cord-002945-29nj4f05	2018	Detection of bovine viral diarrhoea virus 1 subgenotype 1c in extracts from cattle samples using quantitative real time PCR (qPCR). For cattle infected with BVDV-1c strain Trangie, one of the four animals tested positive on Day 2 post-infection, while all the other samples were negative throughout the sampling period (Table 1) . For cattle infected with BVDV-1c strain Trangie, one of the four animals tested positive on Day 2 post-infection, while all the other samples were negative throughout the sampling period (Table 1) . BVDV-1c was not detected via qPCR in the nasal swab or serum samples collected from all animals on Day 21, Day 28, Day 42 and Day 55 post-infection and were deemed to be negative (data not shown). BVDV-1c was not detected via qPCR in the nasal swab or serum samples collected from all animals on Day 21, Day 28, Day 42 and Day 55 post-infection and were deemed to be negative (data not shown).
cord-003767-9xbu4hnq	2019	The synthesis of the findings reveals a predictive virus evolution framework, based on the outerto inner-body changes in the interplay of host environment-transmission modes-organ system involvement-host cell infection cycle-virus genome. Pieced together on this basis was an outer-to inner-body line-up of viruses by organ system or combination of organ systems, guided by the one-to-four virus infiltration score, the corresponding virus organ system tropism, the matching virus transmission modes, length of the infection and shedding periods, infection severity level, and virus environmental survival rate, see Figure 3 and, also, Figure S1d . Pieced together on this basis was an outer-to inner-body line-up of viruses by organ system or combination of organ systems, guided by the one-to-four virus infiltration score, the corresponding virus organ system tropism, the matching virus transmission modes, length of the infection and shedding periods, infection severity level, and virus environmental survival rate, see Figure 3 and, also, Figure S1d .
cord-009445-p2rz81fy	2020	title: Wild Birds in Live Birds Markets: Potential Reservoirs of Enzootic Avian Influenza Viruses and Antimicrobial Resistant Enterobacteriaceae in Northern Egypt Wild migratory birds are often implicated in the introduction, maintenance, and global dissemination of different pathogens, such as influenza A viruses (IAV) and antimicrobial-resistant (AMR) bacteria. Ten samples collected from Northern Shoveler birds (Spatula clypeata) were positive for IAV and PCR sub-typing and pan HA/NA sequencing assays detected H5N8, H9N2, and H6N2 viruses in four, four, and one birds, respectively. Furthermore, wild birds, especially waterfowl, represent the natural reservoir for influenza A viruses (IAV), which mostly present in the low pathogenic (LPAI) forms, including the H5 and H7 subtypes that were transmitted and maintained in domestic birds, to convert to high pathogenic avian influenza (HPAI) [9, 10] . The presence of antimicrobial resistance (AMR) in wild birds screened in Egypt has been confirmed with high homology, with samples collected from adjacent water, and both lack the homology with the human isolates [18] .
cord-013280-kczj24se	2020	Viral capsid protein VP1 and leading protein L pro can inhibit the production of interferon (IFN) and innate immune response by interacting with soluble resistance-related calcium-binding protein (sorcin) or host transcription factor ADNP [12, 13] . Viral capsid protein VP1 and leading protein L pro can inhibit the production of interferon (IFN) and innate immune response by interacting with soluble resistance-related calcium-binding protein (sorcin) or host transcription factor ADNP [12, 13] . FMDV VP1 interacts with host ribosomal protein SA (RPSA) to continually activate the MAPK signal pathway and promote virus replication by inhibiting the RPSA-mediated function [59] (Figure 2 , Table 1 ). It interacts with the VISA protein to inhibit the formation of VISA-regulated complex, thereby inhibiting the dimerization and phosphorylation of IRF3, inhibiting the expression of antiviral genes induced by IFN-β, and promoting FMDV replication [60] (Figure 2 , Table 1 ).
cord-013315-plptulfb	2020	The prompt identification and isolation of the infected animals in the subclinical stage would prevent the spread of the infection.In the present study, an immunoinformatic approach has been used to investigate the immunogenic properties of 10 MAP proteins. For each previously-described immunoreactive protein, we predicted the epitopes capable of eliciting an immune response by binding both B-cells and/or class I MHC antigens. The class I MHC epitopes as of Figure 3 are further aligned against both the mycobacteria and cow databases to assess the specificity of the predicted epitope sequences for MAP. To prove selected epitopes as suitable candidates for the unbiased diagnosis of MAP infection, we aligned the peptides sequences against a database comprising the closest taxonomically-related bacteria. Selected peptide sequences of the immunoreactive proteins were searched against the NCBInr database restricted to Mycobacterium avium subsp. Gene expression profiles during subclinical Mycobacterium avium subspecies paratuberculosis infection in sheep can predict disease outcome
cord-253116-oq0bc35u	2020	Antibody titers of cats not shedding feline coronavirus (FCoV) and of cats with one, two, three, or four fecal samples positive for FCoV RNA by quantitative reverse transcriptase polymerase chain reaction (RT-qPCR). Fecal feline coronavirus (FCoV) load per gram of feces of cats with different antibody titers detected by quantitative reverse transcriptase polymerase chain reaction (RT-qPCR). Mean fecal feline coronavirus (FCoV) load per gram of feces of cats with different frequencies of FCoV shedding detected by quantitative reverse transcriptase polymerase chain reaction (RT-qPCR). In this study, there was a weak positive correlation between the quantity of antibodies and the mean fecal virus load determined by RT-qPCR, indicating that cats with higher antibody titers were more likely to shed FCoV more intensely compared to cats with low antibody titers and cats without antibodies.
cord-255339-oudj079q	2019	The most important zoonotic viral diseases of which eight were diagnosed (in dead or diseased animals or through antibody detection) on the Arabian Peninsula over the last years include rabies, Middle East Respiratory Syndrome (MERS-CoV), influenza virus (IFV), Alkhurma hemorrhagic fever, Crimean-Congo hemorrhagic fever (CCHF), Rift Valley fever (RVF), West Nile fever (WNV), and dengue fever virus. The same WHO epidemiological data suggest that in these 22 countries including Saudi Arabia, in recent years, there has been report of steadily increasing number of sporadic human cases, incidence, and outbreaks of the virus [122] . Surprisingly, the current review showed that during an outbreak, each of these eight most zoonotic viruses (rabies, MERS-CoV, influenza, AHFV, CCHFV, RVFV, DHFV, and WNV) which occurred and/or cases confirmed in Saudi Arabia particularly from (Jeddah and/or Makkah) areas with at least one or all of these eight zoonotic viral pathogenic diseases [33, 44, 46, 78, [96] [97] [98] [99] 121, 130, 156, 171] .
cord-263247-r3t4uowz	2020	In particular, three review articles contributed by leading researchers in the field that cover important concepts, including how different animal models can be developed for understanding Lassa fever''s disease pathogenesis and pathologies and for the evaluation of candidate vaccines and antiviral therapies [1] , how to improve the breadth of host immune responses to Lassa vaccination [2] , as well as how different virus and host factors orchestrate the intricate processes of Lassa virus (LASV) entry and genome replication [3] . In addition to these insightful review articles, two research articles deal with novel strategies of developing vaccines for Lassa fever, including the use of the LASV-like particles composed of the viral matrix (Z) and envelope glycoprotein complex (GPC) expressed by the modified vaccinia Ankara virus to protect mice against lethal virus challenges [4] and the use of a candidate LASV vaccine known as ML29 that is composed of the reassorted genome between the pathogenic LASV and the non-pathogenic Mopeia virus (MOPV), which shows its highly attenuated phenotype in rodents [5] .
cord-266145-xnu8pj24	2020	A composite adherence score was made based on the respondent''s self-reported observance of the following personal preventive measures: physical distancing, face mask use, hand hygiene, coughing hygiene, and the habit of touching one''s face (Table 1) . During the COVID-19 pandemic in Somalia, the participants reported low to moderate levels of worry/fear about their own health, with mean Likert scores on a five-point scale of 2.3 ± 1.6 and 1.9 ± 1.3 during the first and second survey, respectively (p < 0.001). This study shows an overall unsatisfactory level of adherence by Somali residents to the preventive measures put in place by the government to control COVID-19 transmission. The lower adherence scores during the second survey, compared to the first, indicates that compliance to government measures is decreasing as the COVID-19 epidemic evolves in Somalia.
cord-271648-m2c5bvuj	2020	Coronaviruses (CoVs) are RNA viruses that have become a major public health concern since the Severe Acute Respiratory Syndrome-CoV (SARS-CoV) outbreak in 2002. However, unlike SARS-CoV, human-to-human transmission of MERS-CoV is not easy and has not been confirmed except in cases of very close contact with infected patients in health care settings [67] . Similar to the adaptation of SARS-CoV to human host, MERSr-CoVs that are circulating in bats had to undergo several amino acid changes in RBD of S protein to become capable of infecting camels and humans ( Figure 2 ) [74] . S protein of severe acute respiratory syndrome-associated coronavirus mediates entry into hepatoma cell lines and is targeted by neutralizing antibodies in infected patients Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Fully human monoclonal antibody directed to proteolytic cleavage site in severe acute respiratory syndrome (SARS) coronavirus S protein neutralizes the virus in a rhesus macaque SARS model
cord-272295-9sonr8or	2020	Objective: We investigate the prevalence of the self-reported and objective sudden loss of smell (SLS) in patients with severe coronavirus disease 2019 (COVID-19). Potential associations between olfactory evaluation and the clinical outcomes (duration of hospitalization; admission biology; one month serology (IgG), and chest computed tomography findings) were studied. In this study, we investigated the prevalence of self-reported and objective SLS in severe COVID-19 patients. Irrespective of the method used to evaluate the prevalence of SLS (patient-reported outcome questionnaire versus objective tests), these data indicate that SLS could be more prevalent in mild-to-moderate forms of the infection. According to a previous study conducted in the same population and with the same methods, self-reported SLS concerned more than 70% of mild COVID-19 patients, and among them, sixty-two percent had abnormal objective evaluations [3] . Olfactory and gustatory dysfunctions as a clinical presentation of mild-to-moderate forms of the coronavirus disease (COVID-19): A multicenter European study Objective olfactory evaluation of self-reported loss of smell in a case series of 86 COVID-19 patients
cord-274497-tqceazdp	2020	In the present work, the pathogenicity, viral tissue distribution and molecular characterization of ChPV in chicks from a strain isolated in Brazil were determined with a demonstration of Koch''s postulates according to our previous description [21] . In the present work, the pathogenicity, viral tissue distribution and molecular characterization of ChPV in chicks from a strain isolated in Brazil were determined with a demonstration of Koch''s postulates according to our previous description [21] . Experimental infections with isolated ChPV (ABU-P1) have demonstrated that the virus causes enteric diseases, resulting mainly in chickens with diarrhea, cloacal pasting, impaired growth, runting and stunting [32] . Lesions were previously described in commercial chicken flocks affected with RSS and reported by our own group [21] ; the duodenal loop presented the same features, demonstrating Koch''s postulates in relation to ChPV and experimentally infected chickens.
cord-288306-0chcsqe7	2020	The wellestablished diagnostic methods of CSF such as virus isolation, fluorescent antibody test (FAT), antigen capture antibody enzyme-linked immunosorbent assay (ELISA), reverse-transcription polymerase chain reaction (RT-PCR), virus neutralization test (VNT), and antibody ELISA (Table 1) have been widely used and well described in the OIE Terrestrial Manual [17] . The well-established diagnostic methods of CSF such as virus isolation, fluorescent antibody test (FAT), antigen capture antibody enzyme-linked immunosorbent assay (ELISA), reverse-transcription polymerase chain reaction (RT-PCR), virus neutralization test (VNT), and antibody ELISA (Table 1 ) have been widely used and well described in the OIE Terrestrial Manual [17] . Evaluation of a multiplex real-time RT-PCR for quantitative and differential detection of wild-type viruses and C-strain vaccine of Classical swine fever virus The double-antigen ELISA concept for early detection of E rns -specific classical swine fever virus antibodies and application as an accompanying test for differentiation of infected from marker vaccinated animals
cord-292031-weiwksh6	2015	Quantitative microbial risk assessment (QMRA) is a helpful tool to evaluate the scenarios for pathogen contamination that involve surveillance, detection methods, analysis and decision-making. Molecular techniques, such as nucleic acid amplification procedures, offer sensitive and analytical tools for detecting a variety of pathogens, including new emerging strains, present the possibility of automation, and real-time analysis to provide information for microbial risk assessment purposes [33] . Limitations of DNA based methods such as PCR include the inability to discriminate between viable from non-viable cells that both contain DNA, the low concentration of several pathogens in water such as Cryptosporidium, Giardia and viruses, and the lack of data to indicate the real infectious risk to a population. Oligonucleotide microarrays are a powerful genomic technology that is widely utilized to monitor gene expression under different cell growth conditions, detecting specific mutations in DNA sequences and characterizing microorganisms in environmental samples [76] .
cord-293988-f5gvwjyh	2020	The pandemic respiratory disease COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in Wuhan in December 2019 and then spread throughout the world; Italy was the most affected European country. In this study, a domestic cat with clear clinical signs of pneumonia, confirmed by Rx imaging, was found to be infected by SARS-CoV-2 using quantitative RT–qPCR from a nasal swab. The World Health Organization (WHO) declared COVID-19 disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as a worldwide pandemic [1] . As the cat''s pathology evolved rapidly and harmfully (the animal died in as little as three days), with clinical signs and rate of disease progression similar to human COVID-19 patients, and because previously published papers reported different cases of feline infection [10, [13] [14] [15] [16] , a nasal swab was collected in order to verify a possible infection with SARS-CoV-2.
cord-294571-qd0qjo3y	2020	Angiotensin-converting enzyme-2 (ACE2) represents the primary SARS-CoV-2 entry receptor, and its physiological role is crucial in the progress of COVID-19 illness. Previous studies on SARS-CoV-1 reported that the binding of viral spike (S) protein to ACE2 downregulates the expression of ACE2, resulting in a diminished protective role of ACE2 and, subsequently, acute respiratory failure [52] . The levels of ACE2 expression, which could be sex-and age-dependent, have a protective role against lung and kidney injuries that could impact the severity of COVID-19 illness in male vs. The susceptibility of cardio-metabolic patients to develop severe COVID-19 illness and the high mortality rate could be linked to the ACE2 function during SARS-CoV-2 infection and the cardio-metabolic treatments that may interfere with ACE2-virus interaction. Previous studies on SARS-COV-1 reported that the binding of viral S protein to ACE2 downregulates the expression of ACE2, resulting in a diminished protective role of ACE2 and, subsequently, acute respiratory failure [52] .
cord-296419-j5rlgbl8	2017	Building on their earlier work, in 2012 Michael Katze''s lab also compared their human swine microarray pH1N1 (CA 04/09 strain) data to mice and macaque lung responses after infection with the same virus [10] . A recent microarray study comparing highly-pathogenic H5N1 versus low-pathogenic H9N2 in the chicken lung provided valuable insight into inflammatory/cytokine host gene response differences related to infection outcomes [17] . Similar to swine studies, there is also limited proteomic analysis data available for avian species, but Sun and co-workers have identified 38 proteins using 2D-DIGE (differential gel electrophoresis) followed by MALDI-TOF/TOF-MS in the trachea of IAV-infected chickens [20] . Proteomics analysis of differential expression of chicken brain tissue proteins in response to the neurovirulent H5N1 avian influenza virus infection Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems
cord-297469-26d8o1xk	2019	gondii effects of ursolic acid, and analyzed the production of nitric oxide (NO), reactive oxygen species (ROS), and cytokines through co-cultured immune cells, as well as the expression of intracellular organelles of T. Furthermore, ursolic acid effectively increased the production of NO, ROS, interleukin (IL)-10, IL-12, granulocyte macrophage colony stimulating factor (GM-CSF), and interferon-β, while reducing the expression of IL-1β, IL-6, tumor necrosis factor alpha (TNF-α), and transforming growth factor beta 1 (TGF-β1) in T. gondii-infected cells were treated with different concentrations (12.5-200 µg/mL) of ursolic acid (UA) and sulfadiazine (SF) at 37 • C for 24 h, respectively; their survival rates were inhibited a dose-dependent manner. We evaluated the effect of ROS and NO production induced by ursolic acid in immune cells infected with T. We evaluated the effect of ROS and NO production induced by ursolic acid in immune cells infected with T.
cord-298505-r7ihqb96	2020	In fact, in addition to data obtained in experimental animals, there are already reports of successful phage therapy in patients with sepsis [2] . Phage therapy efficacy has also been studied in a mouse model of neonatal sepsis caused by Escherichia coli, Klebsiella pneumoniae, Haemophilus influenzae, Pseudomonas aeruginosa, Citrobacter freundii and Moraxella catarrhalis. High effectiveness of phage therapy in the treatment of experimental sepsis induced by multidrug resistant P. Further progress in phage therapy of sepsis has recently been achieved by introducing engineered phages used to treat a patient with a disseminated drug resistant mycobacterial infection. In recent years, a number of reports derived from experimental studies in animals and human clinics have suggested the potential value of phage therapy in the treatment of sepsis. The anti-inflammatory and the immunomodulating properties of phages could also be useful in the treatment of severe COVID-19 syndrome including viral sepsis (Table 2) .
cord-298862-8bijio30	2020	Buffalopox was first described in India, later in other countries, and has become an emerging contagious viral zoonotic disease infecting milkers with high morbidity among affected domestic buffalo and cattle. Over time, VACV evolved into BPXV by establishing itself in buffaloes to be increasingly pathogenic to this host and to make infections in cattle and humans. The full-length sequences of these four genes of BPXVs-obtained from outbreaks in buffaloes, cattle, and humans in India-were analyzed, to investigate their evolutionary relationship to other OPXVs circulating in the world vis-à The full-length sequences of these four genes of BPXVs-obtained from outbreaks in buffaloes, cattle, and humans in India-were analyzed, to investigate their evolutionary relationship to other OPXVs circulating in the world vis-à-vis the vaccine strains. Sequence and phylogenetic analysis of host-range (E3L, K3L, and C7L) and structural protein (B5R) genes of buffalopox virus isolates from buffalo, cattle, and human in India
cord-302161-ytr7ds8i	2020	Feline Infectious Peritonitis (FIP)—the deadliest infectious disease of young cats in shelters or catteries—is induced by highly virulent feline coronaviruses (FCoVs) emerging in infected hosts after mutations of less virulent FCoVs. Previous studies have shown that some mutations in the open reading frames (ORF) 3c and 7b and the spike (S) gene have implications for the development of FIP, but mainly indirectly, likely also due to their association with systemic spread. Based on the hypothesis that certain mutations are essential for the capacity of FCoVs to spread systemically, the present study investigated a cohort of systemically infected healthy carrier cats at different time points post experimental infection for the presence of a range of mutations in the genes encoding for the S protein, NSP 3abc, and NSP 7b, which have been shown to have implications for the development of FIP.
cord-309147-c3ikb81g	2020	According to available information, SARS-CoV-2 is inferred to be a recombinant virus that originated from bats and was transmitted to humans, possibly using the pangolin as the intermediate host. The interaction of the SARS-CoV-2 spike protein with the human ACE2 (angiotensin-converting enzyme 2) receptor, and its subsequent cleavage by serine protease and fusion, are the main events in the pathophysiology. The recent reports have suggested that SARS-CoV-2 is a modified coronavirus of bat origin [22, 32] , which came to humans as a result of zoonotic transmission [33, 34] . The receptor-binding domain (RBD) of pangolin-CoV has only a one amino acid difference with that of SARS-CoV-2; the infected pangolins exhibit pathological symptoms similar to humans suffering from COVID-19, and their blood circulating antibodies can react with the spike protein of SARS-CoV-2 [35, 36] . Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and corona virus disease-2019 (COVID-19): The epidemic and the challenges
cord-309381-cb80ntxs	2019	IAV RNAs are mainly recognized by the endosomal, membrane-associated PRR Toll-like receptors (TLRs) 3 (double-stranded RNAs, dsRNAs) or 7/8 (ssRNAs), respectively [50, 51] , by the cytoplasmic PRR retinoic acid-inducible gene I (RIG-I), which detects dsRNA and 5 -triphosphates of the negative ssRNA viral genome [50, 52] , generated during replication of multiple viruses, by the NOD-like receptor family member NOD-, LRR-and pyrin domain-containing 3 (NLRP3), which recognizes various stimuli (see below) [53] and by the absent in melanoma 2 (AIM2) protein, recognizing not well-characterized influenza stimuli [54] . Another important SNP (rs34481144) associated with risk of severe influenza in humans from the United States (US) infected with seasonal IAVs is located in the 5 -UTR of the IFITM3 gene [123, 124] .
cord-314825-fzba05wn	2020	
cord-319799-h9kot3og	2017	By combining measures of epigenome reorganization with RNA and proteomic datasets, we articulate a spatial-temporal data integration approach to identify regulatory genomic clusters and regions that play a crucial role in the host''s innate immune response, thereby defining a new viral antagonism mechanism following emerging coronavirus infection. By utilizing Calu3 cells, we have developed a robust human model platform to study innate immune regulatory control and epigenetics following emerging coronavirus and influenza virus infections as well as other highly pathogenic viruses ( Figure 6 ). Utilizing these model systems, we aim to study genome-wide histone modifications, DNA methylation patterns, and the chromatin landscape after virus infection across different cell types in the lung, revealing cell type-specific regulatory features that function to regulate infection outcomes. Utilizing these model systems, we aim to study genome-wide histone modifications, DNA methylation patterns, and the chromatin landscape after virus infection across different cell types in the lung, revealing cell type-specific regulatory features that function to regulate infection outcomes.
cord-322317-wsagoy52	2020	Histology, IHC, and nested RT-PCR (RT-nPCR) for feline coronavirus (FCoV) were performed on spleen, liver, mesenteric lymph node, kidney, large and small intestine, and lung from 14 FIP and 12 non-FIP cats. In the FIP group, the tissues that most often showed typical FIP histological lesions (Table 2) were the lung, kidney, and mesenteric lymph node, followed by the liver and spleen, while the small and large intestine were the organs less frequently affected by lesions imputable to FIP. In particular, this occurred in the same 6 cases from the non FIP group and in 15/21 FIP tissues in which histology was classified as negative and RT-nPCR was positive (spleen of cats n • 1 and 3, liver of cat n • 14, lymph nodes of cats n • 1, 2, and 14, kidney of cats n • 5, 12, and 13, small intestine of cats n • 9 and 12, large intestine of cats n • 2, 9, and 12 and lung of cat n • 14), whose histological findings have been described above.
cord-322807-b24ujorz	2020	The coronavirus genome is highly prone to mutations that lead to genetic drift and escape from immune recognition; thus, it is imperative that sub-strains with different mutations are also accounted for during vaccine development. Typically, surface proteins outside of the viral virion are selected for antigens so that antibodies generated from a vaccine-trained B-cell can bind to the virus for neutralization. This study''s objective is to interrogate currently identified sub-strains of SARS-CoV-2 and identify genetic drifts and potential immune recognition escape sites that would be integral for the development of a successful vaccine. In these countries, the majority of infected patients possess the variant; therefore, vaccine design and convalescent plasma antibody treatment might require further considerations to accommodate the drift. A spike glycoprotein peptide encompassing residues 604-625 derived from a convalescent SARS-CoV-1 patient was successfully able to elicit humoral immune response and prevent infection in non-human primates, underscoring the immunogenic importance of this region [10] .
cord-323380-hm9wd817	2017	This review summarizes the prevalence, reservoirs, sources of human infection and control regimes of common bacterial, parasitic and viral zoonoses in animals and humans in Egypt. In animals, from 1999 to 2016 the prevalence rate of Cryptosporidium infection ranged between 2% and 69% among different species including cattle, buffalo calves, camels, sheep, goats, lambs, dogs, wild rats and quails. In humans, between 1989 and 2016 Cryptosporidium infection has been reported in almost all Egyptian governorates with prevalence rates ranged between 3% and 50% or up to 91% in immunocompromised patients and diarrheic children [169] [170] [171] [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196] [197] . The virus was isolated from various species of domestic animals (e.g., sheep, cows, buffaloes, camels, goats, horses, and rats) as well as humans [288, 289] .The epizootics of RVF in Egypt were reported every year round.
cord-327000-oyg3oyx1	2020	This review highlights the immune evasion mechanisms employed by PEDV, which provides insights for the better understanding of PEDV-host interactions and developing effective vaccines and antivirals against CoVs. Porcine epidemic diarrhea virus (PEDV) is the etiological agent of porcine epidemic diarrhea (PED) that causes an acute and highly contagious enteric disease of swine characterized by vomiting, diarrhea, dehydration, and anorexia in pigs of all ages, especially resulting in severe diarrhea and high mortality rate in piglets. Nsp3 is the largest nsp protein, containing two papain-like protease (PLP1 and PLP2) domains, of which PEDV PLP2 acts as a viral deubiquitinase (DUB), to negatively regulate type I IFN signaling [80] . The evasive strategies utilized by PEDV are classified into four major types: (1) inhibition of RLRs-mediated IFN production pathways, (2) inhibition of the activation of transcription factors responsible for IFN induction, (3) disruption of the signal cascades induced by IFN, and (4) hiding its viral RNA to avoid the exposure of viral RNA to immune sensors.
cord-328395-2cakgmsj	2020	Recent reports suggest that SARS-CoV-2, unlike other related viruses, infects and replicates within endothelial cells, which may explain a significant portion of the observed clinical pathology. This review will focus on the concept of endothelial cell infection and dysfunction as an active driver of COVID-19, which begins as a respiratory illness, with vascular pathology contributing significantly to the most negative patient outcomes. Endothelial cell infection that proceeds via ACE2 shows how SARS-CoV-2 can replicate into a wide range of cells, which may explain some of the clinical symptoms found in COVID-19 patients. Thus far, we have discussed the viral mechanisms of SARS-CoV-2 and resultant COVID-19 sequelae as they relate to endotheliitis and endothelial cell infection mediated by viral spike protein-ACE2 interaction. The successful use of anti-interleukin drugs to treat the inflammatory symptoms seen in severe COVID-19 would have marked effects on endothelial pathology as these cells are highly responsive to cytokine signaling [59] .
cord-330827-gu2mt6zp	2020	The emergence of the 2019 novel coronavirus (2019-nCoV) has recently added to the list of problematic emerging pathogens in the 21st century, which was suspected to originate from the persons exposed to a seafood or wet market in Wuhan, Hubei Province, China, suggesting animal-to-human transmission [2, 3] . Several reports in the last two decades have enough evidence to prove that the plant produced biopharmaceuticals are as effective as the mammalian cell-based proteins and also elicit potent neutralizing antibodies, or shown therapeutic effects against the particular pathogen or infection [17] [18] [19] . Many reports reviewed the importance of plant expression system for the rapid production of candidate vaccines and therapeutic antibodies against infectious diseases [22] [23] [24] [25] [26] [27] . As plant-made biopharmaceuticals provide efficacious and cost-effective strategies to protect against emerging infectious diseases, plant expression systems can be employed for the development of vaccines against nCoV.
cord-331020-lyxje82u	2020	The evolution of new strains of IBV during the last nine decades against vaccine-induced immune response and changing clinical and pathological manifestations emphasize the necessity of the rational development of intervention strategies based on a thorough understanding of IBV interaction with the host. For example, chickens infected with certain strains of IBV such as Mass, QX-like strain or Aust T at ages of 1-14 days develop cystic oviducts without impaired ovarian functions, which leads to false layer syndrome with no egg production [15, [63] [64] [65] . One of the immune cell types that bridges innate and adaptive host responses is the macrophages, and the available data show that certain IBV serotypes (i.e., Mass and Conn) target respiratory tract macrophages and replicate within them, thus leading to a productive infection [59, 88] .
cord-331022-tek4u751	2020	The study also presents the quantity and frequency of T cell responses, particularly CD4(+) and CD8(+); the profile of cytokine production and secretion; and its relation to T cell type, disease severity, and utility in prognostics of the course of SARS, MERS, and COVID-19 outbreaks. Moreover, the kinetics of specific antibody production, the correlation between humoral and cellular immune response and the immunogenicity of the structural HCoVs proteins and their utility in the development of a vaccine against SARS, MERS, and COVID-19 has been updated. The current study reviewed the role of interleukins (ILs) with tumor necrosis factors (TNFs), chemokines and interferons (IFNs) in the immune response to HCoVs. A comparison of the content of proinflammatory Th1 and Th2 cytokines in the serum of SARS patients with healthy controls documented a significantly greater concentration of TNF-α, IL-6, IL-8, IL-10, and IL-12 in the early stage of the SARS-CoV infection [32, 40] .
cord-334907-l4jjb93l	2020	These results demonstrate the important role of viral surface proteins in the regulation of infectivity; in particular, they may further define the influence of HPR on the fusion activity in ISAV, suggesting a novel role for F (i.e., receptor interaction). To assess the role of the F 1 domain on the fusion activity of F, different ISAV HE and F combinations were evaluated in membrane fusion assays, using transfected CHSE/F cells expressing the viral HE and F proteins and R18-labeled salmon RBCs. After adhesion, cells were subjected to trypsin treatment and low pH to activate the fusion mechanism. In ISAV, if the primary receptor (5N-4O sialic acids) binding via HE is not affected by the HPR length/esterase activity, possibly a secondary viral protein-cellular ligand interaction is regulated by those elements.
cord-335774-15fhg8o9	2020	Information regarding the presence and genetic diversity of many orthohantaviruses throughout the distributional range of their hosts is minimal and would significantly benefit from virus isolations to indicate a reservoir role. However, mammals, particularly rodents, are still the most common natural hosts of hantaviruses, encompassing viruses in the largest subfamily (Mammantavirinae) and genus (Orthohantavirus) [9] , and only rodent-borne orthohantaviruses have been linked to human disease [10] . For example, range expansion of a North American grassland rodent species, Baiomys taylori, was recently found in New Mexico, United States, likely due to an increase in grassland areas, particularly along roadsides, due to climate change and habitat disturbance [61] . In the absence of empirical data, we shed light on the diversity, transmission, and risk of spillover for neglected American orthohantaviruses and viral genotypes using the ecology of their hosts and information on ANDV and SNV. Since multiple rodent species are commonly found RT-PCR positive for particular American orthohantavirus strains (Table A1) , virus-host relationships are unclear.
cord-337259-b12fp75d	2020	The diagnosis and epidemiology of the infection in humans and pigs; different aspects of the pathogenesis of the disease; antimicrobial resistance, prevention and control; and finally autogenous vaccine policy were addressed during the meeting and are further discussed below. Most important sequence types (STs) of Streptococcus suis serotype 2 as determined by multilocus sequence typing (MLST): ST1 serotype 2 strains are mostly associated with disease in both pigs (where data are available) and humans in Europe, Asia, Africa, and South America. Most important sequence types (STs) of Streptococcus suis serotype 2 as determined by multilocus sequence typing (MLST): ST1 serotype 2 strains are mostly associated with disease in both pigs (where data are available) and humans in Europe, Asia, Africa, and South America. Secondary infection with Streptococcus suis serotype 7 increases the virulence of highly pathogenic porcine reproductive and respiratory syndrome virus in pigs
cord-342921-lpn6cqz3	2015	Here, we provide complete genomic characterization of a SAFV-3 isolate collected from a two-year-old female from the Amazonian area of Maynas, in Loreto, Peru. To maintain sampling diversity as large as possible, trees were constructed using publicly available reference sequences that represent the totality of the diversity of SAFV strains in terms of genotype, year of isolation, and geographical origin ( Table 1 ). Phylogenetic analyses of both full genome and complete VP1 sequences confirm that the Peruvian SAFV strain collected in 2012 belongs to genotype 3 and is most closely related to Asian strains ( Figure 2 ). To cover as many genotypes, years, and geographical regions as possible, we considered 34 complete genomes (at least 6888 nt covering all 2296 aa of representative SAFV1-11 isolates, including the Peruvian isolate), 17 complete VP1 sequences (810 nt covering all 270 aa), and seven additional partial VP1 sequences (at least 312 nt) specifically from the Americas.
cord-350423-yaeduwvb	2016	Many of the human viruses with oncogenic capabilities, either in their natural host or in experimental systems (hepatitis B and C, human T cell leukaemia virus type 1, Kaposi sarcoma herpesvirus, human immunodeficiency virus, high-risk human papillomaviruses and adenovirus type 9), encode in their limited genome the ability to target cellular proteins containing PSD95/ DLG/ZO-1 (PDZ) interaction modules. Survival of rabies infected neuronal cells is associated with the ability of the viral envelope G protein to interact with the PDZ domain-containing serine threonine kinase MAST2, leading to the disruption of the MAST2-PTEN complex that is intimately involved in the inhibition of neuronal survival [11] . Therefore, in HPV infections the tumour suppressor forms of DLG that are involved in the negative regulation of cell proliferation might be the initial target of the E6 PBM, but during disease progression DLG1, either through mislocalization and/or the stabilization of specific pools, acquires oncogenic functions mediated by interaction with E6 [3, 127] .
cord-351567-ifoe8x28	2020	However, by that time, travelers had carried the virus to many countries, sparking memories of the previous coronavirus epidemics, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), and causing widespread media attention and panic. To assess the magnitude of the risk posed by the SARS-CoV-2, we review four parameters that we believe important: the transmission rate, the incubation period, the case fatality rate (CFR), and the determination of whether asymptomatic transmission can occur. A small study of 17 patients showed that nasal viral load peaks within days of symptom onset, suggesting that transmission of disease is more likely to occur early in the course of infection [40] . Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study The Epidemiological Characteristics of an Outbreak of 2019 Novel Coronavirus Diseases (COVID-19)-China 2020 Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia
cord-355788-6hteott0	2020	In this regard, Newcastle disease virus (NDV), an avian virus, has several well-suited properties for development of a vector vaccine against SARS-CoV-2. Currently, a number of DNA and RNA virus vector platforms are under evaluation for a SARS-CoV-2 vaccine, including attenuated vaccinia virus, replication-defective adenovirus, vesicular stomatitis virus, human parainfluenza viruses, and alphavirus replicons. Keeping these limitations in mind, we think Newcastle disease virus (NDV), as avian virus, has a number of characteristics that make it suitable for use as a vaccine vector for SARS-CoV-2. The effectiveness of NDV-vectored vaccines has already been evaluated against SARS-CoV in monkeys [8] , against MERS-CoV in camels [9] , and against avian infectious bronchitis virus (IBV) in chickens, a natural host challenge model [10] . Immunization of primates with a Newcastle disease virus-vectored vaccine via the respiratory tract induces a high titer of serum neutralizing antibodies against highly pathogenic avian influenza virus