cord-003573-ekxq4l9a	2019	In this study, we used N-terminal extracellular region of the influenza virus M2 protein (M2e) as the target antigen and constructed two optimized M2e DNA vaccines (p-tPA-p3M2e and p-p3M2e) with increased antigenic epitope density and enhanced antigen secretion. Our results show that the serum of mice immunized with p-tPA-p3M2e and p-p3M2e specifically binds to H1N1-infected MDCK cells, indicating that the M2e-specific antibodies induced by p-tPA-p3M2e and p-p3M2e immunization recognize the M2 protein on the surface of cells infected with influenza virus ( Figure S1 ). The above results demonstrate that vaccination with p-tPA-p3M2e protects mice from lethal infection with heterologous avian influenza strains, especially the H9N2 virus. In the present study, high antibody titers were induced in the p-tPA-p3M2e and p-p3M2e immunization groups, both of which demonstrated increased protection against challenge with homologous virus (H1N1). Immunization with p-tPA-p3M2e, without any adjuvant, induced high level, M2e-specific antibody production, humoral/cellular immune responses, and protected BALB/c mice from lethal infections of homo-and hetero-subtypic viruses.
cord-003676-kr4o8hoc	2019	title: Serological evidence and experimental infection of cynomolgus macaques with pteropine orthoreovirus reveal monkeys as potential hosts for transmission to humans In this study, we screened 517 cynomolgus macaques caught in Singapore for evidence of exposure to PRV3M (also known as Melaka virus), which was first isolated from human patients in Melaka, Malaysia. We provide evidence that PRV exposure in the macaque population in Singapore occurs at a relatively high prevalence and this study suggests that cynomolgus macaques may be an intermediate or reservoir host for PRVs. Pteropine orthoreoviruses (PRVs) are a group of emerging bat-borne viruses, belonging to the genus Orthoreovirus within the family Reoviridae. Given the cross-species transmission of PRVs and frequent human-monkey interaction in Singapore and surrounding regions, we initiated this study to determine the seroprevalence of PRV3M in wild cynomolgus macaques and to examine the susceptibility of cynomolgus macaques to experimental infection with PRV3M and their potential role in acting as hosts facilitating cross-species transmission.
cord-264267-weat0qs6	2020	Four polymorphisms (K267E, K267N, A291P and Δ346-348) strongly reduced binding of MERS-CoV S to DPP4 and S protein-driven host cell entry, as determined using soluble S protein and S protein bearing rhabdoviral vectors, respectively. For host cell entry, the surface unit, S1, of MERS-CoV S binds to the cellular type-II transmembrane protein dipeptidyl peptidase 4 (DPP4, CD26) [15] . For the binding studies with solMERS-S1-Fc, a similar protocol was followed as described for the analysis of DPP4 surface expression with the exceptions that sol-MERS-S1-Fc was used instead of the primary antibody (1:10 dilution in PBS/BSA) and that an AlexaFluor488conjugated anti-human antibody (goat, 1:500 dilution in PBS/BSA, ThermoFisher Scientific) was employed as the secondary antibody. Reduced MERS-CoV S-driven host cell entry is caused by inefficient S protein binding to DPP4 harboring polymorphic amino acid residues.
cord-265067-ejpblc6y	2013	China National Health and Family Planning Commission organized experts to do a comprehensive analysis based on the laboratory results, clinical manifestations of patients, epidemiological data, and concluded that the patients were infected with strains of H7N9 avian influenza virus. China National Health and Family Planning Commission notified the World Health Organization that a new H7N9 avian flu virus had caused lethal human infections in China (Gao RB et al., unpublished). The avian influenza viruses that have occasionally infected and caused disease in people without showing human adaptation comprise H5N1, H9N2, and a variety of H7 viruses. At the same time survey for H9N7 among wild birds and poultries has been carried out by the animal Centers for Disease Control and Prevention, and confirmed by the National Key Laboratory of Avian Influenza Institute in Harbin. Avian influenza A H5N1 virus: a continuous threat to humans Infection of immunocompromised patients by avian H9N2 influenza A virus
cord-266987-ikt8r2o1	2020	The laboratory diagnostic methods for human coronavirus infections have evolved substantially, with the development of novel assays as well as the availability of updated tests for emerging ones. It must be appreciated that no matter how accurate and fast laboratory testing methods are, the diagnosis of viral pneumonias such as caused by SARS-CoV-2 involves collecting the correct specimen from the patient at the right time. The authors recommended to use serology to facilitate the diagnosis of SARS-CoV-2 infections when an NP swab specimen was collected inappropriately and the molecular assays were performed unsatisfactorily [42] . Several RT-PCR protocols for detection of SARS-CoV-2 RNA have been posted by the World Health Organization at https://www.who.int/emergencies/ diseases/novel-coronavirus-2019/technical-guidance/ laboratory-guidance. Considering the increased levels of mortality and infectivity associated with three novel-coronavirus outbreaks, these random-access, safe and simple tests, which offer fast and accurate detection and identification, are likely to have an immediate impact on prompt clinical and epidemiological decisions [7, 63] .
cord-269232-rhhmvnlp	2016	Although antibodies against West Nile virus (WNV) have been detected in the sera of dromedaries in the Middle East, North Africa and Spain, no WNV has been isolated or amplified from dromedary or Bactrian camels. Notably, the amino-acid residues at 14 positions in the present dromedary WNV genome differed from those in most of the closely related WNV strains in cluster 2 of lineage 1a, with the majority of these differences observed in the putative E and NS5 proteins. [6] [7] [8] [9] [10] [11] [12] [13] In this article, we report the first isolation of WNV from a dromedary calf in the United Arab Emirates during the process of MERS-CoV screening and the results of the comparative genome and phylogenetic analysis. 20 Notably, 14 amino-acid residues in the present dromedary WNV genome differed from those in most of the closely related WNV strains in cluster 2 of lineage 1a (Figure 3) , with the majority of these differences observed in the putative E and NS5 proteins.
cord-270012-toompiz4	2019	During 2014, enterovirus D68 (EV-D68) outbreaks were described globally, causing severe respiratory diseases in children and, in some cases, subsequent paralysis. In this study, the type characterization of enterovirus (EV) detected in respiratory illnesses and the epidemiology and clinical association of EV-D68 infections in Spain over a five-year period were described. Therefore, the objectives of the present study were first, to identify the genotype of the EV detected in clinical samples collected from hospitalized patients with different respiratory diseases over a 5-year period, and second, to describe the molecular epidemiology and clinical characteristics of EV-D68 infections in Spain. Regarding patients with neurological symptoms, eight children and one adult were diagnosed with meningitis or meningoencephalitis and the remaining eight children were finally described as acute flaccid paralysis (AFP) cases. Two cases of acute severe flaccid myelitis associated with enterovirus D68 infection in children
cord-276914-44ji0g78	2020	However, the concentration of viral RNA in the anal swab (Ct value = 24 + 39) was higher than in the blood (Ct value = 34 + 39) from patient 2, suggesting that the virus might replicate in the digestive tract. Patient 3 (Figure 3(A) ) was transferred to the ICU directly on illness day 11 because of his severe condition, the 2019-nCoV virus was laboratory detected both in pharyngeal (Ct = 30 + 30) and blood samples (Ct = 37 + 39) on day 12, And his infection was confirmed by CDC on day 13. His disease advanced pretty fast and became severe on day 7 and he was transferred to ICU after his blood sample was detected to be virus-positive (Ct = 32 + 37). For patient 1, a high concentration of viral RNA (Ct = 23 + 27, on day 13) was detected in anal swab but not in pharyngeal (the same day) and blood (1 d ahead).
cord-279733-c0w9bw5u	2016	title: Middle East respiratory syndrome coronavirus M protein suppresses type I interferon expression through the inhibition of TBK1-dependent phosphorylation of IRF3 Collectively, our findings suggest a common and conserved mechanism through which highly pathogenic MERS-CoV and SARS-CoV harness their M proteins to suppress type I IFN expression at the level of TBK1-dependent phosphorylation and activation of IRF3 resulting in evasion of the host innate antiviral response. In non-specialized epithelial cells as well as a subset of specialized immune cells that are susceptible to MERS-CoV infection, 16, 18, 27 type I IFN production is an important part of the host innate immune response and is initiated by ubiquitously expressed cytoplasmic viral sensors in the retinoic acid-inducible gene-I (RIG-I)-like receptor (RLR) family in response to the detection of viral pathogen-associated molecular patterns such as double-stranded RNA (dsRNA). Middle east respiratory syndrome coronavirus 4a protein is a double-stranded RNA-binding protein that suppresses PACT-induced activation of RIG-I and MDA5 in the innate antiviral response
cord-281727-elartlro	2020	title: Isolation of infectious SARS-CoV-2 from urine of a COVID-19 patient Here, infectious SARS-CoV-2 was successfully isolated from urine of a COVID-19 patient. A novel coronavirus SARS-CoV-2 emerged to cause a major outbreak of severe pneumonia in humans in China and has spread to over 100 other countries [1] . Although viral RNA can be detected in multiple organs in COVID-19 patients, infectious SARS-CoV-2 has only been isolated from respiratory specimens [3, 4] . The urine sample tested positive for SARS-CoV-2 RNA on day 12 post infection (p.i.) (February 5th) for the first time and had periodically showed positive results in RT-PCR test until March 6th. Although it is hard to determine whether the kidney, the testis or the bladder were infected and produced infectious virus from current study, isolation of infectious SARS-CoV-2 in urine raises the possibility of fecal/urine-respiratory transmission.
cord-282140-teplpmi6	2016	title: Intense circulation of A/H5N1 and other avian influenza viruses in Cambodian live-bird markets with serological evidence of sub-clinical human infections Surveillance for avian influenza viruses (AIVs) in poultry and environmental samples was conducted in four live-bird markets in Cambodia from January through November 2013. Serum samples were collected, after obtaining informed consent, from LBM workers at the start of the study (January 2013) to form a baseline, and 8 weeks after the three major national festivals shown by previous work to be associated with increased A/H5N1 circulation in markets: 25 Lunar New Year, week 6; Khmer New Year, week 15; Pchum Ben, week 40. 25 To our knowledge, AIVs were detected in Cambodian LBMs during 2013 at a higher frequency than any other study published previously, 25 5 6 7 9 11 12 13 14 15 16 17 19 21 23 25 27 29 31 33 35 37 38 39 40 41 42 Avian influenza viruses in Cambodian live-bird markets SV Horm et al chicken swabs positive for influenza A RNA.
cord-284125-35ghtmhu	2013	6 Emerging novel viruses are a major public health concern with the potential of causing high health and socioeconomic impacts, as has occurred with progressive pandemic infectious diseases such as human immunodeficiency viruses (HIV), the recent pandemic caused by the novel quadruple re-assortment strain of influenza A virus (H1N1), and more transient events such as the outbreaks of Nipah virus in 1998/1999 and severe acute respiratory syndrome (SARS) coronavirus in 2003. To minimize the health and socioeconomic impacts of emerging epidemic infectious diseases, major challenges must be overcome in the national and international capacity for early detection, rapid and accurate etiological identification (especially those caused by novel pathogens), rapid response and effective control (Figure 1 ). However, to develop and establish such an effective national public health capacity, especially the laboratory component to support infectious disease surveillance, outbreak investigation and early response, a good understanding of the concepts of emerging infectious diseases and an integrated country and regional public health laboratory system in accordance with the nature and type of emerging pathogens, especially novel ones, are highly recommended.
cord-285965-mar8zt2t	2020	This study aims to analyze the different clinical characteristics between children and their families infected with severe acute respiratory syndrome coronavirus 2. Here, we report the clinical manifestations, laboratory test results, imaging characteristics, and treatment regimen of nine SARS-CoV-2 infected children and their families in Jinan, Shandong province to increase awareness of this disease, especially in children. A retrospective review was conducted of the clinical, lab tests, and radiologic findings for nine children and their families admitted to the Jinan Infectious Diseases Hospital identified to be nucleic acid-positive for SARS-CoV-2 from 24 January 2020 to 24 February 2020. All the patients were recorded with basic information and epidemiological histories [4] including (1) History of travel or residence in Wuhan and surrounding areas or other reported cases within 14 days of onset; (2) History of contact with new coronavirus infection (nucleic acid-positive) 14 days before onset; (3) history of contact with patients with fever or respiratory symptoms from Wuhan and surrounding areas, or from communities with case reports within 14 days before onset; (4) Cluster onset, along with disease condition changes.
cord-288741-69pgy833	2020	LLC-PK and ST cells were infected with PDCoV at a multiplicity of infection (MOI) of 10 in the presence or not of trypsin, and the virus released to the supernatant was collected at 12 and 24 hpi. Immunofluorescence assay LLC-PK and HEK293-APN cells were plated in 24-well plates, and when confluency reached 90%, cells were washed three times with PBS and infected with PDCoV at different MOI in the presence or not of trypsin. After seeding in 6-well plates and the confluency of each cells reached around 90%, PDCoV was used to infect LLC-PK (MOI = 0.5, 1 and 10) and ST cells (MOI = 1, 2 and 5), washed twice with PBS at 2 hpi, and then medium supplemented or not with 5 μg/ml trypsin was added. We first infected LLC-PK cells at different MOIs from 0.5-10, and evaluated PDCoV replication by analyzing the cells at 8, 12 and 24 hpi for the presence of the viral N protein.
cord-290671-6p23qxb8	2020	We have recently designed and engineered a pan-CoV fusion inhibitor, EK1 peptide, which could inhibit infection of five human coronaviruses, including SARS-CoV and MERS-CoV, and three bat-SL-CoVs [7] . Intranasal application of EK1 peptide before or after viral challenge, EK1 peptide can protect human DPP4-transgenic mice from MERS-CoV infection, suggesting its potential prophylactic and therapeutic effect against 2019-nCoV infection. The recently developed SARS-CoV and MERS-CoV neutralizing monoclonal antibodies (mAbs) and nanobodies with protective efficacy are specific to the S1 subunit of S protein, particularly the RBD [5, [8] [9] [10] . One of the rapid approaches is to evaluate the currently available SARS-CoV neutralizing antibodies with cross-neutralizing and protection activity against 2019-nCoV infection. The spike protein of SARS-CoV-a target for vaccine and therapeutic development A novel neutralizing monoclonal antibody targeting the N-terminal domain of the MERS-CoV spike protein
cord-291002-csao3flr	2018	In this study, we describe a previously characterized human monoclonal antibody, HNIgGA6, obtained by isolating rearranged heavy-chain and light-chain genes from patients who had recovered from H7N9 infections. Recent studies have characterized several neutralizing antibodies from human donors that target different epitopes on viral HA proteins, such as CT149 18 , H7.167 19 , m826 20 , HNIgGD5 21 , and HNIgGA6 22 , all of which represent potential interventions in the event of an H7N9 pandemic. Previously, we reported that an H7N9-neutralizing antibody, HNIgGA6, recognized the viral receptor binding site (RBS) on HA1 23 . Human infections with recently-emerging highly pathogenic H7N9 avian influenza virus in China Human monoclonal antibodies targeting the haemagglutinin glycoprotein can neutralize H7N9 influenza virus Molecular determinants of human neutralizing antibodies isolated from a patient infected with Zika virus Broadly neutralizing human antibody that recognizes the receptor-binding pocket of influenza virus hemagglutinin
cord-291076-p350i54m	2015	Unregulated complement activation is likely to play a crucial role in the pathogenesis of acute lung injury (ALI) induced by highly pathogenic virus including influenza A viruses H5N1, H7N9, and severe acute respiratory syndrome (SARS) coronavirus. [1] [2] [3] In addition, the complement system has been implicated in the development of acute lung diseases induced by highly pathogenic viruses including influenza A virus H1N1, 4 H5N1, 5 H7N9, 6 severe acute respiratory syndrome coronavirus (SARS-Cov), 7 Middle East respiratory syndrome coronavirus (MERS-Cov). C5a-mediated release of reactive oxygen species C5a is a strong chemoattractant for neutrophils and monocytes; it then activates these cells to generate oxidative burst with release of 10 A study demonstrated that ROS are primary pathogenic molecules in pneumonia from mice infected with influenza virus. Inhibition of Complement Activation Alleviates Acute Lung Injury Induced by Highly Pathogenic Avian Influenza H5N1 Virus Infection
cord-296511-y2vhh6oq	2016	title: Prevalence and characteristics of hypoxic hepatitis in the largest single-centre cohort of avian influenza A(H7N9) virus-infected patients with severe liver impairment in the intensive care unit 9 Hence, HH is likely one possible cause of severe liver impairment in A(H7N9)-infected patients with respiratory failure. Patients who met all of the following criteria were diagnosed as having HH according to previous reports 7, 8, 12 : (i) a massive but transient elevated ALT level (more than 20-fold the upper limit of normal (ULN)), (ii) the presence of respiratory, cardiac or circulatory failure and (iii) exclusion of other causes of liver injury. The extent of Hypoxic hepatitis in A(H7N9)-infected patients Y Zhang et al 2 ALT elevation was considerably higher in HH patients than in non-HH patients with liver injury (on admission, 1079.50 6 41.72 U/L vs. 8 H7N9 influenza-infected patients with chronic heart disease accompanying acute heart failure are at elevated risk of severe liver damage.
cord-297942-6wdwrttn	2020	To standardize the clinical diagnosis and treatment, Peking Union Medical College Hospital (PUMCH) has established a working group and formulated the following operational recommendation regarding "Diagnosis and Clinical Management of Severe Acute Respiratory Syndrome Coronavirus 2 Infection" (V2.0). According to the definition of the National Health Commission [1] , patients in accordance with one of the following standards should be hospitalized and transferred to Beijing designated medical institution as soon as possible; (1) respiratory rate increased (≥30 per min) or dyspnoea; (2) oxygen saturation ≤ 95% when breathing ambient air, or arterial oxygen tension (PaO₂) over inspiratory oxygen fraction (FIO₂) of less than 300 mm Hg (1 mm Hg equals to 0.133 kPa); (3) lung imaging indicating multilobular lesions or progression of lesions over 50% within 48 h; (4) quick sequential organ failure assessment (qSOFA) score ≥2; (5) community-acquired pneumonia-65 (CURB-65) score ≥ 1; (6) combined pneumothorax; (7) other clinical conditions that require hospitalization.
cord-300641-narpqgmj	2020	To the editor: Originated from Wuhan city in central China and widely spread due to the mass migration for Lunar new year holiday, 17,000+ confirmed novel coronavirus (2019-nCoV)-infected pneumonia (NCIP) cases with 350+ deaths have been identified in the country since December 2019 [1] [2] . Worried on the highly contagious virus that currently lacks effective treatments, 84.9% (83.6-86.2%) subjects (2619) felt "extremely" or "very" nervous about NCIP, and 75.1% (73.6-76.6%) believed that it was at least as terrible as the Severe Acute Respiratory Syndromes (SARS) or avian influenza. Adults living in urban areas had a better awareness of the knowledge on NCIP than those in rural areas (72.7% vs.66.1%, p < 0.001 Protective measures such as washing hands, wearing masks and exercising can effectively prevent people from getting infected [4] [5] . As the NCIP outbreak continues, further understanding of the infection will help to adjust strategies for public'' health education.
cord-304550-6j1pb1pu	2020	Here, we conducted a serial investigation on 21 individuals infected with SARS-CoV-2 in two medical centres from Jiangsu Province, including 11 non-severe COVID-19 patients, and 5 severe COVID-19 patients and 5 asymptomatic carriers based on nucleic acid test and clinical symptoms. In this respective study, we serially analysed the virus RNA test results in swab samples, along with anti-SARS-CoV-2 IgM and IgG responses among 21 COVID-19 patients at the Second Hospital of Nanjing and the Affiliated Hospital of Xuzhou Medical University in Jiangsu Province, China. Our serial SARS-CoV-2 RNA testing identified a prolonged viral shedding for asymptomatic cases compared to COVID-19 patients, suggesting the importance of early identification and timely quarantine for these asymptomatic carriers. It is possible that significantly high level of SARS-CoV-2 viral load observed in severe cases [8, 9] drives an early antibody response produced by immediate activation of extrafollicular B cells during acute infection [10, 11] .
cord-304850-9xetsc2c	2013	7, 8 These and other recent findings remind us of an important issue in viral reservoir ecology: non-persisting viruses are maintained on a social level, requiring large, dense and interconnected host groups for their perpetual transmission. 13 There are prominent examples of bat-borne viruses that can be passed between humans, including Ebola virus, Marburg virus, Nipah virus and the severe acute respiratory syndrome agent. However, there remains a large gap between the many studies describing novel reservoir-borne viruses and our capabilities to use this knowledge to predict or prevent future human disease outbreaks. 13 As we dig deeper into viral reservoir ecology, including its man-made modifications, we may find that changes in host populations affect the transmission and maintenance of viruses with possible consequences for their potential to infect humans (Figure 1 ). Habitat fragmentation Resource abundance Change of social structure Risk Virus replication / transmission Duration of excretion / infectivity Figure 1 Modification of viral maintenance optimum.
cord-312307-0hqqheho	2015	Specimens positive for enteroviruses were further confirmed using standard molecular approaches that involved amplification and sequencing of the human enterovirus VP4/VP2 gene using primers described previously. Based on previously described EV-D68 classification, 11 the newly sequenced strains from Malaysia were found within clade A (MY-Cluster-1) and clade B (MY-Cluster-2). Phylogenetic analysis of the P1 region indicated that 91.7% (11/12) of the Malaysian EV-D68 formed clusters, suggesting the transient EV-D68 outbreaks were most likely caused by at least two viral lineages ( Figure 1) . Such observation suggests an ongoing ''''clade shift'''' or lineage replacement of circulating EV-D68 in causing new outbreak, as observed in other enterovirus-associated outbreaks. Our data suggest that the recent EV-D68 strains associated with unprecedented severe respiratory outbreaks in the USA in 2014 were probably descended from the recent EV-D68 lineages circulating in Thailand and Malaysia. Seven strains of enterovirus D68 detected in the United States during the 2014 severe respiratory disease outbreak
cord-314189-0rg6n7fr	2016	2 Therefore, we hypothesized that intranasal application of a mucosal stimulant that induces antiviral cytokines, except IL-17, may be effective against influenza virus infection. We then examined the viral titers in mouse lungs as previously described 5 and found that PEI significantly reduced lung viral titers on day 2 after H1N1 challenge, whereas the viral titers in the lungs of mice in the CTB-and PBS-pretreated groups showed no significant differences ( Figure 1C ). These results suggest that intranasal application of PEI has efficacy in protecting mice from challenge by influenza virus H1N1. To elucidate the mechanism of action of PEI, we examined the RNA levels of IFN-α4, IFN-β, IFN-γ, GM-CSF, IFITM3 and IL-17 in the lungs of mice pretreated with PEI, CTB, and PBS, respectively, before viral challenge using quantitative reverse transcription-PCR (qRT-PCR). In summary, we demonstrated that PEI, a mucosal stimulant for topical intranasal administration, is highly effective in preventing influenza virus infection.
cord-314254-9ye8tfvz	2014	To date, there is no evidence for an animal reservoir of viruses closely related to hepatitis C virus which may have crossed the species barrier to cause disease in humans and resulted in the current pandemic. Recently, several studies discovered new viruses related to hepatitis C virus, belonging to the hepaciand pegivirus genera, in small wild mammals (rodents and bats) and domesticated animals which live in close contact with humans (dogs and horses). Non-primate hepaciviruses (NPHV) were initially discovered in domestic dogs and subsequently in horses 12, 13 and other diverse and widespread HCV-like viruses have been reported in wild populations of rodents and bats. Furthermore, liver function analyses revealed no indication for hepatic inflammation as c-glutamyl transferase and glutamate dehydrogenase values were within reference range, with the exception of a mildly elevated c-glutamyl transferase New HCV-like viruses in different mammalian hosts Pfaender et al 4 level in one horse.
cord-314350-kcatqzgs	2018	Through in vitro and in vivo experiments, we identified and isolated a novel goose astrovirus different from the CAstVas a causative agent of the gout disease recently circulating in gosling flocks in China. To isolate the novel goose astrovirus, the homogenates of the pooled liver and kidney from the diseased gosling were inoculated into chicken liver cell line LMH. To further confirm the isolation of the virus, the infected LMH cells were analyzed through indirect fluorescent assay (IFA) using the convalescent sera from the survival geese with gout symptom and the mouse sera against the capsid P2 of GD (generated in our laboratory) respectively. Different from those recently reported by other groups, we efficiently isolate such novel goose astrovirus in vitro using the cell culture system (LMH cells) and reproduce the associated gout disease by inoculating the cell cultured virus GD.
cord-314574-3e6u4aza	2020	Considering the relatively high identity of receptor-binding domain (RBD) in 2019-nCoV and SARS-CoV, it is urgent to assess the cross-reactivity of anti-SARS CoV antibodies with 2019-nCoV spike protein, which could have important implications for rapid development of vaccines and therapeutic antibodies against 2019-nCoV. Interestingly, some of the most potent SARS-CoV-specific neutralizing antibodies (e.g. m396, CR3014) that target the ACE2 binding site of SARS-CoV failed to bind 2019-nCoV spike protein, implying that the difference in the RBD of SARS-CoV and 2019-nCoV has a critical impact for the cross-reactivity of neutralizing antibodies, and that it is still necessary to develop novel monoclonal antibodies that could bind specifically to 2019-nCoV RBD. Next, we expressed and purified several representative SARS-CoV-specific antibodies which have been reported to target RBD and possess potent neutralizing activities, including m396 [3] , CR3014 [4] , CR3022 [5] , as well as a MERS-CoV-specific human monoclonal antibody m336 developed by our laboratory [15] , and measured their binding ability to 2019-nCoV RBD by ELISA (Figure 1(e)) .
cord-315355-a25ba7dz	2018	The four SpDCoV strains identified in this study share a slightly higher identity (94.4-94.6% and 96.0-96.4%) to a sparrow CoV strain HKU17-6124 than to PDCoV strains (93.4-93.6% and 95.3-95.8%) in their ORF1ab and N proteins, respectively ( Fig. 1b and Supplementary Table S2 ). In contrast, the four SpDCoV strains share a significantly lower identity to sparrow CoV HKU17 (58.2-58.6%) than to three PDCoV strains (82.7-87.7%) in their S protein (Fig. 1b and Supplementary Table S2 ). In addition, they share a relatively lower identity (90.7-91.5% and 93.5-95.5%) to sparrow CoV HKU17 than the PDCoV strains (94.9-95.8% and 96.1-98.1%) in their E and M proteins, respectively (Supplementary Table S2 ). These findings were also confirmed by phylogenetic tree analysis of amino-acid sequences in which the four SpDCoV strains clustered together and were closely related to PDCoV and sparrow CoV HKU17 strains in ORF1ab, E, M, and N trees ( Fig. 1c and Supplementary Figure S1 ).
cord-318392-r9bbomvk	2017	The genomes of two Coronavirus HKU15 strains detected in the nasopharyngeal samples of two different pigs were sequenced following our previous publications 26, 27 with modifications. Divergence times for the Coronavirus HKU15 strains were calculated based on the complete genome sequence data, utilizing the Bayesian Markov chain Monte Carlo method using BEAST 1.8.0 33 with the substitution model GTR (general time-reversible model)+G (gammadistributed rate variation)+I (estimated proportion of invariable sites), a strict molecular clock, and a constant coalescent. In one (S579N) of the two Coronavirus HKU15 genomes that we sequenced in this study, variant sites were observed at four positions; two of them were due to nucleotide substitutions, and the other two were results of indels at mononucleotide polymeric regions (189th and 376th bases).
cord-325611-tu1bn4hu	2019	We systematically collected samples from a prospective cohort of pediatric patients with respiratory infections, that returned negative results by validated molecular RT–PCR assays, and studied them with a target-independent, high-throughput sequencing-based approach. In this report, we performed a systematic study of respiratory specimens collected from a carefully characterized and highly representative, prospective cohort of pediatric cases suffering unexplained ARI, and we compared the rate of detection of pathogens by utilizing validated molecular assays, and a comprehensive sequence-independent, high-throughput sequencing-based analysis. In order to assess for the clinical relevance of the viral identifications made by HTS in the specimens collected from the unexplained cases of respiratory infections, a second cohort of age-matched healthy individuals from the same epidemiologic environment was also studied with the same methodology. Respiratory viral pathogens identified by target-agnostic HTS analysis and confirmed by contig-specific molecular assays in the respiratory specimens from the cases of respiratory infection and from the control group.
cord-325969-9zhmmvdg	2017	In the first cohort of 159 patients whose nasopharyngeal aspirates (NPAs) tested positive for respiratory viruses during routine testing, the viral load was measured using quantitative reverse transcription PCR. Although NPAs have high viral loads and remain the specimen of choice for most patients with respiratory virus infections, supplementary molecular testing of saliva can improve the clinical management of these patients. The first part of the study consisted of patients whose NPA samples tested positive for respiratory viruses by DFA or the influenza A virus M gene by real-time RT-PCR during routine respiratory virus testing in our clinical microbiology laboratory ( Figure 1 ). In the first part of this study, saliva had a higher viral load than NPA in 17.0% of the patients who tested positive for respiratory viruses by DFA or influenza A virus by RT-PCR in their NPA samples.
cord-326512-iex98lr1	2019	title: Convalescent patient-derived monoclonal antibodies targeting different epitopes of E protein confer protection against Zika virus in a neonatal mouse model To examine antibody response in a patient infected with ZIKV, we used single-cell PCR to clone 31 heavy and light chain-paired monoclonal antibodies (mAbs) that bind to ZIKV envelope (E) proteins isolated from memory B cells of a ZIKV-infected patient. The SHM rates of these heavy chains compared with their predicted germline sequences were relatively low, at 4.51% for 7B3H, 3.47% for 1C11H, and 4.17% for 6A6H, which is lower than that of antibodies isolated from annual trivalent inactivated influenza vaccine (TIV) donors [34] and chronic human immunodeficiency virus (HIV)-1 patients (>30%) [27, 35] . In a separate experiment, an unrelated mAb, 2G11, which is specific for H7N9 influenza virus, showed no protective effects on ZIKV-infected neonatal SCID mice (data not shown). Molecular determinants of human neutralizing antibodies isolated from a patient infected with Zika virus
cord-327024-1k5jucae	2018	18 reported the detection of avian nephritis virus infection in Croatian goose flocks and provided evidence that this AstV was associated with stunting and prehatching mortality of goose embryos. To determine the potential genetic mutation(s) that might occur during the goose embryo passage, the initial virus genome was sequenced using the total RNA extracted from the clinical case tissue homogenate. When the samples were tested by RT-PCR for virus shedding evaluation, the AAstV specific RNA was sequentially detected from the cloacal swabs of infected goslings from 2 to 12 dpi (Fig. 6 ). To evaluate the potential adaptive mutation (s) of the virus that might occur during the process of goose embryo passage, we sequenced the complete genome of initial virus using the total RNA extracted from the clinical case tissue homogenate of kidney, spleen, and liver using the method described above.
cord-327499-4aps0kvp	2020	It was believed that 2019-nCoV was transmitted through respiratory tract and then induced pneumonia, thus molecular diagnosis based on oral swabs was used for confirmation of this disease. Human samples, including oral swabs, anal swabs and blood samples were collected by Wuhan pulmonary hospital with the consent from all patients and approved by the ethics committee of the designated hospital for emerging infectious diseases. We conducted a molecular investigation to patients in Wuhan pulmonary hospital, who were detected as oral swabs positive for 2019-nCoV upon admission. We collected blood, oral swabs and anal swabs for 2019-nCoV qPCR test using previously established method [5] . We detected the virus in oral swabs, anal swabs and blood, thus infected patients can potentially shed this pathogen through respiratory, fecal-oral or body fluid routes. Above all, we strongly suggest using viral IgM and IgG serological test to confirm an infection, considering the unreliable results from oral swabs detection.
cord-329555-y3cp5wza	2019	Here we report simultaneous outbreaks of two distinct human respiratory viruses, human metapneumovirus (MPV; Pneumoviridae: Metapneumovirus) and human respirovirus 3 (HRV3; Paramyxoviridae; Respirovirus, formerly known as parainfluenza virus 3), in two chimpanzee (Pan troglodytes schweinfurthii) communities in the same forest in Uganda in December 2016 and January 2017. Here, we report simultaneous outbreaks of respiratory disease in two nearby chimpanzee communities in Uganda, caused by two distinct negative-sense RNA viruses of human origin. Human respirovirus 3 (HRV3; Paramyxoviridae; Respirovirus, formerly known as parainfluenza virus 3) was detected in 5 of 14 individuals (35.7%) from Kanyawara chimpanzees exhibiting clinical signs during, but not before, the outbreak period (Fisher''s exact P = 0.0005). For example, HRV3 can cause upper respiratory disease and predispose chimpanzees to invasive pneumococcal infection [44] , and the bacterium Streptococcus pneumoniae co-occurs with human metapneumoviruses and respiratory syncytial viruses in both wild and in captive apes [9, 22] .
cord-336157-aqc9zrrm	2015	Slave trading of Africans to the Americas, during the 16th to the 19th century was responsible for the first recorded emergence in the New World of two arthropod-borne viruses (arboviruses), yellow fever virus and dengue virus. [2] [3] Chikungunya virus (CHIKV), West Nile virus (WNV) and dengue virus (DENV) are three of a large number of neglected human pathogenic arthropod-borne viruses (arboviruses) whose combined figures for morbidity and mortality far exceed those for Ebola, severe acute respiratory syndrome and Middle East respiratory syndrome viruses. However, many other arthropod species, in which viruses have been identified, may be involved in perpetuating the virus life cycle without having been associated with overt disease in humans or animals. 55 However, implementation of temporary localized arthropod control measures during epidemics, for example in high density urbanized areas, can still play an important but transient role in reducing the impact on humans and animals of emerging arboviruses.
cord-336671-vfq5ft08	2020	Unexplained pneumonia (UP) caused by a novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged in China in late December 2019 and has infected more than 9000 cases by 31 January 2020. A combinative approach of real-time RT–PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) were used to diagnose this unexplained pneumonia patient. The reasons behind this outbreak are numerous, the highly infectious nature of SARS-CoV-2, limited pathogen detection method for unexplained pneumonia, the high population density of the Hubei Province and across China, etc. On 20 January, Shanghai reported the first imported case of SARS-CoV-2 infection, and through this case, we seek a combinative approach of selected techniques to improve pathogen identification of unexplained pneumonia in the future. We then performed real-time RT-PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) on her respiratory sample and finally diagnosed her with COVID-19.
cord-343196-vlwzzrgc	2018	The MERS-CoV RNA-positive animals belonged to two different dromedary camel herds in Dabel and Lombolio, which are both located within Isiolo country. To experimentally confirm the presence of two independently circulating MERS-CoV strains and to rule out sample cross-contamination, we generated complete MERS-CoV genome sequences using a previously established protocol 10 . Other confirmed MERS-CoVpositive samples were assigned to two different MERS-CoV isolates ("Dabel" or "Lombolio") by amplifying and sequencing single-nucleotide polymorphisms in the spike gene and the open reading frame 3 (Supplementary Table) . The previously described clade C African MERS-CoV strains 4,5 had several mutations in the spike protein, which is responsible for cellular receptor interaction, virus entry, and antibody-directed virus neutralization 12 . An explanation for this observation may again be a lack of testing of imported animals and/or the fact that previous clade A/B MERS-CoV infections may have established herd immunity in the Arabian dromedary populations.
cord-349956-h4i2t2cr	2019	We conducted this study to describe the dynamics of the acquisition of respiratory pathogens, their potential interactions and risk factors for possible lower respiratory tract infection symptoms (LRTI) among French pilgrims during the 2018 Hajj. showed that human rhinovirus (HRV) and influenza viruses were the most common viral respiratory pathogens isolated from ill Hajj pilgrims [6] . Unadjusted associations between respiratory pathogen carriage with multiples factors: sociodemographic characteristics (gender, ≥60 years), chronic respiratory disease, BMI classification, smoking status; individual preventive measures (vaccination against influenza, vaccination against IPD, use of a face mask, hand washing, disinfectant gel and disposable handkerchiefs); antibiotic intake 10 days before each sample; respiratory virus or bacteria and dual carriage were analysed by univariable analysis. aureus carriage increase and the initial wave of respiratory symptoms, suggests that this pathogen association was responsible for the RTIs that affected most pilgrims soon after arriving in Mecca.
cord-354546-lgkqwm6u	2016	7 By far, Aedes aegypti is considered the principal transmission vector of ZIKV, 8 although Aedes albopictus, which caused several outbreaks of dengue fever in Guangdong Province of South China in the last two decades, may play a role in the spread of this virus because A. These four infected individuals were first confirmed by real-time reversetranscription polymerase chain reaction (RT-PCR) in Baiyun International Airport of Guangzhou, where the youngest one (the son) had developed fever, and the family was then isolated by the local department of public health. 28 A previous study Figure 4 Phylogenetic tree based on E gene sequences of Zika virus isolates. First imported familial ZIKV cases in China Y Yin et al showed that a patient had prolonged shedding of viral RNA in saliva and urine for up to 29 days after symptom onset. In previous research, E gene sequences of ZIKV isolates were usually utilized to construct phylogenetic trees 19 based on experience from molecular study of dengue virus.
cord-354790-xx6imhzb	2016	31 In addition to controlling the viral propagation by these mechanisms, the opsonization of viral particles and/or infected cells by therapeutic antiviral mAbs of the IgG type leads to the formation of immune complexes (ICs) recognizable by the FcγRs expressed on antigen-presenting cells (APCs) such as DCs. This can potentially affect the endogenous antiviral adaptive immune response of passive immunotherapy-treated individuals. Moreover, as the in vivo activity of anti-HIV-1 bNAbs, including viral load control, was recently shown to crucially depend on Fc effector functions, 53,54 an important issue is identifying that Fc-FcγRs interactions are involved in the induction of vaccinelike effects by antiviral mAbs. To understand the mechanisms underlying the enhancement of antiviral responses by ICs, several in vitro studies have addressed whether antibody-mediated viral uptake by DCs could lead to stronger activation of these cells and the development of stronger virus-specific CD4 + and CD8 + T-cell responses in an Fc-dependent manner.