cord-000708-iuo2cw23	2012	These studies include the alphaherpesvirinae herpes simplex virus type 1 (HSV-1) and pseudorabies virus (PRV; Loret et al., 2008; Kramer et al., 2011) , the betaherpesvirinae human and murine cytomegaloviruses (HCMV and MCMV, respectively; Kattenhorn et al., 2004; Varnum et al., 2004) and the gammaherpesvirinae Kaposi sarcoma herpesvirus (KSHV), gamma herpesvirus 68 (γHV68), Epstein-Barr virus (EBV), and Alcelaphine (Bortz et al., 2003; Johannsen et al., 2004; Bechtel et al., 2005; Zhu et al., 2005; Dry et al., 2008) . Cellular stress rather than stage of the cell cycle enhances the replication and plating efficiencies of herpes simplex virus type 1 ICP0-viruses Perturbation of cell cycle progression and cellular gene expression as a function of herpes simplex virus ICP0 Herpes simplex virus 1 alpha regulatory protein ICP0 interacts with and stabilizes the cell cycle regulator cyclin D3 Identification and functional evaluation of cellular and viral factors involved in the alteration of nuclear architecture during herpes simplex virus 1 infection
cord-000914-d0bk9gu5	2013	In this article, we highlight emerging evidence supporting the proposition that the signaling pathways anchored by Basigin/CD147 and CD36, two of the known host receptors that control Pf invasion and cyto-adherence, respectively, are also targets for functional subversion by Kaposi''s sarcoma (KS)-associated herpesvirus (KSHV), an inherently persistent cancer-associated herpesvirus that is prevalent in malaria-endemic regions. Remarkably, we have also discovered that cross-linking of CD36 on the surface of KSHV-infected cells with MC179, a recombinant peptide derived from the CIDR1α domain of PfEMP-1 that normally interacts with CD36 to mediate cyto-adherence (Ockenhouse et al., 1989 (Ockenhouse et al., , 1991 Baruch et al., 1997) , not only upregulated CD36 expression (Figure 2A ) but also reactivated the virus from latency through transcriptional activation of KSHV RTA (Figure 2B) , and that the molecular mechanisms that control this process overlap with those that putatively regulate PfEMP-1dependent EBV reactivation from latently infected cells (Chene et al., 2007) .
cord-001726-d7iwkatn	2015	
cord-001933-rnjnxymc	2016	Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; family Hytrosaviridae) is a dsDNA virus whose 190 kb genome encodes more than 60 confirmed proteins (Abd-Alla et al., 2008 , 2009b Kariithi et al., 2013a) . However, detection of hytrosavirus-like infection symptoms, i.e., the salivary gland hypertrophy syndrome (SGH) in the Narcissus bulb fly Merodon equestris (Diptera; Syrphidae; Amargier et al., 1979) and in male accessory gland filaments of the parasitic wasp Diachasmimorpha longicuadata (Hymenoptera; Braconidae; Luo and Zeng, 2010) implies that the Hytrosaviridae potentially contains other members. We hypothesized that GpSGHV infection in Glossina is under the control of host-and/or virus-encoded factors (proteins/peptides) whose interactions influence the expression or lack of overt SGH symptoms. The host (and viral) proteins identified in this study are potential targets for control of GpSGHV infections in tsetse fly mass production facilities. The clear GpSGHV-induced differential modulation of SG protein expression in Glossina raises the question of what host pathways are potentially globally regulated to facilitate successful virus infection.
cord-002068-e071ciil	2016	In the current study we analyzed the transcriptional level of selected immune-response genes we had previously identified from whole-transcriptome profiling of ALV-J-induced tumors in chicken spleen samples (Li et al., 2015) . According to the transcriptome profiles of ALV-J-induced tumor spleen samples and healthy spleen samples from White (Recessive) Plymouth Rock chickens in our previous experiments (Li et al., 2015) , we analyzed the transcriptional level of related innate immune genes. Taken together these results indicated that ALV-J early infection induced no obvious antiviral innate immunity responses in chicks sampled from 1 to 7 d.p.i. However, this was not the case for late infections and there were significant increases in Type I IFN, pro-inflammatory cytokines as well as IL-10.
cord-002085-e7xwb03g	2016	We constructed a DENV database containing the serotype, genotype, year and country/region of collection by collecting all publically available DENV sequence information from the National Center for Biotechnology Information (NCBI) and assigning genotype information. DGV also assigns the serotype and genotype to a user-specified sequence by performing a homology search against the curated DENV database, and shows its homologous sequences with the geographical position and year of collection. The second database is the Dengue virus genotyping database 2 (Yamashita et al., 2013) , which provides a summary table containing the DENV serotype/genotype, year and country of collection and accession number. The Dengue Virus Resource 3 facilitates the retrieval of DENV sequences deposited in GenBank according to serotype, disease symptom, host, region/country, genome region, and collection and/or release data (Resch et al., 2009) . DGV provides a search engine for the assignment of the DENV serotype, genotype, and origin country according to the most homologous sequence on the basis of a blastn search against the DENV database.
cord-002376-970934vm	2016	The quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is nowadays considered as the gold standard method for detection and quantification of enteric RNA viruses such as hepatitis A virus (HAV), hepatitis E virus (HEV) or human noroviruses (NoV) (Mattison et al., 2009; Blaise-Boisseau et al., 2010; Di Pasquale et al., 2010; Vasickova et al., 2012; Hennechart-Collette et al., 2014) . The present article is a followup study of a previously published theoretical concept (Mikel et al., 2015) and describes a method of preparation of MS2 PLP carrying a specific control sequence and their use as a PCV in RT-qPCR detection and quantification of enteric RNA viruses in swab, liver tissue, serum, feces, and vegetable samples. MS2 PLP were added in the amount of 5 × 10 6 particles to the different types of matrices (swabs, liver tissue, serum, feces, and leafy green vegetables) to reveal their ability to serve as PCV in the RT-qPCR detection of enteric RNA viruses.
cord-002795-i1qcanti	2017	Isolated pathogen was detected by polymerase chain reaction (PCR) assay, and the result showed that only GPV was positive; Genomic sequence analysis showed that this new pathogen shared 90.8-94.6% of nucleotide identity with goose parvovirus (GPV). In addition, LAMP has been considered as a time-saving, lowcost, highly specific and sensitive method (Chotiwan et al., 2017) , which can be completed within 60 min under condition of constant temperature, and it has been established to detect GPV, Muscovy duck parvovirus (MDPV), porcine parvovirus (PPV), canine parvovirus (CPV), and others targeting at VP gene (Cho et al., 2006; Chen et al., 2009; Ji et al., 2010; JinLong et al., 2010) . Quantitative loop-mediated isothermal amplification assay was carried out using different viruses including GPV, duck plague virus, duck tembusu virus, duck hepatitis virus, duck reovirus, Muscovy duck parvovirus, and H9N2-AIV to validate specificity of this method.
cord-002806-mu9jt1ul	2017	Many studies have reported the effects of CDV infections on the host cell proteins, such as inhibiting STAT1 and STAT2 nuclear import (Rothlisberger et al., 2010) , inducing cytokine responses in PBMCs (Nielsen et al., 2009) , and inducing lymphocytes apoptosis (Kumagai et al., 2004) . Based on iTRAQ combined with LC-MS/MS, a quantitative proteomic analysis was performed to identify differentially expressed proteins (DEPs) in mink lung epithelial cells (Mv.1.Lu cells) infected with CDV at 24 hours post infection (hpi). Therefore, we utilized an iTRAQ approach to identify the DEPs to further explore the pathogenic mechanism and immunomodulation of CDV infection through an analysis of the effects on host cell proteins in the mink. Collectively, the findings suggested that activation of the innate immune NF-κB signaling pathway and the NLR signaling pathway was involved in mink immune responses against CDV infection, and the NF-κB signaling was associated with the pathological respiratory or other symptoms FIGURE 5 | Confirmation of the iTRAQ-MS data by western blotting or real-time RT-PCR.
cord-003045-r707jl16	2018	The pipeline includes 4 major modules: The first module aligns and filter out human RNA sequences; the second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module quantifies read counts at the individual viral-gene level thus allowing for downstream differential expression analysis of viral genes between case and controls groups. Available online at: https:// www.fda.gov/biologicsbloodvaccines/bloodbloodproducts/approvedproducts/ licensedproductsblas/blooddonorscreening/infectiousdisease/ucm080466.htm Abbreviations: HBV, Hepatitis B virus; HCV, Hepatitis C Virus; HERV K113, Human Endogenous Retrovirus K113; TCGA, The Cancer Genome Atlas; HCC, Hepatocellular carcinoma; NAFLD, nonalcoholic fatty liver disease; Hep B, Hepatitis B; Hep C, Hepatitis C; HepB + HepC, coinfected with both Hepatitis B and C virus; HBsAg, Hepatitis B surface antigen; HBeAg, Hepatitis B type e antigen; NGS, next-generation sequencing; RNA-seq, whole transcriptome sequencing; BAM, Binary version of Sequence alignment/map format; CDS, coding sequence; Cox PH, Cox Proportional Hazard; HBx, viral gene X; STS, Sequence-tagged sites; NCBI, National Center for Biotechnology Information; GFF, general-feature-format.
cord-003207-ow3aez9v	2018	
cord-003239-nph2ezii	2018	
cord-003261-fz8ucwwm	2018	L * is only expressed by TMEV and is important for infection of macrophages, persistence of the virus in mice and inhibiting RNase L (van Eyll and Michiels, 2000; Sorgeloos et al., 2013) , 2B * results from a frameshifting mechanism conserved in cardioviruses that regulates the ratio of structural and non-structural proteins translated over time. (2012) , which was based on Influenza virus infection and suggests that PKR triggers the formation of "antiviral stress granules" that serve as a recruitment platform for dsRNA and RIG-like helicases, thereby enhancing IFN production. Like 3C proteases of other picornaviruses that were shown to target critical factors involved in IFN induction such as RIG-I (Barral et al., 2009) , EMCV 3C was reported to cleave TRAF family member-associated NF-kB activator (TANK) in infected cells, thus disrupting the complex involving TBK1, IKKe and IRF3 and limiting type I IFN production (Huang et al., 2017) .
cord-003327-pad65nww	2018	title: Commentary: Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies by Carrillo-Araujo, M., Tas, N., Alcantara-Hernandez, R. In the Genus Spiroplasma, at least two species have been identified as plant pathogens, Spiroplasma citri, the causative agent of citrus stubborn disease (Saglio et al., 1973) and Spiroplasma kunkelii, which is associated with corn stunt disease (Whitcomb et al., 1986) . Alternatively, microbiome analysis of insectivorous bats that feed on fruit eating insects could allow us to monitor phytoplasma prevalence and spread. Looking at their data from a plant disease perspective, we wondered if frugivorous and nectivorous bats could play a role in the transmission of plant pathogens. Here, we speculate upon the role of frugivorous and nectivorous bats as possible vectors of plant pathogens. jamaicensis ( Figure 1B) and Carollia perspicillata ( Figure 1C ) and nectivorous bats Leptonycteris yerbabuenae ( Figure 1D) and Glossophaga soricina (Figure 1E ) that were sampled by the authors.
cord-003357-4qrg6lqu	2018	
cord-003908-wbawzbhz	2019	
cord-003970-3e58229u	2019	Porcine reproductive and respiratory syndrome virus (PRRSV), the etiological agent of PRRS, is one of the most important endemic viruses affecting the swine industry in the United States (Holtkamp et al., 2013) and globally (Stadejek et al., 2013; VanderWaal and Deen, 2018) . Porcine reproductive and respiratory syndrome virus was first recognized almost simultaneously in Europe (Wensvoort et al., 1991) and North America (Collins et al., 1992) in the late 1980s and early 1990s, but genetic differences suggested a much earlier evolutionary divergence between the North American and European viral types. Here, we describe the temporal dynamics of PRRSV occurrence in a swine-dense region of the United States, characterizing these patterns according to ORF5 genetic lineages and sub-lineages. Porcine reproductive and respiratory syndrome virus diversity of Eastern Canada swine herds in a large sequence dataset reveals two hypervariable regions under positive selection
cord-003976-05tf6oqa	2019	
cord-032614-hp07ky6q	2020	In this study, we characterized the microbiome of ranched southern Bluefin Tuna, Thunnus maccoyii, across four anatomic sites (gill, skin, digesta, and anterior kidney) and evaluated environmental and pathological factors that influence microbiome composition, including the impact of PZQ treatment on microbiome stability. In this study, we characterized the microbiome of ranched southern Bluefin Tuna, Thunnus maccoyii, across four anatomic sites (gill, skin, digesta, and anterior kidney) and evaluated environmental and pathological factors that influence microbiome composition, including the impact of PZQ treatment on microbiome stability. In this study, ranched SBT were sampled to characterize the microbial diversity associated with mucosal body sites, including gill, skin, and gut, providing the first assessment of microbiome diversity in this ecologically and commercially important fish species. In this study we set out to describe how the fish mucosal microbiome is associated by parasitic infection and treatment with praziquantel (PZQ) across three body sites including the gill, skin, and digesta of Southern Bluefin Tuna (SBT).
cord-252485-cxi3cr15	2015	We and other groups have recently reported that recombinant viruses of Sendai virus (SeV), a prototype of the family Paramyxoviridae, in which the C proteins are knocked-out or mutated, generate dsRNA in infected cells at levels similar to the production of IFN-β (Takeuchi et al., 2008; Irie et al., 2010) . These unusual RNAs exhibited distinct properties in infected cells in terms of encapsidation with the viral N protein and subcellular distribution with SG marker proteins and RLRs. Our results suggest that RNA-typedependent mechanisms recognize and accumulate virus-derived, IFN-β-inducible, unusual RNAs into specific compartment to trigger the production of IFN-β, and that SeV may evade detection by the host innate immune system by preventing the production of these RNA species. Since the naked cbDI genomes have been reported readily to form an ideal structure as the RIG-I ligands of 5 -triphosphated, blunt-ended dsRNA (Kolakofsky, 1976) , these results indicated that the major IFN-β-inducing viral RNA species produced in the cells infected with CNT was encapsidated cbDI genomes, whereas those for SeV-4C(-) and NDV were not.
cord-252772-f3fctcru	2020	
cord-254115-hwy962a4	2017	
cord-257656-z7zx46gd	2019	
cord-260336-kwzo8puo	2019	Here we showed that intraperitoneally administered Z2 could also be distributed to testis and epididymis, resulting in the reduction of ZIKV RNA copies in testicular tissue and protection of testis and epididymis against ZIKV-induced pathological damage and poor sperm quality in type I interferon receptor-deficient A129 mice. Student''s unpaired two-tailed t-test was used to monitor the distribution of Z2 in male A129 mouse body and testicular tissue and to analyze the difference of viral RNA level in sera or tissues between Z2-and vehicle-treated A129 mice. ZIKV RNA copies in (A) testes, (B) epididymides, and (C) sperm of Z2-or vehicle-treated ZIKV-infected male A129 mice at day 16 were detected by qRT-PCR. Zika virus infection in the testicular tissue not only damages male testicular tissue, resulting in pathological lesion of testes and epididymides, but also produces ZIKV-infected semen, causing infertility.
cord-262682-gsvswr7v	2018	
cord-263162-37fvlhuo	2019	
cord-264071-hg0qslyx	2019	
cord-267735-y3832u9e	2020	
cord-267960-r5m7o9dp	2020	
cord-269957-vd9ctqro	2019	
cord-271557-xic32wxh	2012	
cord-276493-hoaxv5e0	2020	
cord-277400-w7mvk3x4	2017	
cord-277731-thazunob	2020	
cord-278540-gy65bvot	2019	
cord-281836-j1r771nq	2020	
cord-282305-l5r67gte	2019	
cord-282797-thywse7g	2020	
cord-284889-hth8nf5b	2013	
cord-285868-fz5utxss	2014	
cord-286779-si3qml42	2020	
cord-289623-7oc1ykds	2020	
cord-290505-omszep7u	2019	
cord-291295-7og5umiq	2019	
cord-293675-bojfc3q0	2019	
cord-295121-4xemmaqt	2020	
cord-295240-76ee00i0	2020	
cord-296099-eq9gujk7	2013	
cord-296495-9v0sq8k6	2016	Mycoplasma pneumoniae causes both upper and lower respiratory tract infections, with community-acquired pneumonia (CAP) as the major burden of disease. pneumoniae infections were first reported in 1960 when 16% of 110 children with lower respiratory tract disease were tested positive by a fourfold rise in antibody titers against the Eaton agent (Chanock et al., 1960) . This study described 20 patients with CAP, of which 19 were children 4-15 years of age, diagnosed by a significant rise in antibody titers against M. Emergence of macrolide-resistant strains during an outbreak of Mycoplasma pneumoniae infections in children Results of molecular detection of Mycoplasma pneumoniae among patients with acute respiratory infection and in their household contacts reveals children as human reservoirs Antibiotics for community-acquired lower respiratory tract infections secondary to Mycoplasma pneumoniae in children Role of Mycoplasma pneumoniae and Chlamydia pneumoniae in children with community-acquired lower respiratory tract infections
cord-297662-slmlhqnb	2017	In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis. Since high mannose binding DC-SIGN interacts only with N67 glycans on the viral surface (Pokidysheva et al., 2006) and N153-glycan is dispensable for virus production in mosquito and mammalian cells (Bryant et al., 2007) , this suggests that N153 glycans may serve a distinct function from N67 glycans in DEN pathogenesis possibly via interaction with an unknown fucose binder or act as a viral glycan shield. Finally, N153 deglycosylated (N153 − ) DENV mutant displayed reduced infectivity (10-fold lower) in both mammalian and mosquito cells compared to WT, possibly due to impaired virus entry process (Lee et al., 1997; Hacker et al., 2009) , whereby loss of the N153-glycan affected the conformational stability of E proteins and led to premature exposure of the fusion peptide (Yoshii et al., 2013) . N-linked glycosylation of dengue virus NS1 protein modulates secretion, cell-surface expression, hexamer stability, and interactions with human complement
cord-298032-3zlu8g8y	2018	
cord-298233-qqhgmqrg	2016	More interestingly, a remarkable HEV strain Kernow-C1, which was originally isolated from an HIV-positive patient with chronic HEV infection, contains an insertion of a 174 nt gene fragment of human ribosomal protein S17 in the Pro region (Shukla et al., 2011) . Furthermore, other studies indicate that the expression of viral macro domain in liver cells inhibits apoptosis since it is functionally related to poly(ADP-ribose) polymerase-1 (PARP-1; Allen et al., 2003; Chen et al., 2009) , suggesting a role in apoptosis during viral infection. Identification of critical residues in hepatitis E virus macro domain involved in its interaction with viral methyltransferase and ORF3 proteins ORF3 protein of hepatitis E virus is not required for replication, virion assembly, or infection of hepatoma cells in vitro A PSAP motif in the ORF3 protein of hepatitis E virus is necessary for virion release from infected cells The ORF2 protein of hepatitis E virus binds the 5 region of viral RNA ORF3 protein of hepatitis E virus is essential for virion release from infected cells
cord-298240-vcph52gn	2014	This research topic collated a number of review articles and original research article, in an attempt to highlight how viruses interact with the host UPR in the establishment of acute, chronic and latent infections. The relationship between virus and UPR and its associated autophagy is being addressed in three reviews focusing on RNA viruses, as their life cycles are closely associated with the ER (Blazquez et al., 2014; Fung and Liu, 2014; Jheng et al., 2014) . An important question remains as to whether UPR represents a new tool for sensing viruses or select UPR molecules are merely being co-opted in "microbial stress response." This is being addressed in Judith Smith''s review, in which she provides a critique on the intersection of the UPR with the inflammatory pathways and innate immunity and offers an insight into UPR-PRR synergy as an evolutionary adaptation to ensure specificity of anti-viral responses (Smith, 2014) .
cord-300379-db79kb5c	2019	
cord-302854-buzyani0	2012	
cord-302928-nnly9ju8	2020	Most cited articles and most viewed RTs in the human/animal virus field of the section (top 5, as of February 3, 2020) are as follows, respectively: articles, "Epidemiological aspects and world distribution of HTLV-1 infection" (Gessain and Cassar, 2012) , "Pathology of asthma" (Kudo et al., 2013) , "Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data" (Beerenwinkel et al., 2012) , "ER stress, autophagy, and RNA viruses" (Jheng et al., 2014) , and "Zika virus: the latest newcomer" (Saiz et al., 2016) ; RTs, "Highly mutable animal RNA viruses: adaptation and evolution" , "Virus discovery by metagenomics: the (im)possibilities" (Dutilh et al., 2017) , "Zika virus research" (Bueno-Marí et al., 2018), "Pathophysiology and epidemiology of virus-induced asthma" (Kimura and Ryo, 2014) , and "Forefront studies on HTLV-1 oncogenesis" (Mahieux and Watanabe, 2013) .
cord-305973-i3raopi6	2020	These data demonstrate that DNA vaccines combined with the TcB-based manufacturing platform can be used to rapidly produce potent, human, polyclonal, escape-resistant anti-HTNV, and anti-PUUV neutralizing antibodies that are protective in animal models. Here, we demonstrate that it is possible to combine DNA vaccine technology with the TcB platform to produce potent human polyclonal IgG for use as a pre-or post-exposure prophylactic for HFRS caused by HTNV and PUUV infection. Previous experiments to produce anti-ANDV and anti-SNV TcB human IgG have demonstrated that including an SAB-adj-1 adjuvant at the injection sight increased immunogenicity of the ANDV and SNV DNA vaccines resulting in higher titer virusspecific neutralizing antibodies (Hooper et al., 2014a) . To determine the dose of SAB-159 required to protect against infection, hamsters were administered decreasing concentrations of neutralizing antibody ranging from 12.23 mg/kg to 0.39 mg/kg SAB-159 subcutaneously 1 day prior to a 10 PFU HTNV challenge.
cord-310392-fmobf1f1	2020	
cord-312336-784izxqd	2020	
cord-314567-purplsjn	2018	
cord-315834-ashjw2xs	2019	title: Clinical Features Predicting Mortality Risk in Patients With Viral Pneumonia: The MuLBSTA Score OBJECTIVE: The aim of this study was to further clarify clinical characteristics and predict mortality risk among patients with viral pneumonia. CONCLUSION: Here, we designed an easy-to-use clinically predictive tool for assessing 90-day mortality risk of viral pneumonia. Influenza and other respiratory viruses are common reasons of acute pneumonia which can result in significant morbidity or mortality in the setting of high-risk factors such as extremes of age, pregnancy, obesity or chronic pre-existing conditions. Other reported risk factors for influenza pneumonia such as PO2/FiO2, lymphocyte count, and antigen-specific T cells are likewise useful in predicting mortality and deciding on appropriate management (Viasus et al., 2011; Shi et al., 2017) . In patients hospitalized with viral pneumonia, a simple prognostic tool was made for overall mortality which is useful for prediction several days after admission upon obtaining culture results.
cord-316176-rqc6kvsl	2020	The FilmArray(®) Pneumonia plus Panel (FAPP) is a new multiplex molecular test for hospital-acquired pneumonia (HAP), which can rapidly detect 18 bacteria, 9 viruses, and 7 resistance genes. The FilmArray R Pneumonia plus Panel (FAPP) is a new panel for HAP, which offers potential advantage to detect and quantify in a single test, 27 respiratory pathogens (18 bacteria, 9 viruses) and 7 antibiotic resistance genes. At the time of HAP diagnosis, FAPP yielded positive results with significant levels (i.e., ≥ 10 4 bin in BAL and ≥ 10 5 bin in ETA for semi-quantified bacteria) in 82/100 patients. In this study, this test was compared to routine microbiological methods using 237 prospectively collected BAL and ETA specimens obtained from 100 ICU patients at the time of suspected HAP and, if possible, at a later timepoint during follow-up.
cord-316537-f5rto51t	2016	
cord-317499-mxt7stat	2014	Table 1 shows the frequency of HRV infection in various adult respiratory diseases such as exacerbation of asthma (Nicholson et al., 1993; Atmar et al., 1998; Tan et al., 2003) , common cold (Makela et al., 1998; van Gageldonk-Lafeber et al., 2005) , exacerbation of COPD (Seemungal et al., 2001; Rohde et al., 2003; Tan et al., 2003; Beckham et al., 2005; Papi et al., 2006; Hutchinson et al., 2007; Ko et al., 2007; McManus et al., 2008; Kherad et al., 2010; Dimopoulos et al., 2012; Perotin et al., 2013) , community acquired pneumonia (Jennings et al., 2008; Johnstone et al., 2008; Johansson et al., 2010; Lieberman et al., 2010; Fry et al., 2011; Wootton et al., 2011; Luchsinger et al., 2013; Takahashi et al., 2013; Huijskens et al., 2014) , exacerbation of idiopathic pulmonary fibrosis (Wootton et al., 2011) , and asymptomatic infection (Fry et al., 2011) .
cord-317595-siwzjeea	2018	Herein, we apply an evolutionary approach to shed light into HCV origin, to analyze its adaptation to human populations, and to verify if the emergence of drug-resistant variants is a result of positive selection. We used Single-Likelihood Ancestor Counting (SLAC) and fixed effects likelihood (FEL) (Kosakovsky Pond and Frost, 2005) to calculate the rates of nonsynonymous and synonymous changes at each site in the structural and in the non-structural region alignments (analyses were performed on alignments split on the basis of the recombination breakpoint detected by GARD). The observation that the positively selected sites are involved in HCV binding and infectivity suggests that hepaciviruses contributed to shape the genetic diversity of CD81 in bats. Using an evolutionary model that accounts for variation in the pressure of natural selection across sites and branches, we show that the common ancestor of extant HCV genotypes existed at least 3000 years ago, with a lower bound estimate of ∼5200 years before present.
cord-319460-n4ezxnjc	2016	
cord-319614-4qi59pbz	2019	Experimental data indicate that during persistent infection, lymphocytic choriomeningitis virus (LCMV) may both directly or indirectly modulate regulatory cellular processes and alter cellular functions that are not critical for survival, but are essential for cell homeostasis. Increased levels of ROS were accompanied by changes in the pattern of telomere restriction fragments (TRFs) in infected cells and mediated activation of hypoxia-inducible transcription factor-1 (HIF-1) and phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathways. These data suggest that LCMV maintains its replication in persistently infected cells by regulating redox signaling through modulation of local levels of H 2 O 2 and subsequent activation of cellular processes that it uses for its own benefit. Notably, the treatment with antioxidants also resulted in reduced levels of viral NP in HeLa, as well as in A549 LCMV-infected cells, suggesting a link between ROS-dependent signaling and virus replication (Figures 7B,D and Supplementary Figure S2B ).
cord-321112-w7x1dkds	2019	
cord-322649-c99lszcu	2019	title: Rapid and Sensitive Recombinase Polymerase Amplification Combined With Lateral Flow Strip for Detecting African Swine Fever Virus In this study, we developed a rapid test that combines recombinase polymerase amplification (RPA) of the ASFV p72 gene with lateral flow detection (LFD). Results showed that the sensitivity of recombinase polymerase amplification with lateral flow dipstick (RPA-LFD) for ASFV was 150 copies per reaction within 10 min at 38°C. A dilution range of 10 0 to 10 5 copies per reaction of pMD19-p72 recombinant plasmid was used to evaluate the sensitivity of recombinase polymerase amplification with lateral flow dipstick (RPA-LFD), and the amplicons were evaluated through agarose gel electrophoresis. The sensitivity results showed that the detection limit of the ASFV RPA-LFD assay was 10 2 copies per reaction of the recombinant plasmid pMD19-p72. Development of a TaqMan PCR assay with internal amplification control for the detection of African swine fever virus A recombinase polymerase amplification-based assay for rapid detection of African swine fever virus
cord-324058-20drr99p	2020	We determined the prevalence and type of a wide variety of respiratory pathogens in 12,075 United States subjects tested for SARS-CoV-2 infection in March and April 2020. In the present study, we present data on the prevalence of SARS-CoV-2 and other bacterial, viral and fungal respiratory pathogens in samples taken from over 12,000 United States symptomatic subjects tested for the presence of SARS-CoV-2 in a manner which permitted assessment of the presence of co-pathogens as well as SARS-CoV-2. The t-test for independent group comparison was used to compare age of the study subjects across gender, SARS-CoV-2 ± patients and residential versus outpatients. The higher coinfection rate observed in the present study may be due to the criteria applied to SARS-CoV-2 testing eligibility at the time, which was heavily weighted toward symptomatic patients, and whom would be more likely to have a current infection. The infection rate for these other respiratory pathogens throughout the United States is much greater than that of SARS-CoV-2 itself in subjects seeking SARS-CoV-2 testing.
cord-324651-8teb5jrn	2020	
cord-326217-ji0njeha	2018	We found that both inhibition of GSK3 function by synthetic inhibitors as well as silencing of GSK3β gene expression resulted in a decrease of HCV replication and infectious particle production, whereas silencing of the GSK3α isoform had no relevant effect on the HCV life cycle. To assess whether both GSK3 isoforms are required for HCV replication, we silenced GSK3α and / or GSK3β gene expression by transfecting siRNAs and quantified HCV RNA in Huh-7.5 cells harboring HCV subgenomic replicon (Con1) or infectious HCV (Jc1). Given the well-known dependency of HCV on miR-122 (Jopling et al., 2005 (Jopling et al., , 2008 Machlin et al., 2011) and the regulatory circuit between insulin-like growth factor 1 receptor, GSK3β, and miR-122 identified previously (Zeng et al., 2010) , we assessed the effect of GSK3 inhibition on miR-122 expression in Huh-7.5 cells harboring a subgenomic HCV replicon.
cord-329003-ovnzlpa2	2019	
cord-330942-x238hq9b	2018	
cord-331973-avjw4kx1	2018	Serological tests can successfully identify antibodies to most respiratory pathogens such as RSV, adenovirus, influenza A and B, parainfluenza 1-3 virus, etc., and can detect mixed infections from hospitalized children suffering from acute respiratory infections, with the exception of infants for whom an antibody response is usually undetected (Hall et al., 1991; Chkhaidze et al., 2006) . FA testing, in addition to RT-PCR, is useful for epidemiological studies as it increases the probability of identifying acute viral infections and has been used for accurate assessment of respiratory viruses other than influenza in children (Sawatwong et al., 2012; Feikin et al., 2013; Zhang et al., 2017) . Most of the studies evaluating the clinical performance of these assays have reported high sensitivity (87-100%) and specificity (>98%) for detecting influenza A/B and RSV in pediatric and adult patients (Bell et al., 2014; Nie et al., 2014; Popowitch and Miller, 2015; Gibson et al., 2017; Ling et al., 2018) .
cord-332221-6ea6gz9s	2019	The expression of inflammatory cytokines in the serum was detected by enzyme linked immunosorbent assay; lung injury was observed by hematoxylin-eosin staining; the viral proliferation in the lung was detected by real-time quantitative PCR; and the protein expression of the main molecules in the phosphatidylinositol-3-kinases/protein kinase B (PI3K/AKT) and mitogen-activated protein kinase (MAPK) signaling pathways was detected by Western blot. The expression of inflammatory cytokines in the serum was detected by enzyme linked immunosorbent assay; lung injury was observed by hematoxylin-eosin staining; the viral proliferation in the lung was detected by real-time quantitative PCR; and the protein expression of the main molecules in the phosphatidylinositol-3-kinases/protein kinase B (PI3K/AKT) and mitogen-activated protein kinase (MAPK) signaling pathways was detected by Western blot. To explore the mechanism by which IGF1 regulates acute inflammatory lung injury induced by IAV infection, a Western blot was used to detect the expression of molecules in key signaling pathways in the lung tissue of PR8-infected mice (50LD 50 PR8).
cord-333309-21czobqy	2014	Interaction of lectin-type and other chaperones with ERAD substrates allows association with members of the protein disulfide isomerase (PDI) family, which generally are characterized by one or more thioredoxin-like motifs (CXXC; Brodsky and Skach, 2011) . In contrast to the rhomboid proteases, the Derlins lack proteolytic activity, suggesting that these proteins bind to ERAD substrates and target them to E3 ligases for ubiquitination and to p97 for membrane extraction (Brodsky, 2012) . These ubiquitin ligases are members of the cytosolic SCF (S-phase kinase-associated protein 1 (Skp1)-Cullin 1 (Cul1)-F-box) family, where the F-box components of the SCF complex recognize the N-glycans of the retrotranslocated substrate, e.g., Fbs1 and Fbs2 (Yoshida, 2007) . A proteasomal ATPase contributes to dislocation of endoplasmic reticulum-associated degradation (ERAD) substrates The viral E3 ubiquitin ligase mK3 uses the Derlin/p97 endoplasmic reticulum-associated degradation pathway to mediate down-regulation of major histocompatibility complex class I proteins
cord-336074-76ca1cfy	2016	
cord-337198-4sors3bg	2020	In this study, we evidence that the anti-SARS-CoV2 activity of a clinically achievable hydroxychloroquine concentration is maximized only when administered before and after the infection of Vero E6 and Caco-2 cells. In this study, we tested HCQ against a SARS-CoV-2 Italian clinical isolate, by using different protocols of drug administration corresponding to its possible prophylactic, therapeutic, and prophylactic/therapeutic use in patients. A clinical isolate hCoV-19/Italy/UniSR1/2020 (GISAID accession ID: EPI_ISL_413489) was isolated and propagated in Vero E6 cells, and viral titer was determined by 50% tissue culture infective dose (TCID 50 ) and plaque assay for confirming the obtained titer. HCQ EC 50 against SARS-CoV-2 was obtained by both CPE and RT-PCR analysis on results from full-time experimental setting on Vero E6 cells. Different concentrations of HCQ were tested on Vero E6 to determine the effective concentration of the drug against SARS-CoV-2 in vitro infection (Figure 1) .
cord-338773-ilir895i	2018	Novel sequencing reads related to pestivirus were found in samples collected from different bat and rodent species. Genomic and phylogenetic analyses of these viruses revealed the presences of six novel pestivirus species in bat and rodent hosts. Each peptide of BPV species 1 and 2 aligned best with those of APPV, even when the overall identities FIGURE 1 | Occurrence of pestivirus-related reads in bats and rodents from different locations. This study described the identification of novel BPVs and RPVs in different bat and rodent species across several Chinese regions, which revealed that these two mammals served as natural hosts for pestiviruses. Considering their divergent phylogenetic positions, different genome sizes and structures, and the minimal sequence similarities of BPVs and RPVs when compared to other pestiviruses, we propose classifying members of the genus Pestivirus into three main lineages; bat-swine, rodent, and artiodactylous lineages, based on the order level of their hosts.
cord-343132-qqhivgkq	2020	The results showed that the intracellular extracts of Ln. mesenteroides YPK30 possessed in vitro prophylactic, therapeutic, and direct-inhibitory effects against PEDV in the Vero cell model. As shown in Figure 3 , the metabolic activity of Vero cells pretreated with the intracellular extracts of Ln. mesenteroides, regardless of which strain, were similar to those pretreated with IFN-α2b (p > 0.05) but were significantly higher than the un-pretreated cells (p < 0.05), indicating that all the Ln. mesenteroides strains isolated from kefir grains possessed in vitro prophylactic effects against PEDV. durans, Lb. kefiri, Lc. lactis, and Ln. mesenteroides , were isolated from kefir grains, and the in vitro prophylactic effects of the intracellular extracts of these four species against PEDV infection in Vero cells were compared. Therefore, the in vitro prophylactic and therapeutic effects of the intracellular extracts of Ln. mesenteroides YPK30 against PEDV in Vero cells seem not be attributed to the direct interaction of bacterial components or metabolites with virus.
cord-343357-5nhyumxl	2020	We urge considering infection with porcine respiratory coronavirus of metabolic syndrome pigs, such as the obese Ossabaw pig, as a highly relevant animal model of severe COVID-19. Cytokine storm in the lungs and inflammation are suggested as essential for the escalating and prolonged lung disease observed in severely affected COVID-19 patients, as is also the case for other severe human coronavirus infections like SARS and MERS (Mehta et al., 2020) . We hypothesize that disease severity will increase in obese Ossabaw pigs infected with PRCV compared to pigs of normal weight, and hence will constitute a useful model for severe COVID-19 in humans at risk due to metabolic syndrome associated comorbidities, including aged individuals. With the added benefit of being a well-described pig-specific virus (with no rigorous biosafety demands), we suggest that the obese pig affected by the metabolic syndrome will constitute a highly human-translatable animal model having the potential to significantly facilitate and accelerate SARS-CoV-2/COVID-19 research.
cord-344200-ev4707pq	2020	title: Specific Aptamer-Based Probe for Analyzing Biomarker MCP Entry Into Singapore Grouper Iridovirus-Infected Host Cells via Clathrin-Mediated Endocytosis Aptamer-Q5-complexed major capsid protein (MCP) in the membrane of SGIV-infected cells can be used as a specific molecular probe to investigate the crucial events of MCP endocytosis into SGIV-infected host cells during viral infection. Therefore, MCP enters SGIV-infected host cells via clathrin-mediated endocytosis, which is dependent on dynamin, cholesterol, low pH, and cytoskeletal actin filaments. In this study, an aptamer (Q5)-based specific probe was used to investigate the trafficking mechanism and endocytotic pathway of MCP in host cells during SGIV infection. We analyzed the effects of various inhibitors on the binding of aptamer Cy5-Q5 to its target protein, MCP, in the membranes of SGIV-infected cells with flow cytometry. Relative to the control group of normal GS cells, the GS cells incubated with the safe working concentration of each inhibitor in L-15 medium retained their normal FIGURE 7 | Caveolae/raft-dependent endocytosis is not involved in MCP entry during SGIV infection.
cord-344970-ud1lhkyi	2020	Lipid rafts are specialized plasma membrane microdomains involved in important processes of the virus infections and of the host target cells (Rosenberger et al., 2000) . This minireview reports on the available knowledge about the interplay between coronaviruses, including the SARS-CoV-2, with lipid rafts and autophagic pathways, in order to focus the attention to novel potential targets to inhibit coronavirus infections. As outlined in this review, lipid rafts and autophagic pathways play a pivotal role in coronavirus infection, being critical for viral entry and replication, as well as for viral release from the host cells. In fact, different drugs described as inhibitors or inducers of the autophagy that control host cell pathways process involved in coronavirus infection, have sparked interest for their potential antiviral activity (Shakya et al., 2018; Liu et al., 2019; Xu et al., 2020; Yang et al., 2020 ; Table 1 ).
cord-347917-fmb5nyxu	2020	In this study, genome-wide profiling of lncRNAs in swine testicular (ST) cells infected with PDCoV was performed using RNA-seq. An integrative analysis of lncRNA alterations suggested their putative role in regulating the expression of several key genes in metabolic and TNF signaling pathways during infection. There have been reports of using genome-wide association analysis between lncRNAs and the co-expressed and/or co-regulated protein-coding genes to characterize the function of the lncRNA (Huarte et al., 2010) . GO and KEGG pathway enrichment analysis of target genes revealed that lncRNAs may act in cis or trans to participate in the regulation of expression of multiple important genes in different processes including protein binding, DNA transcription, metabolism, and immune response. The functional association between regulatory lncRNA and protein-coding gene transcripts can be determined by performing expression correlation analysis coupled with ascertaining their putative role in related physiological processes.
cord-351719-xqmir1ca	2020	
cord-353454-zq51hpjs	2016	While plant sources are being extensively explored for the discovery of new chemical entities for various therapeutic purposes, endophytic microorganisms play an important role in this search for natural bioactive compounds, with potential use in the health sector and in drug discovery (Lam, 2007) . Bacterial endophytes are diverse in nature and are known to produce different bioactive metabolites that act as antimicrobial and anticancer compounds, for example, with 76% of them reported from the single genus, Streptomyces (Berdy, 2012) . Endophytes are reported to produce a number of bioactive metabolites in a single plant or microbe which served as an excellent source of drugs for treatment against various diseases and with potential applications in agriculture, medicine, food and cosmetics industries (Strobel and Daisy, 2003; Jalgaonwala et al., 2011; Godstime et al., 2014; Shukla et al., 2014) .
cord-353815-w35spqqt	2020	This review introduces the progress of research on AMPs comprehensively and systematically, including their classification, mechanism of action, design methods, environmental factors affecting their activity, application status, prospects in various fields and problems to be solved. Tryptophan (Trp), as a non-polar amino acid, has a remarkable effect on the interface region of the lipid bilayer, whereas Arg, as a basic amino acid, confers peptide charge and hydrogen bond interactions, which are essential properties to combine with the bacterial membrane''s abundant anionic component. And it seems that Trp residues play the role of natural aromatic activators of Arg-rich AMPs by ion-pair-π interactions (Walrant et al., 2020) , thereby promoting enhanced peptide-membrane interactions (Chan et al., 2006) . Furthermore, L4H4, which is designed based on the linear cationic amphiphilic peptide magainin, also shows good antibacterial activity and cell penetration properties by inserting four histidine sequences in leucine and alanine (Lointier et al., 2020) .
cord-353957-0pjg25kn	2017	Taken together, these results reveal that induced expression of avian IFITM1 and IFITM3 in response to ATMUV infection can effectively restrict the virus replication, and suggest that increasing IFITM proteins in host may be a useful strategy for control of ATMUV infection. Interestingly, we observed that ATMUV infection could trigger duck innate immune response including robust expression of particular type I and type III IFNs and IFITM family proteins. Our previous studies had shown that ATMUV infection effectively triggers the host innate immune response, including robust upregulation of type I and type III IFNs and some critical ISGs in chicken and CEF (Chen et al., 2016a) . To confirm these findings, DF-1 cell lines expressing specific shRNA targeting each of these IFITMs were infected with ATMUV and harvested at 36 hpi, followed by qRT-PCR assay to detect mRNA expression of viral genes.