV) strains TO-163 and SH was examined by neutralization tests. Feline coronaviruses are divided into FIPV types I and II, and FECV types I and II, on the basis of the disease types, that is, whether it causes feline infectious peritonitis (FIP) or not, the ability of the viruses to proliferate in cell cultures, and the antigenic relationship to TGEV and CCV [17] . These MAbs did not neutralize the 6 FIPV type I viruses, but neutralized FECV strain 79-1683, TGEV strains TO-163 and SH, and CCV strain 1-71, which do not cause feline infectious peritonitis (Table 4) .
cord-349907-dwhyx97y	2017	Therefore, in this study, a duplex real-time reverse transcription (RT)-PCR method was developed based on primers and probes that target the conserved spike S2 region of SARS-CoV, SARS-like bat CoVs, MERS-CoV, and MERS-related bat CoVs. For the universal detection of SARS-CoV and SARS-like bat CoVs, consensus primers and probes (Fig. 1a) were designed based on the conserved sequences of the spike S2 region by aligning the following reference sequences: human SARS-CoVs Sino1 (GenBank no. The specificity of the real-time RT-PCR method developed in this study was evaluated using RNAs from several RNA viruses, including MERS-CoV (KOR/KNIH/ 002_05_2015), a recombinant plasmid for the bat CoV HKU4 strain, and RNA from a bat fecal sample containing SARS-like bat CoV. The new real-time RT-PCR method also showed positive results for RNA extracted from a fecal sample containing SARS-like bat CoV (B15-21) [7] .
cord-349964-38rgcc5h	1978	The first antigenically related group was comprised of mouse hepatitis virus, type 3 (MHV-3), hemeagglutinating encephalomyelitis virus 67N (HEV-67N) of swine, calf diarrhea coronavirus (CDCV), and human coronavirus OC43 (HCV-OC43). Utilizing the direct and indirect fluorescent antibody procedure, the antigenic relationship of the feline infectious peritonitis virus (FIPV) to 7 other human and animal coronaviruses was studied. Utilizing the direct and indirect fluorescent antibody procedure, the antigenic relationship of the feline infectious peritonitis virus (FIPV) to 7 other human and animal coronaviruses was studied. Transmissible gastroenteritis virus and FIPV were in turn antigenically related to human eoronavirus 229E (I-ICV-229E) and canine coronavirus (CCV). A possible antigenic relationship between feline infectious peritonitis virus (FIPV) and the transmissible gastroenteritis virus (TGEV) of swine has been recently reported (13, 19, 25) , which further supports the assumption t h a t F I P V is a coronavirus.
cord-353797-yb355mxk	1976	Bovine coronavirus readily multiplied and induced marked cytopathic effect in BEK-1 cultures, thus providing a sensitive, practical assay system for viral infectivity and neutralizing antibody and a satisfactory source of the virus. 1V[~iBus and his associates (4--6) have demonstrated an agent with morphologic features of coronavirus by electron microscopy in fractions prepared by density gradient ultracentrifugation from diarrheal feces of calves with natural and experimentally produced neonatal diarrhea. The agent multiplied but failed to induce readily recognizable cytopathic effect in bovine embryonic kidney cell cultures (3) . This paper describes briefly our recent observation that the virus readily replicates and induces a marked cytopathic effect in cultures of a continuous cell line, BEK-1, derived from bovine embryonic kidney (2), thus providing a sensitive, practical assay method and a satisfactory source of the virus. Coverslip cultures of BEK-1 cells inoculated with the virus were examined after 2 or 3 days of incubation at 34 ° C.
cord-355512-tycuoslv	1992	Hemagglutinating and acetylesterase functions as well as the 124 kDa glycoprotein were present in the highly cell-culture adapted, avirulent bovine coronavirus strain BCV-L9, in the Norden vaccine strain derived from it, and in 5 wild-type, virulent strains that multiplied in HRT-18 cells but were restricted in several types of cultured bovine cells. Purified preparations of the vaccine and the wild-type strains agglutinated chicken erythrocytes at low titers and mouse erythrocytes at 128 to 256 times higher titers whereas receptor destroying enzyme activity was detectable only with chicken erythrocytes. When wild-type strains were propagated in HRT cells at low passage levels, they produced 5×10(5) to 4.5×10(6) plaque forming units per 50 µl which agglutinated erythrocytes from mice but not from chickens. The objective of our investigations was to identify the HE of wild-type BCV strains at low passage levels in H R T cell cultures and to compare it with the HE of prototype BCV-L9 and vaccine strains by relating its functions to the interaction with different erythrocytes, the effects of enzyme inhibitors, and to plaque-forming infectivity.
cord-355535-01h8yyqj	2018	The primary focus was on the prevalence of respiratory viruses, including AdV (adenovirus), BoV (bocavirus), CoV (coronavirus), CMV (cytomegalovirus), EnV (enterovirus), HSV (herpes simplex virus), IfV (influenza virus), MpV (metapneumovirus), PiV (parainfluenzavirus), RV (rhinovirus) and RSV (respiratory syncytial virus) during asthma exacerbations. A standardized form was used for data extraction, including the main characteristics (author, year of publication, sample size, age, definition of exacerbation, quality, detection method, study design and season), primary outcome (the prevalence of viral infection during asthma exacerbations), and secondary outcomes (the prevalence of viruses in different strata). We also did a subgroup analysis to assess the weight of viral infection on asthma exacerbations with respect to geographic region, population, type of respiratory tract secretion examined, and detection method. Because difference in the geographic regions, age, study population, type of respiratory tract secretion, and detection method significantly confound the determination of the prevalence of individual viruses, heterogeneity was not assessed in this study.
cord-356176-1nwjjgul	1978	Chick embryo tracheal organ cultures showed increased resistance to infection by a coronavirus after exposure to ascorbate, while chick respiratory epithelium and allantois-on-shell preparations showed no increase in resistance to infection by an influenza virus or a paramyxovirus. Titrations of avian infectious bronchitis virus were performed by inoculating 4 replicate chick-embryo tracheal organ culture tubes previously selected for ciliat activity, with dilutions of virus made in half-log steps, then continuing to incubate the preparations on a roller drum at 15 rev/hour at 37 ° C. However resistance of CETO cultures to IB virus infection rose with increasing ascorbic acid content (Table t and Fig. 1 ). Our results show t h a t aseorbic acid exerted no direct effect on the infectivity of a n y of the three viruses tested, nor did it affect the resistance of cells to infection by the 0 r t h o m y x o v i r u s (influenza) or the P a r a m y x o v i r u s (NDV).
cord-356192-8b96rgqa	2017	title: Two deletion variants of Middle East respiratory syndrome coronavirus found in a patient with characteristic symptoms Significant sequence variation of Middle East respiratory syndrome coronavirus (MERS CoV) has never been detected since it was first reported in 2012. To predict the function of the E protein of MERS CoV, we aligned the E and ORF5-E protein sequences of MERS CoV with those of two other coronaviruses, SARS-CoV and China Rattus coronavirus HKU24, using MEGA software (version 6.0) [11] . The truncated E protein with a deletion of aa 1-30 lacks the N-terminus and a major part of the hydrophobic transmembrane domain in MERS CoV variant 1, which might directly impair virus packaging and replication [24] . Genomic sequencing and analysis of the first imported Middle East Respiratory Syndrome Coronavirus (MERS CoV) in China Middle East respiratory syndrome coronavirus (MERS-CoV) entry inhibitors targeting spike protein