# pos

id: cord-288306-0chcsqe7
pos: NNP
token:
  https://www.oie.int/animal-health-in-the-world/official-disease-status/classical-swine-fever/map-ofcsf-official-status/

lemma:
  https://www.oie.int/animal-health-in-the-world/official-disease-status/classical-swine-fever/map-ofcsf-official-status/


id: cord-288306-0chcsqe7
pos: NNP
token:
  https://www.oie.int/animalhealth-in-the-world/official-disease-status/classical-swine-fever/map-of-csf-official-status/

lemma:
  https://www.oie.int/animalhealth-in-the-world/official-disease-status/classical-swine-fever/map-of-csf-official-status/


# ent

id: cord-002945-29nj4f05
type: ORG
entity:
  the Veterinary Science Diagnostic Services School of Veterinary Science University of Queensland Gatton


id: cord-009445-p2rz81fy
type: WORK_OF_ART
entity:
  Wild Birds in Live Birds Markets Potential Reservoirs of Enzootic Avian Influenza Viruses and Antimicrobial Resistant Enterobacteriaceae


id: cord-009445-p2rz81fy
type: WORK_OF_ART
entity:
  Wildlife Is Overlooked in the Epidemiology of Medically Important Antibiotic Resistant Bacteria Antimicrobial


id: cord-253116-oq0bc35u
type: PROTEIN
entity:
  fluorescein isothiocyanate FITC conjugated secondary antibody rabbit anti cat IgG H L Nordic MUbio Sustern Netherlands LuBio


id: cord-013315-plptulfb
type: PROTEIN
entity:
  proteins Malate dehydrogenase P61976 Uncharacterized oxidoreductase MAP_3007 Q73VK6 and hypothetical protein EGA31_12440


id: cord-013315-plptulfb
type: WORK_OF_ART
entity:
  the Proteasome Pathogenesis of Bacterial Infections in Animals Membrane and Cytoplasmic Proteins of Mycobacterium


id: cord-013280-kczj24se
type: DNA
entity:
  retinoic acid inducible gene I RIG I TANK binding kinase 1 TBK1 TNF receptor associated factor 6 TRAF6


id: cord-013280-kczj24se
type: PROTEIN
entity:
  eIF4G eukaryotic initiation factor 4G NF κB nuclear factor kappa B IRF3 interferon regulatory factor 3 IRF7 interferon regulatory factor 7


id: cord-274497-tqceazdp
type: ORG
entity:
  the Committee on the Care and Use of Laboratory Animal Resources of the School of Veterinary Medicine University of São Paulo


id: cord-271648-m2c5bvuj
type: ORG
entity:
  Epidemiology Genetic Recombination and Pathogenesis of Coronaviruses Molecular Evolution of Human Coronavirus Genomes Coronaviruses


id: cord-297469-26d8o1xk
type: PROTEIN
entity:
  granulocyte macrophage colony stimulating factor GM CSF transforming growth factor beta 1 TGF β1 and tumor necrosis factor alpha TNF


id: cord-255339-oudj079q
type: WORK_OF_ART
entity:
  Joint WHO FAO Expert Committee on Zoonoses Viral Zoonosis A Comprehensive Review Zoonotic Disease Programs for Enhancing Global Health Security Risk


id: cord-255339-oudj079q
type: ORG
entity:
  the European Union Camelid Infectious Disorders World Health Organization Hemorrhagic Fever Task Force


id: cord-292031-weiwksh6
type: WORK_OF_ART
entity:
  Drinking Water Quality Volume 1 Recommendations World Health Organization WHO Geneva Switzwerland Towards


id: cord-292031-weiwksh6
type: ORG
entity:
  Quantitative Microbial Risk Assessment of Waterborne Disease Guidelines for Safe Recreational Water Environments


id: cord-322317-wsagoy52
type: DNA
entity:
  Tru cut and fine needle aspiration biopsies of liver and kidney for diagnosis of feline infectious peritonitis Limitations


id: cord-322317-wsagoy52
type: DNA
entity:
  viral 3c gene Spike Protein Fusion Peptide and Feline Coronavirus Virulence Feline coronavirus infections


id: cord-319799-h9kot3og
type: PROTEIN
entity:
  signal transducer and activator of transcription 1 STAT1 myeloid differentiation primary response gene 88 MyD88 TLR4 TLR7


id: cord-319799-h9kot3og
type: DNA
entity:
  transcriptional end sites 43 TSS transcription start site TF transcription factor TFBS transcription factor binding site


id: cord-319799-h9kot3og
type: CELL_TYPE
entity:
  primary human airway epithelial cells HAE primary type II pneumocytes AT2 lung fibroblast LF pulmonary endothelial cells MEV


id: cord-302161-ytr7ds8i
type: DNA
entity:
  challenge virus FCoV Zu1 harbors a new recombination site Pathogens 2020 9 x 8 of 21 consensus sequence


id: cord-302161-ytr7ds8i
type: ORG
entity:
  Feline Infectious Peritonitis Feline Infectious Peritonitis ABCD Guidelines on Prevention and Management Risk


id: cord-330827-gu2mt6zp
type: WORK_OF_ART
entity:
  Statement on the second meeting of the International Health Regulations Emergency Committee Regarding the Outbreak of Novel Coronavirus 2019 nCoV Genomic


id: cord-328395-2cakgmsj
type: FAC
entity:
  the Transmembrane Serine Protease TMPRSS2 Efficient Activation of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein


id: cord-328395-2cakgmsj
type: WORK_OF_ART
entity:
  Simultaneous Treatment of Human Bronchial Epithelial Cells with Serine and Cysteine Protease Inhibitors Prevents Severe Acute Respiratory Syndrome Coronavirus Entry


id: cord-328395-2cakgmsj
type: WORK_OF_ART
entity:
  Dexamethasone in Hospitalized Patients with Covid 19 Preliminary Report Pharmacologic Treatments for Coronavirus Disease 2019 COVID 19 A Review Adverse


id: cord-328395-2cakgmsj
type: ORG
entity:
  Hedgehog Pathway Drives Fusion Negative Rhabdomyosarcoma Initiated From Non myogenic Endothelial Progenitors


id: cord-309381-cb80ntxs
type: GGP
entity:
  IL 1R1 interleukin 1 receptor type 1 IL 10RB interleukin 10 receptor subunit beta IL 2RA interleukin 2 receptor subunit alpha IL 10RA interleukin 10 receptor subunit alpha IL 12RB2 interleukin 12 receptor subunit beta 2 IL 1RN interleukin 1 receptor antagonist TNFRSF1B TNF receptor


id: cord-309381-cb80ntxs
type: WORK_OF_ART
entity:
  NEP Modulation of Innate Immune Responses by the Influenza A NS1 and PA X Proteins Interplay of PA X


id: cord-331022-tek4u751
type: GPE
entity:
  Publicly Reported Confirmed Cases Estimation and Application Presymptomatic Transmission of SARS CoV 2


id: cord-331022-tek4u751
type: ORG
entity:
  the Dynamic Changes of Serum Antibody Responses Against Severe Acute Respiratory Syndrome Coronavirus Lack


id: cord-314825-fzba05wn
type: CELL_LINE
entity:
  China H5N1 H9N2 H4N1 H4N6 H5N3 H10N5 H4N8 H6N6 H7N9 United States H4N6 H6N2 H7N2 Canada H4N6 H3N3 South Korea H7N2 H5N2 Nigeria H5N1 and Egypt H5N1 H5N2 H9N2


id: cord-314825-fzba05wn
type: ORG
entity:
  Multitemperature Single Strand Conformational Polymorphism Serological Survey of the Influenza a Virus


id: cord-314825-fzba05wn
type: ORG
entity:
  Sequencing Provides Data for Stratifying Infection Prevention and Control Management of Nosocomial Influenza Rapid


id: cord-314825-fzba05wn
type: DISEASE
entity:
  H1N1 A H1N1 pdm09 None 311 312 Trinidad Tobago H3N2 A H1N1 pdm09 None 313 South America Argentina H1N1 H1N2 H3N2 A H1N1 pdm09 None 314 315 316 317 318 Brazil


id: cord-314825-fzba05wn
type: DISEASE
entity:
  influenza A H1N1 pdm09 viruses with M genes from human pandemic strains among Nigerian pigs Antigenic Detection of Human Strain of Influenza Virus A H3N2 in Swine Populations


id: cord-314825-fzba05wn
type: DISEASE
entity:
  H1N1 human influenza virus isolated from pigs in Japan Genomic reassortants of pandemic A H1N1 2009 virus and endemic porcine H1 and H3 viruses in swine in Japan Influenza A virus infection


id: cord-314825-fzba05wn
type: DISEASE
entity:
  H1N1 swine influenza virus isolated in Korea Phylogenetic analysis of swine influenza viruses recently isolated in Korea Isolation and characterization of novel H3N1 swine influenza viruses from pigs with respiratory diseases


id: cord-314825-fzba05wn
type: DISEASE
entity:
  influenza A virus in swine in two production systems in Guatemala Influenza Other Respir Diaz de Arce H Isolation


id: cord-331020-lyxje82u
type: LAW
entity:
  Pathogenesis of Oviduct Lesions in Immature Chickens Following Exposure to Infectious Bronchitis Virus


id: cord-331020-lyxje82u
type: WORK_OF_ART
entity:
  The Diagnosis of Certain Avian Diseases with the Fluorescent Antibody Technique Standardization of the Fluorescent Antibody Technique for the Detection of Avian Respiratory Viruses Effects of Infectious Bronchitis in Baby Chicks Persistence of Virus in the Tissues and Development of the Oviduct in the Fowl Following Infection at Day Old with Infectious Bronchitis Virus Induction


id: cord-327000-oyg3oyx1
type: LAW
entity:
  PEDV The Accessory Protein ORF3 Contributes to Porcine Epidemic Diarrhea Virus Replication by Direct Binding


id: cord-327000-oyg3oyx1
type: WORK_OF_ART
entity:
  Localization and Effect on Type I Interferon Response of Porcine Epidemic Diarrhea Virus Nsp7 Host Factors in Coronavirus Replication Coronavirus Endoribonuclease Activity in Porcine Epidemic Diarrhea Virus


id: cord-327000-oyg3oyx1
type: CHEMICAL
entity:
  N genes Figure 1 39 40 41 The N terminal ORF1a and ORF1b encode two large replicase polyprotein precursors pp1a and pp1ab


id: cord-351567-ifoe8x28
type: WORK_OF_ART
entity:
  Camostat Mesilate Pancrelipase and Rabeprazole Combination Therapy Improves Epigastric Pain in Early Chronic Pancreatitis


id: cord-335774-15fhg8o9
type: DISEASE
entity:
  infectious to humans but incorrectly dismissed due to a lack of sequencing Conversely additional orthohantaviruses or viral


# bib

id: cord-002945-29nj4f05
title: In Vivo Characterisation of Five Strains of Bovine Viral Diarrhoea Virus 1 (Subgenotype 1c)
author: Ambrose, Rebecca K.
date: 2018-01-19
txt: ./txt/cord-002945-29nj4f05.txt
cache: ./cache/cord-002945-29nj4f05.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5874738/
doi: 10.3390/pathogens7010012
summary:
  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).

abstract:
  Bovine viral diarrhoea virus 1 (BVDV-1) is strongly associated with several important diseases of cattle, such as bovine respiratory disease, diarrhoea and haemoragic lesions. To date many subgenotypes have been reported for BVDV-1, currently ranging from subgenotype 1a to subgenotype 1u. While BVDV-1 has a world-wide distribution, the subgenotypes have a more restricted geographical distribution. As an example, BVDV-1 subgenotypes 1a and 1b are frequently detected in North America and Europe, while the subgenotype 1c is rarely detected. In contrast, BVDV-1 subgenotype 1c is by far the most commonly reported in Australia. Despite this, uneven distribution of the biological importance of the subgenotypes remains unclear. The aim of this study was to characterise the in vivo properties of five strains of BVDV-1 subgenotype 1c in cattle infection studies. No overt respiratory signs were reported in any of the infected cattle regardless of strain. Consistent with other subgenotypes, transient pyrexia and leukopenia were commonly identified, while thrombocytopenia was not. The quantity of virus detected in the nasal secretions of transiently infected animals suggested the likelihood of horizontal transmission was very low. Further studies are required to fully understand the variability and importance of the BVDV-1 subgenotype 1c.


id: cord-003767-9xbu4hnq
author: Slingenbergh, Jan
date: 2019-05-25
txt: ./txt/cord-003767-9xbu4hnq.txt
cache: ./cache/cord-003767-9xbu4hnq.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6631033/
doi: 10.3390/pathogens8020072
summary:
  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 .

title:
  Animal Virus Ecology and Evolution Are Shaped by the Virus Host-Body Infiltration and Colonization Pattern

abstract:
  The current classification of animal viruses is largely based on the virus molecular world. Less attention is given to why and how virus fitness results from the success of virus transmission. Virus transmission reflects the infection-shedding-transmission dynamics, and with it, the organ system involvement and other, macroscopic dimensions of the host environment. This study describes the transmission ecology of the world main livestock viruses, 36 in total, a mix of RNA, DNA and retroviruses. Following an iterative process, the viruses are virtually ranked in an outer- to inner-body fashion, by organ system, on ecological grounds. Also portrayed are the shifts in virus host tropism and virus genome. The synthesis of the findings reveals a predictive virus evolution framework, based on the outer- to inner-body changes in the interplay of host environment-transmission modes-organ system involvement-host cell infection cycle-virus genome. Outer-body viruses opportunistically respond to the variation in the external environment. For example, respiratory and enteric viruses tend to be associated with poultry and pig mass rearing. Ruminant and equine viruses tend to be more deep-rooted and host-specific, and also establish themselves in the vital inner-body systems. It is concluded that the framework may assist the study of new emerging viruses and pandemic risks.


id: cord-009445-p2rz81fy
author: Nabil, Nehal M.
date: 2020-03-06
txt: ./txt/cord-009445-p2rz81fy.txt
cache: ./cache/cord-009445-p2rz81fy.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7157678/
doi: 10.3390/pathogens9030196
summary:
  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] .

title:
  Wild Birds in Live Birds Markets: Potential Reservoirs of Enzootic Avian Influenza Viruses and Antimicrobial Resistant Enterobacteriaceae in Northern Egypt

abstract:
  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. Trapping of migratory birds during their resting periods at the northern coast of Egypt is a common and ancient practice performed mainly for selling in live bird markets (LBM). In the present study, samples were collected from 148 wild birds, representing 14 species, which were being offered for sale in LBM. All birds were tested for the presence of AIV and enterobacteriaceae. 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. Sequencing of the full haemagglutinin (HA) gene revealed a high similarity with currently circulating IAV in Egypt. From all the birds, E. coli was recovered from 37.2% and Salmonella from 20.2%, with 66–96% and 23–43% isolates being resistant to at least one of seven selected critically important antimicrobials (CIA), respectively. The presence of enzootic IAV and the wide prevalence of AMR enterobacteriaceae in wild birds highlight the potential role of LBM in the spread of different pathogens from and to wild birds. Continued surveillance of both AIV and antimicrobial-resistant enterobacteriaceae in wild birds’ habitats is urgently needed.


id: cord-013280-kczj24se
title: Molecular Mechanisms of Immune Escape for Foot-and-Mouth Disease Virus
author: Yang, Bo
date: 2020-09-04
txt: ./txt/cord-013280-kczj24se.txt
cache: ./cache/cord-013280-kczj24se.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7558374/
doi: 10.3390/pathogens9090729
summary:
  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 ).

abstract:
  Foot-and-mouth disease virus (FMDV) causes a highly contagious vesicular disease in cloven-hoofed livestock that results in severe consequences for international trade, posing a great economic threat to agriculture. The FMDV infection antagonizes the host immune responses via different signaling pathways to achieve immune escape. Strategies to escape the cell immune system are key to effective infection and pathogenesis. This review is focused on summarizing the recent advances to understand how the proteins encoded by FMDV antagonize the host innate and adaptive immune responses.


id: cord-013315-plptulfb
author: Tilocca, Bruno
date: 2020-08-27
txt: ./txt/cord-013315-plptulfb.txt
cache: ./cache/cord-013315-plptulfb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7558617/
doi: 10.3390/pathogens9090705
summary:
  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

title:
  Immunoinformatic-Based Prediction of Candidate Epitopes for the Diagnosis and Control of Paratuberculosis (Johne’s Disease)

abstract:
  Paratuberculosis is an infectious disease of ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP). MAP is an intracellular pathogen with a possible zoonotic potential since it has been successfully isolated from the intestine and blood of Crohn’s disease patients.Since no cure is available, after the detection of the disease, animal culling is the sole applicable containment strategy. However, the difficult detection of the disease in its subclinical form, facilitates its spread raising the need for the development of effective diagnosis and vaccination strategies. 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. These proteins were chosen according to a previously published immunoproteomics approach. 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 retrieved peptide sequences were analyzed for their specificity and cross-reactivity. The final aim is to employ the discovered peptides sequences as a filtered library useful for early-stage diagnosis and/or to be used in novel multi-subunit or recombinant vaccine formulations.


id: cord-253116-oq0bc35u
title: Correlation of Feline Coronavirus Shedding in Feces with Coronavirus Antibody Titer
author: Felten, Sandra
date: 2020-07-22
txt: ./txt/cord-253116-oq0bc35u.txt
cache: ./cache/cord-253116-oq0bc35u.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32707796/
doi: 10.3390/pathogens9080598
summary:
  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.

abstract:
  Background: Feline coronavirus (FCoV) infection is ubiquitous in multi-cat households. Responsible for the continuous presence are cats that are chronically shedding a high load of FCoV. The aim of the study was to determine a possible correlation between FCoV antibody titer and frequency and load of fecal FCoV shedding in cats from catteries. Methods: Four fecal samples from each of 82 cats originating from 19 German catteries were examined for FCoV viral loads by quantitative reverse transcriptase polymerase chain reaction (RT-qPCR). Additionally, antibody titers were determined by an immunofluorescence assay. Results: Cats with antibodies were more likely to be FCoV shedders than non-shedders, and there was a weak positive correlation between antibody titer and mean fecal virus load (Spearman r = 0.2984; p = 0.0072). Antibody titers were significantly higher if cats shed FCoV more frequently throughout the study period (p = 0.0063). When analyzing only FCoV shedders, cats that were RT-qPCR-positive in all four samples had significantly higher antibody titers (p = 0.0014) and significantly higher mean fecal virus loads (p = 0.0475) than cats that were RT-qPCR-positive in only one, two, or three samples. Conclusions: The cats’ antibody titers correlate with the likelihood and frequency of FCoV shedding and fecal virus load. Chronic shedders have higher antibody titers and shed more virus. This knowledge is important for the management of FCoV infections in multi-cat environments, but the results indicate that antibody measurement cannot replace fecal RT-qPCR.


id: cord-255339-oudj079q
author: Al-Tayib, Omar A.
date: 2019-02-22
txt: ./txt/cord-255339-oudj079q.txt
cache: ./cache/cord-255339-oudj079q.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens8010025
doi: 10.3390/pathogens8010025
summary:
  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] .

title:
  An Overview of the Most Significant Zoonotic Viral Pathogens Transmitted from Animal to Human in Saudi Arabia

abstract:
  Currently, there has been an increasing socioeconomic impact of zoonotic pathogens transmitted from animals to humans worldwide. Recently, in the Arabian Peninsula, including in Saudi Arabia, epidemiological data indicated an actual increase in the number of emerging and/or reemerging cases of several viral zoonotic diseases. Data presented in this review are very relevant because Saudi Arabia is considered the largest country in the Peninsula. We believe that zoonotic pathogens in Saudi Arabia remain an important public health problem; however, more than 10 million Muslim pilgrims from around 184 Islamic countries arrive yearly at Makkah for the Hajj season and/or for the Umrah. Therefore, for health reasons, several countries recommend vaccinations for various zoonotic diseases among preventive protocols that should be complied with before traveling to Saudi Arabia. However, there is a shortage of epidemiological data focusing on the emerging and reemerging of zoonotic pathogens transmitted from animal to humans in different densely populated cities and/or localities in Saudi Arabia. Therefore, further efforts might be needed to control the increasing impacts of zoonotic viral disease. Also, there is a need for a high collaboration to enhance the detection and determination of the prevalence, diagnosis, control, and prevention as well as intervention and reduction in outbreaks of these diseases in Saudi Arabia, particularly those from other countries. Persons in the health field including physicians and veterinarians, pet owners, pet store owners, exporters, border guards, and people involved in businesses related to animal products have adopted various preventive strategies. Some of these measures might pave the way to highly successful prevention and control results on the different transmission routes of these viral zoonotic diseases from or to Saudi Arabia. Moreover, the prevention of these viral pathogens depends on socioeconomic impacts, available data, improved diagnosis, and highly effective therapeutics or prophylaxis.


id: cord-263247-r3t4uowz
title: Lassa Fever: Viral Replication, Disease Pathogenesis, and Host Immune Modulations
author: Ly, Hinh
date: 2020-06-03
txt: ./txt/cord-263247-r3t4uowz.txt
cache: ./cache/cord-263247-r3t4uowz.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens9060437
doi: 10.3390/pathogens9060437
summary:
  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] .

abstract:
  Despite major discoveries made in the last few decades about Lassa fever, there are still many unresolved key issues that hamper the development of effective vaccines and therapies against this deadly disease that is endemic in several West African countries. Some of these issues include the lack of a detailed understanding of the viral and participating host factors in completing the virus life cycle, in mediating disease pathogenesis or protection from disease, and in activating or suppressing host innate and cellular immunity against virus infection, as well as of the animal models required for testing vaccines and therapeutics. This Special Issue is devoted to understanding some of these important issues and to exploring the current status of the research and development in combating Lassa fever.


id: cord-266145-xnu8pj24
title: COVID-19 in Somalia: Adherence to Preventive Measures and Evolution of the Disease Burden
author: Ahmed, Mohammed A. M.
date: 2020-09-06
txt: ./txt/cord-266145-xnu8pj24.txt
cache: ./cache/cord-266145-xnu8pj24.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32899931/
doi: 10.3390/pathogens9090735
summary:
  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.

abstract:
  Following the COVID-19 outbreak in Somalia, strict preventive measures were implemented by the government. We assessed adherence to the government recommendations via two consecutive online cross-sectional surveys between April and July 2020. A five-point adherence score was constructed based on self-reported observance of five preventive measures (physical distancing, face mask use, hand hygiene, mouth covering when coughing/sneezing, and avoidance of touching the face). 4124 and 4703 responses were analyzed during the first and second survey, respectively. The mean adherence score decreased from 3.54 ± 1.5 in the first survey to 3.40 ± 1.6 during the second survey; p < 0.001. More participants experienced at least one flu-like symptom during the second survey (38.2%) compared to the first (16.2%); however, the proportion of positive COVID-19 tests in the first (26.9%) and second survey (26.5%) was similar. The ordinal logistic regression model identified the following predictors for high adherence scores: female gender (odds ratio (OR) = 1.715 (1.581–1.861), p < 0.001); being a healthcare worker/student (OR = 2.180 (2.000–2.377), p < 0.001); obtaining COVID-19 information from official sources (OR = 1.460 (1.341–1.589), p < 0.001); and having postgraduate education (OR = 1.679 (1.220–2.307), p < 0.001). Conversely, obtaining COVID-19 information from social media and residing in urban settings were associated with lower adherence. Targeted and context-specific adaptations of the COVID-19 response may be required in Somalia.


id: cord-271648-m2c5bvuj
author: Ashour, Hossam M.
date: 2020-03-04
txt: ./txt/cord-271648-m2c5bvuj.txt
cache: ./cache/cord-271648-m2c5bvuj.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens9030186
doi: 10.3390/pathogens9030186
summary:
  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

title:
  Insights into the Recent 2019 Novel Coronavirus (SARS-CoV-2) in Light of Past Human Coronavirus Outbreaks

abstract:
  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. The continuous evolution of coronaviruses was further highlighted with the emergence of the Middle East Respiratory Syndrome-CoV (MERS-CoV) outbreak in 2012. Currently, the world is concerned about the 2019 novel CoV (SARS-CoV-2) that was initially identified in the city of Wuhan, China in December 2019. Patients presented with severe viral pneumonia and respiratory illness. The number of cases has been mounting since then. As of late February 2020, tens of thousands of cases and several thousand deaths have been reported in China alone, in addition to thousands of cases in other countries. Although the fatality rate of SARS-CoV-2 is currently lower than SARS-CoV, the virus seems to be highly contagious based on the number of infected cases to date. In this review, we discuss structure, genome organization, entry of CoVs into target cells, and provide insights into past and present outbreaks. The future of human CoV outbreaks will not only depend on how the viruses will evolve, but will also depend on how we develop efficient prevention and treatment strategies to deal with this continuous threat.


id: cord-272295-9sonr8or
title: Objective Olfactory Findings in Hospitalized Severe COVID-19 Patients
author: Lechien, Jerome R.
date: 2020-07-31
txt: ./txt/cord-272295-9sonr8or.txt
cache: ./cache/cord-272295-9sonr8or.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32752123/
doi: 10.3390/pathogens9080627
summary:
  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

abstract:
  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). Methods: Severe COVID-19 patients with self-reported SLS were recruited at hospitalization discharge. Epidemiological and clinical data were collected. The Sino-nasal Outcome Test-22 (SNOT-22) was used to evaluate rhinological complaints. Subjective olfactory and gustatory functions were assessed with the National Health and Nutrition Examination Survey (NHNES). Objective SLS was evaluated using psychophysical tests. 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. Results: Forty-seven patients completed the study (25 females). Subjectively, eighteen (38.3%) individuals self-reported subjective partial or total SLS. Among them, only three and four were anosmic and hyposmic, respectively (38.9%). Considering the objective evaluation in the entire cohort, the prevalence of SLS was 21.3%. Elderly patients and those with diabetes had lower objective olfactory evaluation results than young and non-diabetic individuals. Conclusions: The prevalence of SLS in severe COVID-19 patients appears to be lower than previously estimated in mild-to-moderate COVID-19 forms. Future comparative studies are needed to explore the predictive value of SLS for COVID-19 severity.


id: cord-274497-tqceazdp
author: N. Nuñez, Luis Fabian
date: 2020-07-25
txt: ./txt/cord-274497-tqceazdp.txt
cache: ./cache/cord-274497-tqceazdp.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32722416/
doi: 10.3390/pathogens9080606
summary:
  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.

title:
  Molecular Characterization and Pathogenicity of Chicken Parvovirus (ChPV) in Specific Pathogen-Free Chicks Infected Experimentally

abstract:
  Chicken parvovirus (ChPV) is an agent frequently associated with runting stunting syndrome (RSS). This syndrome has been reported in association with ChPV in many countries, including Brazil; however, studies characterizing the virus on a molecular level are scarce, and ChPV pathogenicity in day-old chicks remains unclear. The aim of the present work was to establish the molecular characteristics of ChPV, determine the pathogenicity of ChPV in SPF chicks and detect and quantify ChPV by qPCR in several tissues and chicks of different ages. The experimental challenge was performed at one day of age, and daily and weekly observations were performed and five birds from each experimental group (mock and infected birds) were euthanized to perform the different analysis. ChPV genome copies were detected and quantified by qPCR in gut, spleen, thymus, kidney, pancreas, proventriculus and bursa. Clinically, the infected group presented with diarrhea 24 h post-infection, which persisted until 42 days of age. The small intestine was distended, and its contents were aqueous and foamy. Enteritis and dilated crypts with cyst shapes were observed in intestinal segments. Acute pancreatitis associated with lymphocytic nodules, infiltrating lymphocytes and plasma cells between the pancreatic acinus was observed. Koch’s postulate was demonstrated and the genetic characterization of the VP1 gene showed that the Brazilian ChPV isolate belongs to the ChPV II group.


id: cord-288306-0chcsqe7
title: Recent Advances in the Diagnosis of Classical Swine Fever and Future Perspectives
author: Wang, Lihua
date: 2020-08-15
txt: ./txt/cord-288306-0chcsqe7.txt
cache: ./cache/cord-288306-0chcsqe7.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens9080658
doi: 10.3390/pathogens9080658
summary:
  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

abstract:
  Classical swine fever (CSF) is a highly contagious viral disease of pigs, including wild boar. It is regarded as one of the major problems in the pig industry as it is still endemic in many regions of the world and has the potential to cause devastating epidemics, particularly in countries free of the disease. Rapid and reliable diagnosis is of utmost importance in the control of CSF. Since clinical presentations of CSF are highly variable and may be confused with other viral diseases in pigs, laboratory diagnosis is indispensable for an unambiguous diagnosis. On an international level, well-established diagnostic tests 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 have been described in detail in the OIE Terrestrial Manual. However, improved CSF diagnostic methods or alternatives based on modern technologies have been developed in recent years. This review thus presents recent advances in the diagnosis of CSF and future perspectives.


id: cord-292031-weiwksh6
title: Waterborne Pathogens: Detection Methods and Challenges
author: Ramírez-Castillo, Flor Yazmín
date: 2015-05-21
txt: ./txt/cord-292031-weiwksh6.txt
cache: ./cache/cord-292031-weiwksh6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26011827/
doi: 10.3390/pathogens4020307
summary:
  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] .

abstract:
  Waterborne pathogens and related diseases are a major public health concern worldwide, not only by the morbidity and mortality that they cause, but by the high cost that represents their prevention and treatment. These diseases are directly related to environmental deterioration and pollution. Despite the continued efforts to maintain water safety, waterborne outbreaks are still reported globally. Proper assessment of pathogens on water and water quality monitoring are key factors for decision-making regarding water distribution systems’ infrastructure, the choice of best water treatment and prevention waterborne outbreaks. Powerful, sensitive and reproducible diagnostic tools are developed to monitor pathogen contamination in water and be able to detect not only cultivable pathogens but also to detect the occurrence of viable but non-culturable microorganisms as well as the presence of pathogens on biofilms. 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. This review aims to present a research outlook on waterborne outbreaks that have occurred in recent years. This review also focuses in the main molecular techniques for detection of waterborne pathogens and the use of QMRA approach to protect public health.


id: cord-293988-f5gvwjyh
title: New SARS-CoV-2 Infection Detected in an Italian Pet Cat by RT-qPCR from Deep Pharyngeal Swab
author: Musso, Nicolò
date: 2020-09-11
txt: ./txt/cord-293988-f5gvwjyh.txt
cache: ./cache/cord-293988-f5gvwjyh.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32932800/
doi: 10.3390/pathogens9090746
summary:
  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.

abstract:
  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. Despite close pet–human contact, little is known about the predisposition of pets to SARS-CoV-2. Among these, felines are the most susceptible. 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. This is the first Italian study responding to the request of the scientific community to focus attention on the possible role of pets as a viral reservoir. An important question remains unanswered: did the cat actually die due to SARS-CoV-2 infection?


id: cord-294571-qd0qjo3y
title: Molecular Aspects of COVID-19 Differential Pathogenesis
author: Rothan, Hussin A.
date: 2020-07-06
txt: ./txt/cord-294571-qd0qjo3y.txt
cache: ./cache/cord-294571-qd0qjo3y.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32640525/
doi: 10.3390/pathogens9070538
summary:
  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] .

abstract:
  In the absence of therapeutic interventions, and a possible vaccine candidate, the spread of COVID-19 disease and associated fatalities are on the rise. The high mutation frequency in the genomic material of these viruses supports their ability to adapt to new environments, resulting in an efficient alteration in tissue tropism and host range. Therefore, the coronavirus’ health threats could be relevant for the long-term. The epidemiological data indicate that age, sex, and cardio-metabolic disease have a significant impact on the spread and severity of COVID-19. In this review, we highlight recent updates on the pathogenesis of SARS-CoV-2 among men and women, including children. We also discuss the role of the cellular receptors and coreceptors used by the virus to enter host cells on differential infection among men, women, and cardio-metabolic patients.


id: cord-296419-j5rlgbl8
title: Influenza-Omics and the Host Response: Recent Advances and Future Prospects
author: Powell, Joshua D.
date: 2017-06-10
txt: ./txt/cord-296419-j5rlgbl8.txt
cache: ./cache/cord-296419-j5rlgbl8.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens6020025
doi: 10.3390/pathogens6020025
summary:
  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

abstract:
  Influenza A viruses (IAV) continually evolve and have the capacity to cause global pandemics. Because IAV represents an ongoing threat, identifying novel therapies and host innate immune factors that contribute to IAV pathogenesis is of considerable interest. This review summarizes the relevant literature as it relates to global host responses to influenza infection at both the proteome and transcriptome level. The various-omics infection systems that include but are not limited to ferrets, mice, pigs, and even the controlled infection of humans are reviewed. Discussion focuses on recent advances, remaining challenges, and knowledge gaps as it relates to influenza-omics infection outcomes.


id: cord-297469-26d8o1xk
author: Choi, Won Hyung
date: 2019-05-09
txt: ./txt/cord-297469-26d8o1xk.txt
cache: ./cache/cord-297469-26d8o1xk.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31075881/
doi: 10.3390/pathogens8020061
summary:
  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.

title:
  The Mechanism of Action of Ursolic Acid as a Potential Anti-Toxoplasmosis Agent, and Its Immunomodulatory Effects

abstract:
  This study was performed to investigate the mechanism of action of ursolic acid in terms of anti-Toxoplasma gondii effects, including immunomodulatory effects. We evaluated the anti-T. 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. gondii. The subcellular organelles and granules of T. gondii, particularly rhoptry protein 18, microneme protein 8, and inner membrane complex sub-compartment protein 3, were markedly decreased when T. gondii was treated with ursolic acid, and their expressions were effectively inhibited. 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 immune cells. These results demonstrate that ursolic acid not only causes anti-T. gondii activity/action by effectively inhibiting the survival of T. gondii and the subcellular organelles of T. gondii, but also induces specific immunomodulatory effects in T. gondii-infected immune cells. Therefore, this study indicates that ursolic acid can be effectively utilized as a potential candidate agent for developing novel anti-toxoplasmosis drugs, and has immunomodulatory activity.


id: cord-298505-r7ihqb96
title: Sepsis, Phages, and COVID-19
author: Górski, Andrzej
date: 2020-10-15
txt: ./txt/cord-298505-r7ihqb96.txt
cache: ./cache/cord-298505-r7ihqb96.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33076482/
doi: 10.3390/pathogens9100844
summary:
  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) .

abstract:
  Phage therapy has emerged as a potential novel treatment of sepsis for which no decisive progress has been achieved thus far. Obviously, phages can help eradicate local bacterial infection and bacteremia that may occur in a syndrome. For example, phages may be helpful in correcting excessive inflammatory responses and aberrant immunity that occur in sepsis. Data from animal studies strongly suggest that phages may indeed be an efficient means of therapy for experimentally induced sepsis. In recent years, a number of reports have appeared describing the successful treatment of patients with sepsis. Moreover, novel data on the anti-viral potential of phages may be interpreted as suggesting that phages could be used as an adjunct therapy in severe COVID-19. Thus, clinical trials assessing the value of phage therapy in sepsis, including viral sepsis, are urgently needed.


id: cord-298862-8bijio30
title: Buffalopox Virus: An Emerging Virus in Livestock and Humans
author: Eltom, Kamal H.
date: 2020-08-20
txt: ./txt/cord-298862-8bijio30.txt
cache: ./cache/cord-298862-8bijio30.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens9090676
doi: 10.3390/pathogens9090676
summary:
  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

abstract:
  Buffalopox virus (BPXV) is the cause of buffalopox, which was recognized by the FAO/WHO Joint Expert Committee on Zoonosis as an important zoonotic disease. 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. BPXV is a member of the genus Orthopoxvirus and a close variant of the vaccinia virus (VACV). Recent genome data show that BPXV shares a most recent common ancestor of VACV Lister strain, which had been used for inoculating buffalo calves to produce a Smallpox vaccine. 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. Together with the current pandemic of SARS-COV2/COVID 19, BPXV infections illustrate how vulnerable the human population is to the emergence and re-emergence of viral pathogens from unsuspected sources. In view that majority of the world population are not vaccinated against smallpox and are most vulnerable in the event of its re-emergence, reviewing and understanding the biology of vaccinia-like viruses are necessary for developing a new generation of safer smallpox vaccines in the smallpox-free world.


id: cord-302161-ytr7ds8i
author: Lutz, Mirjam
date: 2020-07-24
txt: ./txt/cord-302161-ytr7ds8i.txt
cache: ./cache/cord-302161-ytr7ds8i.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens9080603
doi: 10.3390/pathogens9080603
summary:
  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.

title:
  FCoV Viral Sequences of Systemically Infected Healthy Cats Lack Gene Mutations Previously Linked to the Development of FIP

abstract:
  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. The aim of the present study was to determine whether FCoV detected in organs of experimentally FCoV infected healthy cats carry some of these mutations. Viral RNA isolated from different tissues of seven asymptomatic cats infected with the field strains FCoV Zu1 or FCoV Zu3 was sequenced. Deletions in the 3c gene and mutations in the 7b and S genes that have been shown to have implications for the development of FIP were not detected, suggesting that these are not essential for systemic viral dissemination. However, deletions and single nucleotide polymorphisms leading to truncations were detected in all nonstructural proteins. These were found across all analyzed ORFs, but with significantly higher frequency in ORF 7b than ORF 3a. Additionally, a previously unknown homologous recombination site was detected in FCoV Zu1.


id: cord-309147-c3ikb81g
title: Origin, Potential Therapeutic Targets and Treatment for Coronavirus Disease (COVID-19)
author: Nadeem, Muhammad Shahid
date: 2020-04-22
txt: ./txt/cord-309147-c3ikb81g.txt
cache: ./cache/cord-309147-c3ikb81g.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32331255/
doi: 10.3390/pathogens9040307
summary:
  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

abstract:
  The ongoing episode of coronavirus disease 19 (COVID-19) has imposed a serious threat to global health and the world economy. The disease has rapidly acquired a pandemic status affecting almost all populated areas of the planet. The causative agent of COVID-19 is a novel coronavirus known as SARS-CoV-2. The virus has an approximate 30 kb single-stranded positive-sense RNA genome, which is 74.5% to 99% identical to that of SARS-CoV, CoV-pangolin, and the coronavirus the from horseshoe bat. 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 serine protease inhibitors, spike protein-based vaccines, or ACE2 blockers may have therapeutic potential in the near future. At present, no vaccine is available against COVID-19. The disease is being treated with antiviral, antimalarial, anti-inflammatory, herbal medicines, and active plasma antibodies. In this context, the present review article provides a cumulative account of the recent information regarding the viral characteristics, potential therapeutic targets, treatment options, and prospective research questions.


id: cord-309381-cb80ntxs
title: Host Single Nucleotide Polymorphisms Modulating Influenza A Virus Disease in Humans
author: Nogales, Aitor
date: 2019-09-30
txt: ./txt/cord-309381-cb80ntxs.txt
cache: ./cache/cord-309381-cb80ntxs.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens8040168
doi: 10.3390/pathogens8040168
summary:
  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] .

abstract:
  A large number of human genes associated with viral infections contain single nucleotide polymorphisms (SNPs), which represent a genetic variation caused by the change of a single nucleotide in the DNA sequence. SNPs are located in coding or non-coding genomic regions and can affect gene expression or protein function by different mechanisms. Furthermore, they have been linked to multiple human diseases, highlighting their medical relevance. Therefore, the identification and analysis of this kind of polymorphisms in the human genome has gained high importance in the research community, and an increasing number of studies have been published during the last years. As a consequence of this exhaustive exploration, an association between the presence of some specific SNPs and the susceptibility or severity of many infectious diseases in some risk population groups has been found. In this review, we discuss the relevance of SNPs that are important to understand the pathology derived from influenza A virus (IAV) infections in humans and the susceptibility of some individuals to suffer more severe symptoms. We also discuss the importance of SNPs for IAV vaccine effectiveness.


id: cord-314825-fzba05wn
author: Chauhan, Ravendra P.
date: 2020-05-08
txt: ./txt/cord-314825-fzba05wn.txt
cache: ./cache/cord-314825-fzba05wn.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32397138/
doi: 10.3390/pathogens9050355
title:
  A Systematic Review Analyzing the Prevalence and Circulation of Influenza Viruses in Swine Population Worldwide

abstract:
  The global anxiety and a significant threat to public health due to the current COVID-19 pandemic reiterate the need for active surveillance for the zoonotic virus diseases of pandemic potential. Influenza virus due to its wide host range and zoonotic potential poses such a significant threat to public health. Swine serve as a “mixing vessel” for influenza virus reassortment and evolution which as a result may facilitate the emergence of new strains or subtypes of zoonotic potential. In this context, the currently available scientific data hold a high significance to unravel influenza virus epidemiology and evolution. With this objective, the current systematic review summarizes the original research articles and case reports of all the four types of influenza viruses reported in swine populations worldwide. A total of 281 articles were found eligible through screening of PubMed and Google Scholar databases and hence were included in this systematic review. The highest number of research articles (n = 107) were reported from Asia, followed by Americas (n = 97), Europe (n = 55), Africa (n = 18), and Australia (n = 4). The H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses were the most common influenza A virus subtypes reported in swine in most countries across the globe, however, few strains of influenza B, C, and D viruses were also reported in certain countries. Multiple reports of the avian influenza virus strains documented in the last two decades in swine in China, the United States, Canada, South Korea, Nigeria, and Egypt provided the evidence of interspecies transmission of influenza viruses from birds to swine. Inter-species transmission of equine influenza virus H3N8 from horse to swine in China expanded the genetic diversity of swine influenza viruses. Additionally, numerous reports of the double and triple-reassortant strains which emerged due to reassortments among avian, human, and swine strains within swine further increased the genetic diversity of swine influenza viruses. These findings are alarming hence active surveillance should be in place to prevent future influenza pandemics.


id: cord-319799-h9kot3og
title: Epigenetic Landscape during Coronavirus Infection
author: Schäfer, Alexandra
date: 2017-02-15
txt: ./txt/cord-319799-h9kot3og.txt
cache: ./cache/cord-319799-h9kot3og.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28212305/
doi: 10.3390/pathogens6010008
summary:
  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.

abstract:
  Coronaviruses (CoV) comprise a large group of emerging human and animal pathogens, including the highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) strains. The molecular mechanisms regulating emerging coronavirus pathogenesis are complex and include virus–host interactions associated with entry, replication, egress and innate immune control. Epigenetics research investigates the genetic and non-genetic factors that regulate phenotypic variation, usually caused by external and environmental factors that alter host expression patterns and performance without any change in the underlying genotype. Epigenetic modifications, such as histone modifications, DNA methylation, chromatin remodeling, and non-coding RNAs, function as important regulators that remodel host chromatin, altering host expression patterns and networks in a highly flexible manner. For most of the past two and a half decades, research has focused on the molecular mechanisms by which RNA viruses antagonize the signaling and sensing components that regulate induction of the host innate immune and antiviral defense programs upon infection. More recently, a growing body of evidence supports the hypothesis that viruses, even lytic RNA viruses that replicate in the cytoplasm, have developed intricate, highly evolved, and well-coordinated processes that are designed to regulate the host epigenome, and control host innate immune antiviral defense processes, thereby promoting robust virus replication and pathogenesis. In this article, we discuss the strategies that are used to evaluate the mechanisms by which viruses regulate the host epigenome, especially focusing on highly pathogenic respiratory RNA virus infections as a model. 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.


id: cord-322317-wsagoy52
author: Stranieri, Angelica
date: 2020-10-18
txt: ./txt/cord-322317-wsagoy52.txt
cache: ./cache/cord-322317-wsagoy52.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33081040/
doi: 10.3390/pathogens9100852
summary:
  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.

title:
  Concordance between Histology, Immunohistochemistry, and RT-PCR in the Diagnosis of Feline Infectious Peritonitis

abstract:
  Histology, immunohistochemistry (IHC), and reverse transcription polymerase chain reaction (RT-PCR) have been used to diagnose feline infectious peritonitis (FIP), but no information regarding the comparison of their diagnostic performances on the same organ is available. The aims of this study were to determine the concordance among these tests and to evaluate which combination of tests and organs can be used in vivo. 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. Sensitivity, specificity, predictive values, likelihood ratios, and concordance were calculated. IHC and RT-nPCR had the highest concordance in lung and liver, histology and IHC in the other organs. The sensitivity of histology, IHC, and RT-nPCR on the different organs ranged from 41.7 to 76.9%, 46.2 to 76.9%, and 64.3 to 85.7%, respectively, and their specificity ranged from 83.3 to 100.0%, 100% and 83.3 to 100.0%. Therefore, IHC is recommended when histology is consistent with FIP. If RT-nPCR is performed as the first diagnostic approach, results should always be confirmed with IHC. Lung or liver provide accurate information regardless of the method, while IHC is preferred to RT-nPCR to confirm FIP in the kidney or intestine.


id: cord-322807-b24ujorz
title: Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment
author: Koyama, Takahiko
date: 2020-04-26
txt: ./txt/cord-322807-b24ujorz.txt
cache: ./cache/cord-322807-b24ujorz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32357545/
doi: 10.3390/pathogens9050324
summary:
  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] .

abstract:
  New coronavirus (SARS-CoV-2) treatments and vaccines are under development to combat COVID-19. Several approaches are being used by scientists for investigation, including (1) various small molecule approaches targeting RNA polymerase, 3C-like protease, and RNA endonuclease; and (2) exploration of antibodies obtained from convalescent plasma from patients who have recovered from COVID-19. 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. As the disease has grown to become a pandemic, B-cell and T-cell epitopes predicted from SARS coronavirus have been reported. Using the epitope information along with variants of the virus, we have found several variants which might cause drifts. Among such variants, 23403A>G variant (p.D614G) in spike protein B-cell epitope is observed frequently in European countries, such as the Netherlands, Switzerland, and France, but seldom observed in China.


id: cord-323380-hm9wd817
author: Helmy, Yosra A.
date: 2017-07-21
txt: ./txt/cord-323380-hm9wd817.txt
cache: ./cache/cord-323380-hm9wd817.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens6030033
doi: 10.3390/pathogens6030033
summary:
  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.

title:
  A Comprehensive Review of Common Bacterial, Parasitic and Viral Zoonoses at the Human-Animal Interface in Egypt

abstract:
  Egypt has a unique geographical location connecting the three old-world continents Africa, Asia and Europe. It is the country with the highest population density in the Middle East, Northern Africa and the Mediterranean basin. 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. There is a gap of knowledge conerning the epidemiology of zoonotic diseases at the human-animal interface in different localities in Egypt. Some zoonotic agents are “exotic” for Egypt (e.g., MERS-CoV and Crimean-Congo hemorrhagic fever virus), others are endemic (e.g., Brucellosis, Schistosomiasis and Avian influenza). Transboundary transmission of emerging pathogens from and to Egypt occurred via different routes, mainly importation/exportation of apparently healthy animals or migratory birds. Control of the infectious agents and multidrug resistant bacteria in the veterinary sector is on the frontline for infection control in humans. The implementation of control programs significantly decreased the prevalence of some zoonoses, such as schistosomiasis and fascioliasis, in some localities within the country. Sustainable awareness, education and training targeting groups at high risk (veterinarians, farmers, abattoir workers, nurses, etc.) are important to lessen the burden of zoonotic diseases among Egyptians. There is an urgent need for collaborative surveillance and intervention plans for the control of these diseases in Egypt.


id: cord-327000-oyg3oyx1
title: Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response
author: Li, Shasha
date: 2020-05-11
txt: ./txt/cord-327000-oyg3oyx1.txt
cache: ./cache/cord-327000-oyg3oyx1.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens9050367
doi: 10.3390/pathogens9050367
summary:
  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.

abstract:
  Porcine epidemic diarrhea virus (PEDV), a swine enteropathogenic coronavirus (CoV), is the causative agent of porcine epidemic diarrhea (PED). PED causes lethal watery diarrhea in piglets, which has led to substantial economic losses in many countries and is a great threat to the global swine industry. Interferons (IFNs) are major cytokines involved in host innate immune defense, which induce the expression of a broad range of antiviral effectors that help host to control and antagonize viral infections. PEDV infection does not elicit a robust IFN response, and some of the mechanisms used by the virus to counteract the host innate immune response have been unraveled. PEDV evades the host innate immune response by two main strategies including: 1) encoding IFN antagonists to disrupt innate immune pathway, and 2) hiding its viral RNA to avoid the exposure of viral RNA to immune sensors. 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.


id: cord-328395-2cakgmsj
title: Endothelial Cell Contributions to COVID-19
author: Oxford, Alexandra E.
date: 2020-09-25
txt: ./txt/cord-328395-2cakgmsj.txt
cache: ./cache/cord-328395-2cakgmsj.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens9100785
doi: 10.3390/pathogens9100785
summary:
  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] .

abstract:
  Understanding of the clinical, histological and molecular features of the novel coronavirus 2019 (Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)) has remained elusive. Coronavirus disease 2019 (COVID-19) caused by this virus has unusual clinical presentation with regard to other related coronaviruses. 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. Likewise, mounting evidence associates vascular and endothelial cell dysfunction with increased mortality. This review focuses on understanding how endothelial cell pathology is caused by SARS-CoV-2 at the molecular and cellular levels and how these events relate to COVID-19. A detailed examination of current knowledge regarding canonical inflammatory reaction pathways as well as alteration of endothelial cell-derived exosomes and transdifferentiation by SARS-CoV-2 is included in this assessment. Additionally, given an understanding of endothelial contributions to COVID-19, potential therapeutic aims are discussed, particularly as would affect endothelial function and pathology.


id: cord-330827-gu2mt6zp
title: Emergence of Novel Coronavirus 2019-nCoV: Need for Rapid Vaccine and Biologics Development
author: Shanmugaraj, Balamurugan
date: 2020-02-22
txt: ./txt/cord-330827-gu2mt6zp.txt
cache: ./cache/cord-330827-gu2mt6zp.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens9020148
doi: 10.3390/pathogens9020148
summary:
  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.

abstract:
  Novel Coronavirus (2019-nCoV) is an emerging pathogen that was first identified in Wuhan, China in late December 2019. This virus is responsible for the ongoing outbreak that causes severe respiratory illness and pneumonia-like infection in humans. Due to the increasing number of cases in China and outside China, the WHO declared coronavirus as a global health emergency. Nearly 35,000 cases were reported and at least 24 other countries or territories have reported coronavirus cases as early on as February. Inter-human transmission was reported in a few countries, including the United States. Neither an effective anti-viral nor a vaccine is currently available to treat this infection. As the virus is a newly emerging pathogen, many questions remain unanswered regarding the virus’s reservoirs, pathogenesis, transmissibility, and much more is unknown. The collaborative efforts of researchers are needed to fill the knowledge gaps about this new virus, to develop the proper diagnostic tools, and effective treatment to combat this infection. Recent advancements in plant biotechnology proved that plants have the ability to produce vaccines or biopharmaceuticals rapidly in a short time. In this review, the outbreak of 2019-nCoV in China, the need for rapid vaccine development, and the potential of a plant system for biopharmaceutical development are discussed.


id: cord-331020-lyxje82u
author: M. Najimudeen, Shahnas
date: 2020-09-24
txt: ./txt/cord-331020-lyxje82u.txt
cache: ./cache/cord-331020-lyxje82u.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens9100779
doi: 10.3390/pathogens9100779
summary:
  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] .

title:
  Infectious Bronchitis Coronavirus Infection in Chickens: Multiple System Disease with Immune Suppression

abstract:
  In the early 1930s, infectious bronchitis (IB) was first characterized as a respiratory disease in young chickens; later, the disease was also described in older chickens. The etiology of IB was confirmed later as being due to a coronavirus: the infectious bronchitis virus (IBV). Being a coronavirus, IBV is subject to constant genome change due to mutation and recombination, with the consequence of changing clinical and pathological manifestations. The potential use of live attenuated vaccines for the control of IBV infection was demonstrated in the early 1950s, but vaccine breaks occurred due to the emergence of new IBV serotypes. Over the years, various IBV genotypes associated with reproductive, renal, gastrointestinal, muscular and immunosuppressive manifestations have emerged. IBV causes considerable economic impacts on global poultry production due to its pathogenesis involving multiple body systems and immune suppression; hence, there is a need to better understand the pathogenesis of infection and the immune response in order to help developing better management strategies. 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.


id: cord-331022-tek4u751
title: Immune Response to COVID-19: Can We Benefit from the SARS-CoV and MERS-CoV Pandemic Experience?
author: Sinderewicz, Emilia
date: 2020-09-09
txt: ./txt/cord-331022-tek4u751.txt
cache: ./cache/cord-331022-tek4u751.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens9090739
doi: 10.3390/pathogens9090739
summary:
  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] .

abstract:
  The global range and high fatality rate of the newest human coronavirus (HCoV) pandemic has made SARS-CoV-2 the focus of the scientific world. Next-generation sequencing of the viral genome and a phylogenetic analysis have shown the high homology of SARS-CoV-2 to other HCoVs that have led to local epidemics in the past. The experience acquired in SARS and MERS epidemics may prove useful in understanding the SARS-CoV-2 pathomechanism and lead to effective treatment and potential vaccine development. This study summarizes the immune response to SARS-CoV, MERS-CoV, and SARS-CoV-2 and focuses on T cell response, humoral immunity, and complement system activation in different stages of HCoVs infections. 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. The role of interferons in the therapy of these infections is also discussed. 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.


id: cord-334907-l4jjb93l
title: Interaction of the Amino-Terminal Domain of the ISAV Fusion Protein with a Cognate Cell Receptor
author: Ojeda, Nicolás
date: 2020-05-27
txt: ./txt/cord-334907-l4jjb93l.txt
cache: ./cache/cord-334907-l4jjb93l.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32471165/
doi: 10.3390/pathogens9060416
summary:
  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.

abstract:
  The infectious salmon anemia virus (ISAV), etiological agent of the disease by the same name, causes major losses to the salmon industry. Classified as a member of the Orthomyxoviridae family, ISAV is characterized by the presence of two surface glycoproteins termed hemagglutinin esterase (HE) and fusion protein (F), both of them directly involved in the initial interaction of the virus with the target cell. HE mediates receptor binding and destruction, while F promotes the fusion process of the viral and cell membranes. The carboxy-terminal end of F (F(2)) possesses canonical structural characteristics of a type I fusion protein, while no functional properties have been proposed for the amino-terminal (F(1)) region. In this report, based on in silico modeling, we propose a tertiary structure for the F(1) region, which resembles a sialic acid binding domain. Furthermore, using recombinant forms of both HE and F proteins and an in vitro model system, we demonstrate the interaction of F with a cell receptor, the hydrolysis of this receptor by the HE esterase, and a crucial role for F(1) in the fusion mechanism. Our interpretation is that binding of F to its cell receptor is fundamental for membrane fusion and that the esterase in HE modulates this interaction.


id: cord-335774-15fhg8o9
title: Ecology of Neglected Rodent-Borne American Orthohantaviruses
author: Mull, Nathaniel
date: 2020-04-26
txt: ./txt/cord-335774-15fhg8o9.txt
cache: ./cache/cord-335774-15fhg8o9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32357540/
doi: 10.3390/pathogens9050325
summary:
  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.

abstract:
  The number of documented American orthohantaviruses has increased significantly over recent decades, but most fundamental research has remained focused on just two of them: Andes virus (ANDV) and Sin Nombre virus (SNV). The majority of American orthohantaviruses are known to cause disease in humans, and most of these pathogenic strains were not described prior to human cases, indicating the importance of understanding all members of the virus clade. In this review, we summarize information on the ecology of under-studied rodent-borne American orthohantaviruses to form general conclusions and highlight important gaps in knowledge. 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. Additionally, few studies have investigated the mechanisms underlying transmission routes and factors affecting the environmental persistence of orthohantaviruses, limiting our understanding of factors driving prevalence fluctuations. As landscapes continue to change, host ranges and human exposure to orthohantaviruses likely will as well. Research on the ecology of neglected orthohantaviruses is necessary for understanding both current and future threats to human health.


id: cord-337259-b12fp75d
author: Segura, Mariela
date: 2020-05-14
txt: ./txt/cord-337259-b12fp75d.txt
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url: https://doi.org/10.3390/pathogens9050374
doi: 10.3390/pathogens9050374
summary:
  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

title:
  Update on Streptococcus suis Research and Prevention in the Era of Antimicrobial Restriction: 4th International Workshop on S. suis †

abstract:
  Streptococcus suis is a swine pathogen and a zoonotic agent afflicting people in close contact with infected pigs or pork meat. Sporadic cases of human infections have been reported worldwide. In addition, S. suis outbreaks emerged in Asia, making this bacterium a primary health concern in this part of the globe. In pigs, S. suis disease results in decreased performance and increased mortality, which have a significant economic impact on swine production worldwide. Facing the new regulations in preventive use of antimicrobials in livestock and lack of effective vaccines, control of S. suis infections is worrisome. Increasing and sharing of knowledge on this pathogen is of utmost importance. As such, the pathogenesis and epidemiology of the infection, antimicrobial resistance, progress on diagnosis, prevention, and control were among the topics discussed during the 4th International Workshop on Streptococcus suis (held in Montreal, Canada, June 2019). This review gathers together recent findings on this important pathogen from lectures performed by lead researchers from several countries including Australia, Canada, France, Germany, Japan, Spain, Thailand, The Netherlands, UK, and USA. Finally, policies and recommendations for the manufacture, quality control, and use of inactivated autogenous vaccines are addressed to advance this important field in veterinary medicine.


id: cord-342921-lpn6cqz3
title: Full Genomic Characterization of a Saffold Virus Isolated in Peru
author: Leguia, Mariana
date: 2015-11-20
txt: ./txt/cord-342921-lpn6cqz3.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26610576/
doi: 10.3390/pathogens4040816
summary:
  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.

abstract:
  While studying respiratory infections of unknown etiology we detected Saffold virus in an oropharyngeal swab collected from a two-year-old female suffering from diarrhea and respiratory illness. The full viral genome recovered by deep sequencing showed 98% identity to a previously described Saffold strain isolated in Japan. Phylogenetic analysis confirmed the Peruvian Saffold strain belongs to genotype 3 and is most closely related to strains that have circulated in Asia. This is the first documented case report of Saffold virus in Peru and the only complete genomic characterization of a Saffold-3 isolate from the Americas.


id: cord-350423-yaeduwvb
title: Viral Interactions with PDZ Domain-Containing Proteins—An Oncogenic Trait?
author: James, Claire D.
date: 2016-01-18
txt: ./txt/cord-350423-yaeduwvb.txt
cache: ./cache/cord-350423-yaeduwvb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26797638/
doi: 10.3390/pathogens5010008
summary:
  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] .

abstract:
  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. In many cases (but not always), the viruses have evolved to bind the PDZ domains using the same short linear peptide motifs found in host protein-PDZ interactions, and in some cases regulate the interactions in a similar fashion by phosphorylation. What is striking is that the diverse viruses target a common subset of PDZ proteins that are intimately involved in controlling cell polarity and the structure and function of intercellular junctions, including tight junctions. Cell polarity is fundamental to the control of cell proliferation and cell survival and disruption of polarity and the signal transduction pathways involved is a key event in tumourigenesis. This review focuses on the oncogenic viruses and the role of targeting PDZ proteins in the virus life cycle and the contribution of virus-PDZ protein interactions to virus-mediated oncogenesis. We highlight how many of the viral associations with PDZ proteins lead to deregulation of PI3K/AKT signalling, benefitting virus replication but as a consequence also contributing to oncogenesis.


id: cord-351567-ifoe8x28
title: SARS-CoV-2 and Coronavirus Disease 2019: What We Know So Far
author: Rabi, Firas A.
date: 2020-03-20
txt: ./txt/cord-351567-ifoe8x28.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens9030231
doi: 10.3390/pathogens9030231
summary:
  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

abstract:
  In December 2019, a cluster of fatal pneumonia cases presented in Wuhan, China. They were caused by a previously unknown coronavirus. All patients had been associated with the Wuhan Wholefood market, where seafood and live animals are sold. The virus spread rapidly and public health authorities in China initiated a containment effort. 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. Based on clinical criteria and available serological and molecular information, the new disease was called coronavirus disease of 2019 (COVID-19), and the novel coronavirus was called SARS Coronavirus-2 (SARS-CoV-2), emphasizing its close relationship to the 2002 SARS virus (SARS-CoV). The scientific community raced to uncover the origin of the virus, understand the pathogenesis of the disease, develop treatment options, define the risk factors, and work on vaccine development. Here we present a summary of current knowledge regarding the novel coronavirus and the disease it causes.


id: cord-355788-6hteott0
title: Newcastle Disease Virus as a Vaccine Vector for SARS-CoV-2
author: Shirvani, Edris
date: 2020-07-29
txt: ./txt/cord-355788-6hteott0.txt
cache: ./cache/cord-355788-6hteott0.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens9080619
doi: 10.3390/pathogens9080619
summary:
  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

abstract:
  The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 16 million infections and more than 600,000 deaths worldwide. There is an urgent need to develop a safe and effective vaccine against SARS-CoV-2. Currently, several strategies are being pursued to develop a safe and effective SARS-CoV-2 vaccine. However, each vaccine strategy has distinct advantages and disadvantages. Therefore, it is important to evaluate multiple vaccine platforms to select the most efficient vaccine platform for SARS-CoV-2. 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. Here, we elaborate on the idea of considering NDV as a vaccine vector for SARS-CoV-2.


