# bib

id: cord-328381-bfvdhai8
title: Susceptibility of different eukaryotic cell lines to SARS-coronavirus
author: Hattermann, K.
date: 2005-01-13
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url: https://www.ncbi.nlm.nih.gov/pubmed/15645376/
doi: 10.1007/s00705-004-0461-1
summary:
  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).

abstract:
  In order to define and characterize target cells of SARS-coronavirus (SARS-CoV) we studied the susceptibility of 23 different permanent and primary eukaryotic cell lines to SARS-coronavirus. Beneath Vero E6 cells SARS- Coronavirus infection could also be demonstrated in two pig cell lines (POEK, PS) and one human cell line (Huh-7) using the indirect immunofluorescence assay and a newly established quantitative real-time PCR. 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. Our results show that there is a correlation between the abundance of ACE2 mRNA and SARS-CoV susceptibility.


id: cord-329145-424vv8a8
author: Kuhn, Jens H.
date: 2012-09-23
txt: ./txt/cord-329145-424vv8a8.txt
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url: https://doi.org/10.1007/s00705-012-1454-0
doi: 10.1007/s00705-012-1454-0
summary:
  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.

title:
  Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae

abstract:
  The task of international expert groups is to recommend the classification and naming of viruses. The International Committee on Taxonomy of Viruses Filoviridae Study Group and other experts have recently established an almost consistent classification and nomenclature for filoviruses. Here, further guidelines are suggested to include their natural genetic variants. First, this term is defined. Second, a template for full-length virus names (such as “Ebola virus H.sapiens-tc/COD/1995/Kikwit-9510621”) is proposed. These names contain information on the identity of the virus (e.g., Ebola virus), isolation host (e.g., members of the species Homo sapiens), sampling location (e.g., Democratic Republic of the Congo (COD)), sampling year, genetic variant (e.g., Kikwit), and isolate (e.g., 9510621). 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). We suggest that these comprehensive names are to be used specifically in the methods section of publications. Suitable abbreviations, also proposed here, could then be used throughout the text, while the full names could be used again in phylograms, tables, or figures if the contained information aids the interpretation of presented data. The proposed system is very similar to the well-known influenzavirus nomenclature and the nomenclature recently proposed for rotaviruses. If applied consistently, it would considerably simplify retrieval of sequence data from electronic databases and be a first important step toward a viral genome annotation standard as sought by the National Center for Biotechnology Information (NCBI). Furthermore, adoption of this nomenclature would increase the general understanding of filovirus-related publications and presentations and improve figures such as phylograms, alignments, and diagrams. Most importantly, it would counter the increasing confusion in genetic variant naming due to the identification of ever more sequences through technological breakthroughs in high-throughput sequencing and environmental sampling.


id: cord-330035-0d6w8xyd
title: Cellular cholesterol is required for porcine nidovirus infection
author: Jeon, Ji Hyun
date: 2017-09-07
url: https://doi.org/10.1007/s00705-017-3545-4
doi: 10.1007/s00705-017-3545-4
abstract:
  Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine epidemic diarrhea virus (PEDV) are porcine nidoviruses that are considered emerging and re-emerging viral pathogens of pigs that pose a significant economic threat to the global pork industry. Although cholesterol is known to affect the replication of a broad range of viruses in vitro, its significance and role in porcine nidovirus infection remains to be elucidated. Therefore, the present study was conducted to determine whether cellular or/and viral cholesterol levels play a role in porcine nidovirus infection. Our results showed that depletion of cellular cholesterol by treating cells with methyl-β-cyclodextrin (MβCD) dose-dependently suppressed the replication of both nidoviruses. Conversely, cholesterol depletion from the viral envelope had no inhibitory effect on porcine nidovirus production. The addition of exogenous cholesterol to MβCD-treated cells moderately restored the infectivity of porcine nidoviruses, indicating that the presence of cholesterol in the target cell membrane is critical for viral replication. The antiviral activity of MβCD on porcine nidovirus infection was found to be predominantly exerted when used as a treatment pre-infection or prior to the viral entry process. Furthermore, pharmacological sequestration of cellular cholesterol efficiently blocked both virus attachment and internalization and, accordingly, markedly affected subsequent post-entry steps of the replication cycle, including viral RNA and protein biosynthesis and progeny virus production. Taken together, our data indicate that cell membrane cholesterol is required for porcine nidovirus entry into cells, and pharmacological drugs that hamper cholesterol-dependent virus entry may have antiviral potential against porcine nidoviruses.


id: cord-330825-apfcql4m
title: Phylogenetic tracking of current porcine epidemic diarrhea virus (PEDV) strains in the Philippines
author: Paraguison-Alili, Rubigilda
date: 2016-06-28
txt: ./txt/cord-330825-apfcql4m.txt
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url: https://doi.org/10.1007/s00705-016-2938-0
doi: 10.1007/s00705-016-2938-0
summary:
  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

abstract:
  To trace the possible route of introduction of porcine epidemic diarrhea virus (PEDV), the phylogenetic relationships of PEDV strains in the regions of epidemicity in the Philippines to PEDV strains that are endemic in other countries were investigated. Partial nucleotide sequences of the S1 spike gene was determined from the PEDV-positive samples and compared with S1 sequences from other countries. Phylogenetic analysis indicated that PEDV strains in the Philippines segregate into two groups. Members of group 1 are related to strains from the USA, Taiwan, Japan and Canada, while those in group 2 are related to strains from China and Vietnam.


id: cord-332811-kjgah8ts
author: Lee, Do Hyun
date: 2015-06-23
txt: ./txt/cord-332811-kjgah8ts.txt
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url: https://doi.org/10.1007/s00705-015-2494-z
doi: 10.1007/s00705-015-2494-z
summary:
  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

title:
  Immunoprophylactic effect of chicken egg yolk antibody (IgY) against a recombinant S1 domain of the porcine epidemic diarrhea virus spike protein in piglets

abstract:
  Porcine epidemic diarrhea virus (PEDV) is a highly contagious enteric pathogen of swine causing high mortality rates in piglets. PEDV outbreaks have occurred continuously in most swine-producing Asian countries and have recently emerged in the United States, leading to large economic losses for both the Asian and US pig industries. The spike (S) protein of PEDV consists of the S1 and S2 domains, responsible for virus binding and fusion, respectively. The involvement of the S1 domain in specific high-affinity interactions with the cellular receptor and induction of neutralizing antibodies in the natural host makes it a logical target for the development of effective vaccines and therapeutics against PEDV. Passive immunization by oral administration of egg yolk antibodies (IgY) obtained from immunized chickens provides an alternative source of specific antibodies for the prevention and treatment of PEDV in newborn piglets. In this study, we produced an IgY against the PEDV S1 protein and investigated its immunoprophylactic effect in neonatal 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. The purified recombinant S1 protein was found to mediate potent immune responses in immunized hens. We next tested the ability of oral passive immunization with anti-PEDV S1 IgY to protect piglets against PEDV. Specific chicken IgY against the S1 protein was orally administered to neonatal piglets, and their responses subsequent to a virulent PEDV challenge were monitored. The results showed that oral administration of anti-PEDV S1 IgY efficiently protects neonatal piglets against PEDV, suggesting its potential as a prophylactic or therapeutic agent against acute PEDV infection.


id: cord-333043-fe24ezt6
title: “Runde“ virus, a coronavirus-like agent associated with seabirds and ticks
author: Traavik, T.
date: 1977
txt: ./txt/cord-333043-fe24ezt6.txt
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url: https://www.ncbi.nlm.nih.gov/pubmed/72555/
doi: 10.1007/bf01314476
summary:
  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.

abstract:
  From 206I. uriae collected in the seabird colonies at Runde, Norway, two identical virus strains demonstrating no antigenic relationships to major arbovirus groups were isolated. The new strains demonstrated a corona-virus like morphology, haemagglutinated chicken red cells and were sensitive to sodium desoxycholate. Multiplication with CPE was demonstrated in BHK 21/c13 and BSC-1 cells, and without CPE in Vero and GMK cell cultures. The mouse pathogenicity was relatively low. In gel precipitation three to five specific lines were seen. Precipitating antibodies have been found in seabird species commonly infested byI. uriae. The ecological circumstances of the isolates indicate an earlier unrecognized arbovirus circulating between seabirds andI. uriae. This corona-like virus has been tentatively termed Runde virus.


id: cord-333331-ddcz7zck
title: Detection of hepatitis C virus by an improved loop-mediated isothermal amplification assay
author: Yang, Jin
date: 2011-05-12
txt: ./txt/cord-333331-ddcz7zck.txt
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url: https://doi.org/10.1007/s00705-011-1001-4
doi: 10.1007/s00705-011-1001-4
summary:
  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

abstract:
  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. Based on an accelerating primer (AP), the present assay, named AP-LAMP, has the advantages of rapidity and sensitivity over the routine LAMP method. The possible AP-based amplification pathway during the reaction was revealed by restriction enzyme digestion and eletrophoresis. The detection limit of the AP-LAMP assay was approximately 84 IU/ml, and no cross-detection was observed. The assay was evaluated further with 126 clinical specimens, and the results indicated the suitability and simplicity of the test as a rapid diagnostic tool for detection of HCV RNA.


id: cord-333403-imx3990a
title: Characterization of a temperature sensitive feline infectious peritonitis coronavirus
author: Christianson, K. K.
date: 1989
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url: https://www.ncbi.nlm.nih.gov/pubmed/2558634/
doi: 10.1007/bf01311080
summary:
  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] .

abstract:
  The characteristics of a temperature sensitive feline infectious peritonitis virus (TS-FIPV) were examined. TS-FIPV, unlike its parent strain, DF2 wild type FIPV (WT-FIPV), propagated at 31 °C (permissive temperature) but not at 39 °C (nonpermissive temperature). This temperature preference of TS-FIPV was also demonstrated in cats by the ability of the virus to replicate only at the lower temperature in the upper respiratory tract and not at systemic sites where higher temperatures (38–39 °C) prevail. 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 was more thermolabile than WT-FIPV which indicated alterations in the structural proteins of TS-FIPV, and a difference in the envelope protein of the two viruses was revealed by Western blot analysis. Plaque assay characterization showed that TS-FIPV produced small plaques in comparison to the large plaques of WT-FIPV. These unique characteristics possessed by TS-FIPV may account for its nonvirulent nature and ability to stimulate protective immune responses in cats.


id: cord-333636-h2sg6shp
author: Kochan, G.
date: 2003
url: https://www.ncbi.nlm.nih.gov/pubmed/12664296/
doi: 10.1007/s00705-002-0949-5
title:
  Characterization of the RNA-binding activity of VP3, a major structural protein of Infectious bursal disease virus

abstract:
  Infectious bursal disease virus (IBDV) is the agent of an immune-depressive disease affecting the poultry industry worldwide. Infection of IBDV leads to expression of five mature virus-encoded proteins. Proteolytic processing of the virus-encoded polyprotein generates VP3 which coats the inner surface of the IBDV capsid. In this report, we describe the characterization of the RNA-binding activity of VP3. For these studies, the VP3 coding region was fused to a histidine tag and expressed in insect cells using a recombinant baculovirus. The histidine-tagged VP3 was affinity-purified and used to study its ability to bind RNA molecules using three complementary methods: (i) Northwestern blotting; (ii) binding of VP3 protein-RNA complexes to nitrocellulose membranes; and (iii) electrophoretic mobility shift assays. The results demonstrated that VP3 efficiently bound ssRNA and dsRNA. Under the experimental conditions used in this study, the formation of VP3-RNA complexes did not depend upon the presence of specific RNA sequences. A series of histidine-tagged VP3 deletion mutants spanning the whole VP3 coding region were generated. The use of these mutants revealed that the VP3 RNA-binding domain layed in a highly conserved 69 aa stretch close to the N-terminus of the protein.


id: cord-334090-66d8c75g
title: Genotyping of infectious bronchitis viruses from broiler farms in Iraq during 2014-2015
author: Seger, Waleed
date: 2016-02-18
txt: ./txt/cord-334090-66d8c75g.txt
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url: https://www.ncbi.nlm.nih.gov/pubmed/26887967/
doi: 10.1007/s00705-016-2790-2
summary:
  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] .

abstract:
  Infectious bronchitis virus (IBV) is one of the most critical pathogens in the poultry industry, causing serious economic losses in all countries including Iraq. IBV has many genotypes that do not confer any cross-protection. This virus has been genotyped by sequence analysis of the S1 glycoprotein gene. A total of 100 tracheal and kidney tissue specimens from different commercial broiler flocks in the middle and south of Iraq were collected from September 2013 to September 2014. Thirty-two IBV-positive samples were selected from among the total and were further characterized by nested PCR. Phylogenetic analysis revealed that isolates belong to four groups (group I, variant 2 [IS/1494-like]; group II, 793/B-like; group III, QX-like; group IV, DY12-2-like). Sequence analysis revealed nucleotide sequence identities within groups I, II, and III of 99.68 %-100 %, 99.36 %-100 %, and 96.42 %-100 %, respectively. Group I (variant 2) was the dominant IBV genotype. One Chinese-like recombinant virus (DY12-2-like) that had not been reported in the Middle East was detected. In addition, the presence of QX on broiler chicken farms in the area studied was confirmed. This is the first comprehensive study on the genotyping of IBV in Iraq with useful information regarding the molecular epidemiology of IBV. The phylogenetic relationship of the strains with respect to different time sequences and geographical regions displayed complexity and diversity. Further studies are needed and should include the isolation and full-length molecular characterization of IBV in this region.


id: cord-334810-hw1aijwf
author: Banyard, Ashley C.
date: 2009-10-20
txt: ./txt/cord-334810-hw1aijwf.txt
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url: https://doi.org/10.1007/s00705-009-0504-8
doi: 10.1007/s00705-009-0504-8
summary:
  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)

title:
  Repeated detection of European bat lyssavirus type 2 in dead bats found at a single roost site in the UK

abstract:
  In August 2007, European bat lyssavirus type 2 (EBLV-2) was isolated from a Daubenton’s bat found at Stokesay Castle. In September 2008, another bat from the same vicinity of Stokesay Castle also tested positive for EBLV-2. This is the first occurrence of repeated detection of EBLV-2 from a single site. Here, we report the detection of low levels of viral RNA in various bat organs by qRT-PCR and detection of viral antigen by immunohistochemistry. We also report sequence data from both cases and compare data with those derived from other EBLV-2 isolations in the UK.


id: cord-335690-66t5fjld
title: RNA binding properties of core protein of the flavivirus Kunjin
author: Khromykh, A. A.
date: 1996
txt: ./txt/cord-335690-66t5fjld.txt
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mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/8645104/
doi: 10.1007/bf01718326
summary:
  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) .

abstract:
  Kunjin virus (KUN) C is a typical flavivirus core protein which is truncated in vivo to a mature form of 105 residues enriched in lysine and arginine. In order to study the possible association of KUN C with RNA in vitro, we prepared several recombinant C proteins with specific deletions, each fused at the amino-terminus to glutathione-S-transferase (GST) and expressed inE. coli. They were reacted with KUN RNA probes transcribed in vitro from cDNA representing the 5′ untranslated region (5′ UTR, 93 of 96 nucleotides), the 3′ UTR (624 nucleotides), and the 5′ UTR plus most of the C coding region (t′ core, 440 nucleotides). Fusion protein C107 (incorporating mature C) bound strongly to all KUN RNA probes with apparent specificity, being completely resistant to inhibition by 800 mM NaCl, and to competition by a large excess of tRNA. In reactions with labelled KUN RNA probes putative binding sites were identified in the isolated amino-terminal (32 residues) and carboxyterminal (26 residues) basic amino acid domains; this binding was strongly competed by unlabelled KUN UTR probes but weakly or not at all by tRNA. These small domains probably acted co-operatively in binding of mature C to KUN RNA probes. The KUN RNA-core protein binding reactions are similar to those reported with other viral coat or capsid proteins and viral RNAs.


id: cord-338607-22f04uqe
author: Verbeek, A.
date: 1991
txt: ./txt/cord-338607-22f04uqe.txt
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mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/1662038/
doi: 10.1007/bf01316754
summary:
  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.

title:
  Genomic relationship between turkey and bovine enteric coronaviruses identified by hybridization with BCV or TCV specific cDNA probes

abstract:
  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 plasmid probes p 52, p 27, and p 247, holding inserts derived from (probably nonstructural) genes, and plasmids pN 17 and pN 9 holding the N and M gene, respectively, permitted the detection of isolates of both BCV and TCV with similar sensitivities. Similarly, probing supernatants of cell cultures infected with several isolates of TCV, using probes pN 17 and pM 78, respectively holding the N gene of BCV and TCV, resulted in equally intense detection signals. Only a slight detection of MHV-3, which is antigenically related to BCV, was observed, whereas the probes did not allow the detection of IBV, TGEV, and HCV-229E, which are placed in antigenic groups separate from those of BCV and TCV. Detection of TCV was improved by hybridization with BCV-specific single-stranded (ss) probes holding sequences of the N and M genes and synthesized by the polymerase chain reaction. Diagnosis of TCV in 134 clinical samples by hybridization was better with PCR-produced ss BCV-specific probes than with ds PCR-produced probes or a combination of six recombinant plasmid probes holding non-overlapping BCV-specific cDNA sequences. Detection signals were absent when probing clinical samples with(32)P-labelled pUC-DNA.


id: cord-338641-s006a7m0
author: Black, W. D.
date: 2006-08-24
txt: ./txt/cord-338641-s006a7m0.txt
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mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16932985/
doi: 10.1007/s00705-006-0810-3
summary:
  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] .

title:
  Reverse transcriptase-polymerase chain reaction for the detection equine rhinitis B viruses and cell culture isolation of the virus

abstract:
  Equine rhinitis B virus (ERBV), genus Erbovirus, family Picornaviridae occurs as two serotypes, ERBV1 and ERBV2. An ERBV-specific nested reverse transcriptase-polymerase chain reaction (RT-PCR) that amplified a product within the 3D(pol) and 3′ non-translated region of the viral genome was developed. The RT-PCR detected all 24 available ERBV1 isolates and one available ERBV2 isolate. The limit of detection for the prototype strain ERBV1.1436/71 was 0.1 50% tissue culture infectious doses. 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. The sequences of these six ERBV RT-PCR positive samples had 93–96% nucleotide identity with six other partially sequenced ERBV1 isolates and one ERBV2. ERBV was isolated from one of the six samples at fourth cell culture passage when it was shown that the addition of 20 mg/mL MgCl(2) to the cell culture medium enhanced the growth of the virus. This isolated virus was antigenically similar to ERBV2.313/75. Determination of the nucleotide sequence of the P1 region of the genome also indicated that the isolate was ERBV2, and it was therefore designated ERBV2.1576/99. This is the first reported isolation of ERBV in Australia. The study highlights the utility of PCR for the identification of viruses in clinical samples that may initially be considered negative by conventional cell culture isolation.


id: cord-338916-fqxjzavm
title: Detection of coronavirus genomes in Moluccan naked-backed fruit bats in Indonesia
author: Anindita, Paulina Duhita
date: 2015-02-04
url: https://doi.org/10.1007/s00705-015-2342-1
doi: 10.1007/s00705-015-2342-1
abstract:
  Bats have been shown to serve as natural reservoirs for numerous emerging viruses including severe acute respiratory syndrome coronavirus (SARS-CoV). In the present study, we report the discovery of bat CoV genes in Indonesian Moluccan naked-backed fruit bats (Dobsonia moluccensis). A partial RNA-dependent RNA polymerase gene sequence was detected in feces and tissues samples from the fruit bats, and the region between the RdRp and helicase genes could also be amplified from fecal samples. Phylogenetic analysis suggested that these bat CoVs are related to members of the genus Betacoronavirus.


id: cord-339178-d6f6a5ds
title: A new coronavirus-like particle associated with diarrhea in swine
author: Pensaert, M. B.
date: 1978
txt: ./txt/cord-339178-d6f6a5ds.txt
cache: ./cache/cord-339178-d6f6a5ds.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/83132/
doi: 10.1007/bf01317606
summary:
  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.

abstract:
  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.


id: cord-339991-k8z6v2vx
author: Rong, Q.
date: 2003
txt: ./txt/cord-339991-k8z6v2vx.txt
cache: ./cache/cord-339991-k8z6v2vx.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/12556996/
doi: 10.1007/s00705-002-0912-5
summary:
  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

title:
  Multiple mechanisms for HSV-1 induction of interferon α production by peripheral blood mononuclear cells

abstract:
  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). GM-CSF activated the MOMC (G-MOMC) to produce greater amounts of interferon while differentiation to DC, by the addition of granulocyte macrophage colony stimulating factor (GM-CSF) and calcium ionophore (GA-MOMC), reduced the levels of interferon production upon challenge with some HSV strains. UV-inactivated virus induced more interferon than infectious virus. L-fucose, an antagonist of the mannose receptor, inhibited the induction of IFN-α by UV-inactivated virus and gB(−) virus (defective in penetration) in MOMC and GA-MOMC but not G-MOMC. L-fucose had little effect on interferon induction by infectious HSV-1. The insensitivity of the G-MOMC to fucose inhibition distinguishes these interferon producing cells from the pDC2 cells previously described as natural interferon producing cells. The mannose receptor appears to be involved in the response to non-infectious forms of HSV but infectious virus appears to use a different pathway. These studies suggest that non-infectious virions and HSV infected cell debris effectively stimulate monocytes and pre-dendritic cells to produce IFN-α to initiate host protection against HSV infection.


id: cord-340065-f4ffvkr9
author: Horváth, Trén
date: 1981
url: https://www.ncbi.nlm.nih.gov/pubmed/7247729/
doi: 10.1007/bf01314440
title:
  Ultrastructural changes in the small intestinal epithelium of suckling pigs affected with a transmissible gastroenteritis (TGE)-like disease

abstract:
  The small intestine of piglets collected during a sudden outbreak of diarrhoeal disease resembling transmissible gastroenteritis (TGE) was examined by light and electron microscopy. The principal histopathological changes were moderate infiltration by mononuclear cells in the lamina propria of the villi and cytoplasmic vacuolation. These were most pronounced in the epithelial cells covering the villous tips. By scanning electron microscopy, the intestinal villi were swollen and the transverse furrows disappeared. Microvilli were reduced in number leaving denuded areas on the brush border of the villous epithelial cells. The ultrastructural changes were restricted to the cytoplasm of affected villous epithelial cells. The cell organelles were missing in rounded areas leaving cleared areas in the cytoplasm. Parallel fascicles and bundles were seen in these areas. Viral particles with an average diameter of 70 nm were found within the dilated apical tubulo-vesicular system, free in the cytoplasm, among the microvilli or lying free in the intestinal lumen. Viral particles surrounded a non-membrane bound viroplasm in some cases. The negatively stained particles showed a typical coronavirus morphology. These particles were found to be distinct from the known coronaviruses of swine, TGE virus and hemagglutinating encephalomyelitis virus by immune electron microscopy.


id: cord-340422-8f5xe4zc
author: Rowland, R. R. R.
date: 2001
url: https://www.ncbi.nlm.nih.gov/pubmed/11338389/
doi: 10.1007/s007050170161
title:
  Inhibition of porcine reproductive and respiratory syndrome virus by interferon-gamma and recovery of virus replication with 2-aminopurine

abstract:
  Porcine reproductive and respiratory syndrome virus (PRRSV) belongs to a group of RNA viruses that establish persistent infections. A proposed strategy for evading immunity during persistent PRRSV infection is by preventing the induction of IFN activity in pigs and/or by blocking the activation of antiviral proteins in permissive cells. IFN-γ mRNA expression was observed in the lymph nodes and lungs of pigs infected with wild-type PRRSV strain SDSU-23983. Pretreatment of MARC-145 cells with IFN-γ inhibited wild-type (SDSU-23983 P6) and culture-adapted (SDSU-23983 P136) PRRS viruses in a dose-dependent manner and at relatively low concentrations. The effect of IFN-γ on virus replication included reductions in the number of infected cells, virus yield, and RNA content in single cells. Virus replication was partially restored by the addition of 2-aminopurine (2-AP), an inhibitor of dsRNA inducible protein kinase (PKR). The addition of 2-AP also restored the viral RNA content per cell to near normal levels, suggesting that inhibition of viral RNA synthesis was through PKR. The principal difference between P6 and P136 isolates was the recovery of P136 replication with lower concentrations of 2-AP. Immunostaining with anti-PKR antibody showed a redistribution of PKR from the cytoplasm into nucleoli of infected cells.


id: cord-340905-8nyew5i5
author: Chen, Yi-Ning
date: 2015-08-08
txt: ./txt/cord-340905-8nyew5i5.txt
cache: ./cache/cord-340905-8nyew5i5.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26254026/
doi: 10.1007/s00705-015-2556-2
summary:
  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.

title:
  Genotyping of turkey coronavirus field isolates from various geographic locations in the Unites States based on the spike gene

abstract:
  Turkey flocks have experienced turkey coronaviral enteritis sporadically in the United States since the 1990s. Twenty-four field isolates of turkey coronavirus (TCoV) from multiple states in the United States were recovered from 1994 to 2010 to determine the genetic relationships among them. The entire spike (S) gene of each TCoV isolate was amplified and sequenced. Pairwise comparisons were performed using the Clustal W program, revealing 90.0 % to 98.4 % sequence identity in the full-length S protein, 77.6 % to 96.6 % in the amino terminus of the S1 subunit (containing one hypervariable region in S1a), and 92.1 % to 99.3 % in the S2 subunit at the deduced amino acid sequence level. The conserved motifs, including two cleavage recognition sequences of the S protein, two heptad repeats, the transmembrane domain, and the Golgi retention signal were identified in all TCoV isolates. Phylogenetic analysis based on the full-length S gene was used to distinguish North American TCoV isolates from French TCoV isolates. Among the North American TCoV isolates, three distinct genetic groups with 100 % bootstrap support were observed. North Carolina isolates formed group I, Texas isolates formed group II, and Minnesota isolates formed Group III. The S genes of 24 TCoV isolates from the United States remained conserved because they contained predominantly synonymous substitutions. The findings of the present study suggest endemic circulation of distinct TCoV genotypes in different geographic locations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-015-2556-2) contains supplementary material, which is available to authorized users.


id: cord-341278-klv9jdm8
title: The role of gamma interferon in infection of susceptible mice with murine coronavirus, MHV-JHM
author: Smith, Abigail L.
date: 1991
txt: ./txt/cord-341278-klv9jdm8.txt
cache: ./cache/cord-341278-klv9jdm8.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/1662041/
doi: 10.1007/bf01316746
summary:
  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] .

abstract:
  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. Since gamma interferon (IFN) has been implicated as an up-regulator of IgG 2 a production, attempts were made to determine whether levels of this cytokine were modified in sera of infected mice. 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. Immunotherapy with recombinant IFN-γ ameliorated disease as reflected by mortality rates and virus titers in target organs.


id: cord-341342-kyavg4vu
author: Masters, P. S.
date: 1992
txt: ./txt/cord-341342-kyavg4vu.txt
cache: ./cache/cord-341342-kyavg4vu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/1322650/
doi: 10.1007/bf01309634
summary:
  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).

title:
  Localization of an RNA-binding domain in the nucleocapsid protein of the coronavirus mouse hepatitis virus

abstract:
  The interaction between the nucleocapsid (N) protein of mouse hepatitis virus (MHV) and RNA was studied in an effort to define portions of the N molecule that participate in binding to RNA. N mRNAs transcribed from SP6 and T7 vectors were translated in a rabbit reticulocyte lysate. Analysis of synthesized N protein in a nondenaturing gel system showed that it bound in vitro to an endogenous RNA in the reticulocyte lysate but not to its own mRNA. A set of deletion mutants was constructed in order to localize the RNA-binding activity of the N protein. It was found that removal of as much as 135 amino-terminal or 57 carboxy-terminal amino acids from the molecule had little or no effect on RNA binding. Moreover, deletion mutants lacking both termini still retained RNA-binding ability. By contrast, internal deletions or truncations extending beyond these two limits effectively abolished RNA binding by N protein. Thus, the RNA-binding region of N has been mapped to the second (central) of the three structural domains of the molecule.


id: cord-341383-e2jrhycj
author: Dong, Wei
date: 2016-05-02
txt: ./txt/cord-341383-e2jrhycj.txt
cache: ./cache/cord-341383-e2jrhycj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27138548/
doi: 10.1007/s00705-016-2866-z
summary:
  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) .

title:
  Epidemiological and clinical characteristics of respiratory viral infections in children in Shanghai, China

abstract:
  Acute respiratory tract infections (ARTIs) due to various viruses are not only the most common causes of upper and lower respiratory infection but are also major causes of morbidity and mortality in children. 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. Nasopharyngeal swabs from 2819 children with ARTIs were collected from August 2011 to December 2014, and used for detection of respiratory viruses by multiplex RT-PCR. Seventeen respiratory viruses were detected among 691 (24.5 %) of 2819 patients. The highest prevalence of respiratory viruses was detected in the age group of less than 1 year (29.0 %), and the prevalence decreased with age. This suggests that children less than one year old are the most susceptible to infection. Influenza virus (IFV) was the most frequently detected virus (5.8 %), followed by parainfluenza virus (PIV) (5.7 %), enterovirus (EV) (4.3 %), and respiratory syncytial virus (RSV) (3.6 %). Statistical analysis showed that epidemics of IFV, PIV and EV had distinct seasonal variations. Mean monthly temperature appeared to be the only meteorological factor associated with IFV and PIV infection. These findings will provide valuable information for decision-making, prevention and treatment of ARTIs in children. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-016-2866-z) contains supplementary material, which is available to authorized users.


id: cord-341469-7guojyay
author: Park, Seong-Jun
date: 2011-01-06
txt: ./txt/cord-341469-7guojyay.txt
cache: ./cache/cord-341469-7guojyay.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00705-010-0892-9
doi: 10.1007/s00705-010-0892-9
summary:
  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.

title:
  Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field isolates in Korea

abstract:
  Porcine epidemic diarrhea virus (PEDV) has caused enteric disease with devastating impact since the first identification of PEDV in 1992 in Korea. In this study, we investigated molecular epidemiology, showed genetic diversity, and analyzed phylogenetic relationships of Korean PEDV field isolates with other PEDV reference strains. Genetic analysis of the complete M and ORF3 genes showed that each PEDV group had several unique characteristics, and this indicated that specific groups of PEDVs may be differentiated from the other PEDVs by specific nucleotide differences. 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. These results raise questions as to whether a new type of PEDV vaccine may be necessary for preventing PEDV infection more effectively in Korea.


id: cord-342568-3sj235rm
author: Bald-Blume, Niklas
date: 2017-02-11
txt: ./txt/cord-342568-3sj235rm.txt
cache: ./cache/cord-342568-3sj235rm.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28190200/
doi: 10.1007/s00705-017-3256-x
summary:
  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.

title:
  Development of a molecular assay for the general detection of tospoviruses and the distinction between tospoviral species

abstract:
  A Luminex xTAG-based assay for plant-infecting tospoviruses was developed. The test enables the detection of tospoviruses in general and the differentiation of the four important member species of this genus: Tomato spotted wilt virus, Impatiens necrotic spot virus, the proposed ‘Capsicum chlorosis virus’ and Watermelon silver mottle virus. The generic tospovirus primers used in this method are also applicable for detection of tospoviruses by basic RT-PCR. We also describe an economic alternative method for the distinction of the four tospoviruses mentioned and of additional member viruses, based on a restriction fragment length polymorphism (RFLP). The sophisticated Luminex xTAG technology allows the simultaneous detection of various targets. This study is part of a project that aims to develop a method for the simultaneous detection of various plant pathogens (viral, bacterial and fungal) in plant material.


id: cord-343131-tu6g977q
title: A divergent clade of circular single-stranded DNA viruses from pig feces
author: Cheung, Andrew K.
date: 2013-04-24
txt: ./txt/cord-343131-tu6g977q.txt
cache: ./cache/cord-343131-tu6g977q.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00705-013-1701-z
doi: 10.1007/s00705-013-1701-z
summary:
  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.

abstract:
  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). Phylogenetic analysis placed these viruses into a highly divergent clade of this rapidly growing new viral family. 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. Furthermore, these viruses also exhibit three additional overlapping open reading frames in the large intergenic region between the capsid and replication initiator protein genes.


id: cord-343256-n593kh7u
author: Percy, D. H.
date: 1991
txt: ./txt/cord-343256-n593kh7u.txt
cache: ./cache/cord-343256-n593kh7u.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/1877886/
doi: 10.1007/bf01310668
summary:
  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 ).

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

abstract:
  Sialodacryoadenitis virus (SDAV) and Parker's rat coronavirus (PRC) are two recognized viral strains which cause spontaneous disease in the laboratory rat. Currently there is no recognized practical procedure which will accurately differentiate infections with these strains. Using SDAV- and 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. There was no detectable difference in the sensitivity or specificity of these systems in detecting antibody to the homologous or heterologous virus. Thus there was no evidence that SDAV- and PRC-infected cells would serve to differentiate antibody to the homologous virus using the IFA technique. In addition, antibody titers were similar when mouse hepatitis virus (MHV)-infected cells were used as the source of antigen for the IFA technique. 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.


id: cord-343349-ftzjdvfj
title: Experimental infection of adult axenic rats with Parker''s Rat Coronavirus
author: Bhatt, P. N.
date: 1977
txt: ./txt/cord-343349-ftzjdvfj.txt
cache: ./cache/cord-343349-ftzjdvfj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/907478/
doi: 10.1007/bf01314779
summary:
  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.

abstract:
  The pathogenesis of Parker's Rat Coronavirus (PRCV) was studied in axenic CD rats. Three to four 9 to 10 week old rats were euthanized daily for eight days after intranasal inoculation. Rats remained free of clinical disease. 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. Acute rhinitis developed by day two and was associated with mild focal necrosis of respiratory mucosal epithelium. Mild nonsuppurative tracheitis and multifocal interstitial pneumonia appeared by day five and persisted through day eight. Dacryoadenitis did not occur, sialoadenitis was detected in only three rats and virus was recovered from only one submaxillary salivary gland. This experiment indicates that PRCV can be a primary pathogen for the respiratory system of adult rats. In contrast to sialodacryoadenitis (SDA) virus the tropism of PRCV for salivary and lacrimal glands is low.


id: cord-343780-084lq92r
title: Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan
author: Hsu, Tien-Huan
date: 2018-07-26
txt: ./txt/cord-343780-084lq92r.txt
cache: ./cache/cord-343780-084lq92r.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00705-018-3964-x
doi: 10.1007/s00705-018-3964-x
summary:
  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) .

abstract:
  Porcine deltacoronavirus (PDCoV) was initially documented in Hong Kong and later in the United States, South Korea, and Thailand. 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. The rRT-PCR results were positive for PDCoV (29/172, 16.9%), PEDV (36/172, 20.9%), TGEV (2/172, 1.2%), and coinfections (16/172, 9.3%). After cloning and sequencing, PDCoV nucleocapsid genes were analyzed. Phylogeny results indicated that the nucleotide sequences of all isolates were like those reported in other countries. To further trace PDCoV in the period of 2011 to 2015, an enzyme-linked immunosorbent assay (ELISA) was used to detect antibodies against PDCoV. The results showed that 279 of 1,039 (26.9%) sera were positive for the PDCoV nucleocapsid protein, implying that PDCoV might have existed in Taiwan before 2011.


id: cord-344464-if6js43s
author: Cowley, J. A.
date: 2002
txt: ./txt/cord-344464-if6js43s.txt
cache: ./cache/cord-344464-if6js43s.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/12376758/
doi: 10.1007/s00705-002-0847-x
summary:
  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.

title:
  The complete genome sequence of gill-associated virus of Penaeus monodon prawns indicates a gene organisation unique among nidoviruses(*): Brief Report

abstract:
  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. The putative 1640 amino acid (aa) ORF3 protein (MW = 182049 Da, pI = 6.62) contains 15 potential N-linked glycosylation sites, 15 potential O-linked glycosylation sites and six highly hydrophobic regions predicted to represent transmembrane (TM) domains. Three of the predicted TM domains occur in the amino-terminal 228 aa, two in the central portion, and one near the carboxy-terminus of ORF3. Only one short (83 aa) open reading frame (ORF4) was identified between ORF3 and the 3′-poly(A) tail. 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.


id: cord-345552-h6fwi0qn
title: Hydropathic characteristics of adenovirus hexons
author: Li, Q.-G.
date: 1997-07-01
txt: ./txt/cord-345552-h6fwi0qn.txt
cache: ./cache/cord-345552-h6fwi0qn.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/9267445/
doi: 10.1007/s007050050162
summary:
  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

abstract:
  The complete nucleotide sequence and the predicted amino acid sequence of the adenovirus type 7 hexon gene were determined. The hydro-pathy of the 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 was analysed. The presence of purines and pyrimid-ines in the second position of the codons was correlated to hydrophilicity and hydrophobicity, respectively. Comparison of the hydrophilicity plots of eight hexons showed seven hypervariable regions to be distributed on the surface. A large portion of the hypervariable regions manifests hydrophilicity. The strength of the surface charge accumulated on the hydrophilic and hydrophobic regions correlated to the tissue tropism of the different adenovirus types. Analysis of codon usage for adenovirus hexons showed that among synony-mous codons those with cytidine in the third position were preferably used to a great extent. Analysis of the nucleotide and amino acid sequence pair distances and the phylogenetic tree of 14 hexon proteins showed members of subgenera B, D and E to be closely related, especially Ad4 and Ad16, and subgenus A to be closely related to subgenus F.


id: cord-345856-ckm0ol20
title: Antiviral activity of Arbidol against Coxsackie virus B5 in vitro and in vivo
author: Zhong, Qiong
date: 2009-03-17
txt: ./txt/cord-345856-ckm0ol20.txt
cache: ./cache/cord-345856-ckm0ol20.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00705-009-0346-4
doi: 10.1007/s00705-009-0346-4
summary:
  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.

abstract:
  We investigated the antiviral activity of Arbidol, an antiviral chemical compound, against Coxsackie virus B5 (CVB(5)) in vitro and in vivo. 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. BALB/c mice were used as an animal model to test the Arbidol activity in vivo. 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. Our results demonstrate that in vitro and in vivo infection with CVB(5) can be effectively treated by Arbidol.


id: cord-345940-adg264vb
author: Wanitchang, Asawin
date: 2018-08-22
txt: ./txt/cord-345940-adg264vb.txt
cache: ./cache/cord-345940-adg264vb.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00705-018-4001-9
doi: 10.1007/s00705-018-4001-9
summary:
  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) .

title:
  Characterization of influenza A virus pseudotyped with the spike protein of porcine epidemic diarrhea virus

abstract:
  The coronavirus spike protein and the influenza virus hemagglutinin are class I viral membrane fusion proteins. While the two proteins display strong structural conservation and the mechanisms underlying membrane fusion are similar, they share no sequence similarity. Whether they are functionally interchangeable is currently unknown. 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. Treatment with endocytosis inhibitors did not affect syncytium formation by infected cells. Moreover, the infectivity of scIAV-S was associated with the degree of cell adaptation of PEDV-S. Intriguingly, scIAV-S lacking functional neuraminidase (NA) exhibited substantially higher infectivity, suggesting a pivotal role of the sialic acid in the binding/entry of PEDV. Together, scIAV-S offers a robust platform for the investigation of the entry mechanism of PEDV or, possibly, of other coronaviruses.


id: cord-345957-wuk2arf9
title: Detection and genetic characterization of bovine kobuvirus from calves in Egypt
author: Mohamed, Fakry F.
date: 2018-02-08
txt: ./txt/cord-345957-wuk2arf9.txt
cache: ./cache/cord-345957-wuk2arf9.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00705-018-3758-1
doi: 10.1007/s00705-018-3758-1
summary:
  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 ).

abstract:
  Kobuviruses are small non-enveloped RNA viruses that probably cause diarrhea in cattle and swine. Since its discovery in 2003, few studies have addressed bovine kobuvirus (BKoV; a species of Aichivirus B) infections. BKoV has been reported in Europe, Asia, and South America, suggesting a worldwide distribution. To investigate the presence of BKoV in Egypt, 36 fecal specimens from diarrheic calves in two different Egyptian provinces (Cairo and Sharkia) were screened by RT-PCR and 24 (66.7%) were found positive for BKoV. RNA from one of the positive samples (BKoV/Egy-1/KY407744) was subjected to next-generation sequencing to determine the complete BKoV genome sequence. 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). Additionally, five VP1 and seven 3D sequences were obtained from other samples by using RT-PCR and Sanger sequencing. A discrepancy in the phylogenetic topography of VP1 and 3D was observed, where the Egyptian VP1 sequences were classified as a distinct cluster within the proposed lineage 1 (genotype A), which also contained strains from the UK, Brazil, and Japan. While, the 3D sequences from Cairo were related to those of Chinese strains unlike Sharkia ones that were more closer to Korean strains. To the best of our knowledge, this is the first detection and genomic characterization of BKoV in Egypt or indeed Africa. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-018-3758-1) contains supplementary material, which is available to authorized users.


id: cord-346321-drhiqch0
author: Hohdatsu, T.
date: 1994
txt: ./txt/cord-346321-drhiqch0.txt
cache: ./cache/cord-346321-drhiqch0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/7832635/
doi: 10.1007/bf01310791
summary:
  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.

title:
  The role of IgG subclass of mouse monoclonal antibodies in antibody-dependent enhancement of feline infectious peritonitis virus infection of feline macrophages

abstract:
  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. Even among the MAbs that have been shown to recognize the same antigenic site, IgG 2a MAbs enhanced FIPV infection strongly, whereas IgG 1 MAbs did not. These IgG 2a MAbs enhanced the infection even when macrophages pretreated with the MAb were washed and then inoculated with the virus. Immunofluorescence flow cytometric analysis of the macrophages treated with each of the MAbs showed that the IgG 2a MAbs but not the IgG 1 MAbs bound to feline alveolar macrophages. Treatment of the IgG 2a MAb with protein A decreased the binding to the macrophages and, in parallel, diminished the ADE activity. Although no infection was observed by inoculation of FIPV to human monocyte cell line U937 cells, FIPV complexed with either the IgG 2a MAb or the IgG 1 MAb caused infection in U937 cells which are shown to express Fc gamma receptor (Fc γ R) I and II that can bind mouse IgG 2a and IgG 1, respectively. These results suggest that the enhancing activity of MAb is closely correlated with IgG subclass and that the correlation is involved in binding of MAb to Fc γ R on feline macrophage.


id: cord-346629-770qyee8
title: Phylogenetic analysis of avian infectious bronchitis virus strains isolated in Japan
author: Mase, M.
date: 2004-07-15
txt: ./txt/cord-346629-770qyee8.txt
cache: ./cache/cord-346629-770qyee8.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15290359/
doi: 10.1007/s00705-004-0369-9
summary:
  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

abstract:
  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). Among them, three major genetic groups were associated with the recent outbreaks of IB in Japan. One group is indigenous to Japan and could not be placed within the known existing groups in other countries. The remaining two groups, which have emerged recently, are related to isolates in China and Taiwan.


id: cord-346928-g1dqiki6
author: Costantini, V.
date: 2003-11-26
txt: ./txt/cord-346928-g1dqiki6.txt
cache: ./cache/cord-346928-g1dqiki6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15098110/
doi: 10.1007/s00705-003-0245-z
summary:
  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] .

title:
  Respiratory and fecal shedding of Porcine respiratory coronavirus (PRCV) in sentinel weaned pigs and sequence of the partial S-gene of the PRCV isolates

abstract:
  Porcine respiratory coronavirus (PRCV), a spike (S) gene deletion mutant of Transmissible gastroenteritis virus (TGEV), causes mild or subclinical respiratory infections in pigs. The shedding of PRCV/TGEV was studied at different days post-arrival in fecal and nasal swabs from PRCV/TGEV seronegative sentinel pigs introduced into a PRCV seropositive herd with questionable TGEV serology and diarrhea. Nasal shedding of PRCV was detected in 57% and 63% of samples by nested-RT-PCR and cell culture immunofluorescence (CCIF), respectively. However fecal shedding of PRCV was detected in 37% of the samples by nested-RT-PCR and 19% by CCIF. Four respiratory and 5 fecal PRCV strains were isolated in swine testicle cells including nasal/fecal PRCV pairs (isolated at the same time) from 3 pigs. Comparison of nasal/fecal PRCV pairs from individual pigs revealed different deletions in the spike (S) gene (648 or 681 nt) in 2 pairs and a consistent change in nt 790/791 (aa T to V) for all pairs. 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. The nasal isolate was shed both nasally and in feces, but the fecal isolate was shed only marginally in feces, and not nasally. Our results show that nested-RT-PCR was as sensitive as CCIF for PRCV detection in nasal swabs, but was more sensitive than CCIF for PRCV detection in fecal samples; alternatively PRCV shed in feces was more labile with loss of infectivity. The S-gene sequence differences found between the fecal and respiratory PRCV isolates may influence their tissue tropism. These new PRCV isolates should be useful to understand the molecular basis of coronavirus tropism and evolution in infected swine.


id: cord-347443-0evqo01m
author: Litwin, Christine M.
date: 2013-07-24
txt: ./txt/cord-347443-0evqo01m.txt
cache: ./cache/cord-347443-0evqo01m.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/23881085/
doi: 10.1007/s00705-013-1794-4
summary:
  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.

title:
  Seasonality and prevalence of respiratory pathogens detected by multiplex PCR at a tertiary care medical center

abstract:
  Respiratory tract infections (RTIs) are a leading cause of mortality and morbidity. Seasonality has been reported for many viruses, including influenza virus, respiratory syncytial virus (RSV), and the recently described human metapneumovirus (hMPV). We hypothesize that the availability of rapid, multiplex PCR diagnostics will provide better clinical care and new insights into the etiology and clinical spectrum of RTIs. We conducted a retrospective analysis of the incidence of respiratory pathogens at a 500-bed adult and 154-bed pediatric hospital tertiary care center. A total of 939 specimens from patients with an age range of 5 days to 91 years (median, 2 years) were tested by a multiplex respiratory pathogen PCR from November 14, 2011 to November 13, 2012. Sixty-five percent of specimens were positive for at least one pathogen. As the age of the patient increased, the positivity rate for the PCR decreased proportionately. Rhinoviruses/enteroviruses (Rhino/Entero) were the most prevalent (34.3 %) followed by RSV (19.2 %) and hMPV (6.2 %). Twelve percent of the positive samples were positive for multiple analytes, with Rhino/Entero and RSV being the most common combination. The peak months were September and May for Rhino/Entero infections, January for RSV and February for coronavirus. hMPV peaked 2 months after RSV, as has been observed recently in other studies. Multiplex PCR provides rapid diagnostic information that can be used to make knowledgeable clinical decisions and potentially reduce the use of antibiotics. Active respiratory PCR surveillance could also predict seasonal respiratory epidemics to allow for adequate planning of additional infection control measures.


id: cord-348147-leni23pa
title: Genetic diversity and recombination of murine noroviruses in immunocompromised mice
author: Müller, B.
date: 2007-05-29
txt: ./txt/cord-348147-leni23pa.txt
cache: ./cache/cord-348147-leni23pa.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/17533553/
doi: 10.1007/s00705-007-0989-y
summary:
  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.

abstract:
  Murine noroviruses (MNV) are newly identified pathogens which infect laboratory mice. In this study, we found a high prevalence (64.3%) of MNV in various breeding colonies of immunocompromised, transgenic and wild-type mouse lines. All mice survived infection with no signs of clinical disease. Faeces samples were collected from animals housed in two separate laboratory mouse colonies in Berlin, Germany, and screened using quantitative reverse transcription (RT)-PCR. We have determined the complete nucleotide sequences of 3 novel MNV strains. Furthermore, we sequenced two subgenomic regions within open reading frames (ORFs) 1 and 2 that are suitable for genotyping. Sequence analysis of the full-length and partial genomes obtained from naturally infected mice yielded valuable data on genetic diversity of murine noroviruses. The discordance of genotype affiliation of some MNVs shown in ORF1 and ORF2 suggests intertypic recombination events in vivo.


id: cord-348163-9q1rt8i7
title: Beyond RGD: virus interactions with integrins
author: Hussein, Hosni A. M.
date: 2015-09-01
txt: ./txt/cord-348163-9q1rt8i7.txt
cache: ./cache/cord-348163-9q1rt8i7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26321473/
doi: 10.1007/s00705-015-2579-8
summary:
  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.

abstract:
  Viruses successfully infect host cells by initially binding to the surfaces of the cells, followed by an intricate entry process. As multifunctional heterodimeric cell-surface receptor molecules, integrins have been shown to usefully serve as entry receptors for a plethora of viruses. However, the exact role(s) of integrins in viral pathogen internalization has yet to be elaborately described. Notably, several viruses harbor integrin-recognition motifs displayed on viral envelope/capsid-associated proteins. The most common of these motifs is the minimal peptide sequence for binding integrins, RGD (Arg-Gly-Asp), which is known for its role in virus infection via its ability to interact with over half of the more than 20 known integrins. Not all virus-integrin interactions are RGD-dependent, however. Non-RGD-binding integrins have also been shown to effectively promote virus entry and infection as well. Such virus-integrin binding is shown to facilitate adhesion, cytoskeleton rearrangement, integrin activation, and increased intracellular signaling. Also, we have attempted to discuss the role of carbohydrate moieties in virus interactions with receptor-like host cell surface integrins that drive the process of internalization. As much as possible, this article examines the published literature regarding the role of integrins in terms of virus infection and virus-encoded glycosylated proteins that mediate interactions with integrins, and it explores the idea of targeting these receptors as a therapeutic treatment option.


id: cord-348179-i8w7huke
title: Increased risk of hepatitis E virus infection in schizophrenia
author: Xue, Yong
date: 2012-10-07
txt: ./txt/cord-348179-i8w7huke.txt
cache: ./cache/cord-348179-i8w7huke.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00705-012-1494-5
doi: 10.1007/s00705-012-1494-5
summary:
  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.

abstract:
  Until now, the risk of HEV infection in schizophrenia was unknown. The present results showed that the seroprevalence of anti-HEV IgG and anti-HEV IgM in schizophrenia were significantly higher than that in healthy controls. Anti-HEV IgG positivity increased with age and with the duration of disease in schizophrenia patients. 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). Compared with the schizophrenia patients who tested anti-HEV IgG negative, the levels of interleukin-4 and interleukin-10 (Th2 cytokines) were significantly higher, while the interleukin-12 (Th1 cytokine) level was significantly lower, in those with anti-HEV IgG positivity. Of five schizophrenia patients who were anti-HEV IgM positive, four had elevated CD4(+)/CD8(+) T-cell ratios. HEV RNA was isolated from one of these four patients and classified as genotype 4. Anti-HEV IgM positivity was not detected among healthy controls. Therefore, schizophrenia patients exhibited a higher risk of HEV infection than controls.


id: cord-348867-c0xpzd4d
title: First complete genome sequence of parainfluenza virus 5 isolated from lesser panda
author: Zhai, Jun-Qiong
date: 2017-01-30
txt: ./txt/cord-348867-c0xpzd4d.txt
cache: ./cache/cord-348867-c0xpzd4d.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00705-017-3245-0
doi: 10.1007/s00705-017-3245-0
summary:
  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

abstract:
  Parainfluenza virus 5 (PIV5) is widespread in mammals and humans. Up to now, there is little information about PIV5 infection in lesser pandas. 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. The full-length genome of ZJQ-221 was found to be 15,246 nucleotides and consisted of seven non-overlapping genes encoding eight proteins (i.e., NP, V, P, M, F, SH, HN and L). 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. The findings of this study confirm the presence of PIV5 in lesser panda and indicate this mammal as a possible natural reservoir. Furthermore they highlight the urgent need to strengthen viral surveillance and control of PIV5 in zoo animals. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-017-3245-0) contains supplementary material, which is available to authorized users.


id: cord-349800-s9w2yr08
author: Hohdatsu, T.
date: 1991
txt: ./txt/cord-349800-s9w2yr08.txt
cache: ./cache/cord-349800-s9w2yr08.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/1706593/
doi: 10.1007/bf01310494
summary:
  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) .

title:
  Characterization of monoclonal antibodies against feline infectious peritonitis virus type II and antigenic relationship between feline, porcine, and canine coronaviruses

abstract:
  Seven monoclonal antibodies (MAbs) with neutralizing activity against feline infectious peritonitis virus (FIPV) strain 79-1149 (type II) were prepared. When the polypeptide specificity recognized by these monoclonal antibodies (MAbs) was investigated by Western immunoblotting, all of the MAbs reacted with peplomer glycoprotein (S) of the virus. By competitive binding assay these MAbs were found to recognize at least 3 different epitopes. 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. All MAbs neutralized FECV strain 79-1683, CCV strain 1-71, and TGEV strains TO-163 and SH, while they did not neutralize the 6 FIPV type I viruses. Moreover, the MAb against TGEV strain TO-163, which has strong neutralizing activity against 7 TGEV viruses, neutralized CCV strain 1-71, FECV strain 79-1683, and FIPV strain 79-1146, but did not neutralize the 6 FIPV type I viruses. These results demonstrated that there are at least 3 epitopes involved in the neutralization of FIPV type II strain 79-1146, and that these epitopes are not present in FIPV type I viruses but are present in FECV strain 79-1683 which does not induce feline infectious peritonitis, TGEV strains TO-163 and SH, and CCV strain 1-71. These results suggest the presence of 2 serotypes of FIPV which can be clearly distinguished by the neutralization test using MAbs.


id: cord-349907-dwhyx97y
author: Noh, Ji Yeong
date: 2017-02-20
txt: ./txt/cord-349907-dwhyx97y.txt
cache: ./cache/cord-349907-dwhyx97y.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00705-017-3281-9
doi: 10.1007/s00705-017-3281-9
summary:
  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] .

title:
  Simultaneous detection of severe acute respiratory syndrome, Middle East respiratory syndrome, and related bat coronaviruses by real-time reverse transcription PCR

abstract:
  Since severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses (CoVs) share similar characteristics with respect to clinical signs, etiology, and transmission, methods for a rapid and accurate differential diagnosis are important. Therefore, the aim of this study was to develop a duplex real-time reverse transcription (RT)-PCR method for the simultaneous detection of these viruses. Primers and probes that target the conserved spike S2 region of human SARS-CoV, MERS-CoV, and their related bat CoVs were designed. The results of real-time RT-PCR showed specific reactions for each virus with adequate detection limits of 50–100 copies/mL and 5–100 copies/mL using pUC57-SARS-pS2 (a template for SARS-CoV) and pGEM-MERS-S2 (a template for MERS-CoV), respectively. In addition, this real-time RT-PCR system was able to detect the target viruses SARS-like bat CoV and MERS-CoV in bat fecal samples and sputum of MERS patients, respectively. Therefore, this newly developed real-time RT-PCR method is expected to detect not only SARS-CoV and MERS-CoV in humans but also several bat CoVs that are closely related to these viruses in bats.


id: cord-349964-38rgcc5h
title: Antigenic relationship of the feline infectious peritonitis virus to coronaviruses of other species
author: Pedersen, N. C.
date: 1978
txt: ./txt/cord-349964-38rgcc5h.txt
cache: ./cache/cord-349964-38rgcc5h.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/81044/
doi: 10.1007/bf01315534
summary:
  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.

abstract:
  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. FIPV was found to be closely related to transmissible gastroenteritis virus (TGEV) of swine. Transmissible gastroenteritis virus and FIPV were in turn antigenically related to human coronavirus 229E (HCV-229E) and canine coronavirus (CCV). An interesting finding in the study was that the 8 coronaviruses selected for this study fell into one of two antigenically distinct groups. Viruses in each group were antigenically related to each other to varying degrees, but were antigenically unrelated to coronaviruses of the second group. 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). The second antigenically related group was comprised of FIPV, TGEV, HCV-229E and CCV.


id: cord-353797-yb355mxk
title: Replication of bovine coronavirus in cell line BEK-1 culture
author: Inaba, Y.
date: 1976
txt: ./txt/cord-353797-yb355mxk.txt
cache: ./cache/cord-353797-yb355mxk.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/179503/
doi: 10.1007/bf01317959
summary:
  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.

abstract:
  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.


id: cord-355512-tycuoslv
author: Storz, J.
date: 1992
txt: ./txt/cord-355512-tycuoslv.txt
cache: ./cache/cord-355512-tycuoslv.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/1642550/
doi: 10.1007/bf01309637
summary:
  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.

title:
  Comparison of hemagglutinating, receptor-destroying, and acetylesterase activities of avirulent and virulent bovine coronavirus strains

abstract:
  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. The BCV-L9 and the wild-type strain BCV-LY-138 agglutinated chicken and mouse erythrocytes. The acetylesterase facilitated break-down of the BCV-erythrocyte complex with chicken but only to a minimal extent with mouse erythrocytes in the receptor-destroying enzyme test. 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. Diisopropylfluoro-phosphate moderately increased the hemagglutination titers, but completely inhibited the receptor destroying enzyme of purified virus of all strains. It had virtually no influence on the plaque-forming infectivity of the different BCV strains. The acetylesterase of strain BCV-L9 reacting in the receptor-destroying enzyme test was stable for 3h at 37 and 42°C. It was inactivated within 30 min at 56°C while the hemagglutinin function of this strain was stable for 3 h at 37, 42, and 56°C, but it was inactivated at 65°C within 1 h.


id: cord-355535-01h8yyqj
author: Zheng, Xue-yan
date: 2018-01-11
txt: ./txt/cord-355535-01h8yyqj.txt
cache: ./cache/cord-355535-01h8yyqj.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00705-017-3700-y
doi: 10.1007/s00705-017-3700-y
summary:
  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.

title:
  Regional, age and respiratory-secretion-specific prevalence of respiratory viruses associated with asthma exacerbation: a literature review

abstract:
  Despite increased understanding of how viral infection is involved in asthma exacerbations, it is less clear which viruses are involved and to what extent they contribute to asthma exacerbations. Here, we sought to determine the prevalence of different respiratory viruses during asthma exacerbations. Systematic computerized searches of the literature up to June 2017 without language limitation were performed. 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. We also examined the prevalence of viral infection stratified by age, geographic region, type of respiratory secretion, and detection method. Sixty articles were included in the final analysis. During asthma exacerbations, the mean prevalence of AdV, BoV, CoV, CMV, EnV, HSV, IfV, MpV, PiV, RV and RSV was 3.8%, 6.9%, 8.4%, 7.2%, 10.1%, 12.3%, 10.0%, 5.3%, 5.6%, 42.1% and 13.6%, respectively. EnV, MPV, RV and RSV were more prevalent in children, whereas AdV, BoV, CoV, IfV and PiV were more frequently present in adults. RV was the major virus detected globally, except in Africa. RV could be detected in both the upper and lower airway. Polymerase chain reaction was the most sensitive method for detecting viral infection. Our findings indicate the need to develop prophylactic polyvalent or polyvirus (including RV, EnV, IfV and RSV) vaccines that produce herd immunity and reduce the healthcare burden associated with virus-induced asthma exacerbations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-017-3700-y) contains supplementary material, which is available to authorized users.


id: cord-356176-1nwjjgul
author: Atherton, J. G.
date: 1978
txt: ./txt/cord-356176-1nwjjgul.txt
cache: ./cache/cord-356176-1nwjjgul.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/205194/
doi: 10.1007/bf01317848
summary:
  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).

title:
  The effect of ascorbic acid on infection of chick-embryo ciliated tracheal organ cultures by coronavirus

abstract:
  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.


id: cord-356192-8b96rgqa
author: Xie, Qian
date: 2017-04-18
txt: ./txt/cord-356192-8b96rgqa.txt
cache: ./cache/cord-356192-8b96rgqa.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00705-017-3361-x
doi: 10.1007/s00705-017-3361-x
summary:
  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

title:
  Two deletion variants of Middle East respiratory syndrome coronavirus found in a patient with characteristic symptoms

abstract:
  Significant sequence variation of Middle East respiratory syndrome coronavirus (MERS CoV) has never been detected since it was first reported in 2012. A MERS patient came from Korea to China in late May 2015. The patient was 44 years old and had symptoms including high fever, dry cough with a little phlegm, and shortness of breath, which are roughly consistent with those associated with MERS, and had had close contact with individuals with confirmed cases of MERS.After one month of therapy with antiviral, anti-infection, and immune-enhancing agents, the patient recovered in the hospital and was discharged. A nasopharyngeal swab sample was collected for direct sequencing, which revealed two deletion variants of MERS CoV. Deletions of 414 and 419 nt occurred between ORF5 and the E protein, resulting in a partial protein fusion or truncation of ORF5 and the E protein. Functional analysis by bioinformatics and comparison to previous studies implied that the two variants might be defective in their ability to package MERS CoV. However, the mechanism of how these deletions occurred and what effects they have need to be further investigated. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-017-3361-x) contains supplementary material, which is available to authorized users.


