# ent

id: cord-267168-qjktnnn6
type: DNA
entity:
  LongAmp Taq DNA Polymeranse 2 5 U dNTP mix 0 33 mM 1 LongAmp Taq Reaction buffer New England BioLabs M0323S Ipswich MA USA 0 4 μM


id: cord-267168-qjktnnn6
type: DNA
entity:
  Klenow Fragment 3 5 exo Thermo Fisher Scientific Waltham MA USA KAPA HyperPlus Library Prep kit KAPA Biosystems Roche Sequencing Pleasanton CA USA


id: cord-267168-qjktnnn6
type: LAW
entity:
  A Language and Environment for Statistical Computing R Foundation for Statistical Computing Exploring


id: cord-267168-qjktnnn6
type: ORG
entity:
  the Swedish Kennel Club Research Foundation Jan Skogborgs Foundation Sveland Foundation for Animal Health and Welfare MSD Animal Health


id: cord-331237-t3z1hbox
type: WORK_OF_ART
entity:
  Investigating the Role of Bats in Emerging Zoonoses Balancing Ecology Conservation and Public Health Interests Leptospirosis


id: cord-257584-v38tjof3
type: DNA
entity:
  human coronaviruses human coronavirus NL63 HCoV NL63 human coronavirus 229E HCoV 229E human coronavirus OC43 HCoV OC43


id: cord-257584-v38tjof3
type: DISEASE
entity:
  coronaviruses human coronavirus NL63 HCoV NL63 human coronavirus 229E HCoV 229E human coronavirus OC43 HCoV OC43


id: cord-267136-1abp6oom
type: PROTEIN
entity:
  Urbani CUHK W1 TOR2 HKU 39849 BJ01 BJ02 BJ03 BJ04 GD01 TW1 TWC SIN2774 SIN2748 SIN2679 SIN2677 SIN2500 HSR1 CUHK Su10 Frankfurt1


id: cord-318625-hf7fgtnp
type: PROTEIN
entity:
  membrane fusion Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion Structural


id: cord-318625-hf7fgtnp
type: PROTEIN
entity:
  PDB ID 6VSB 5 249 261 13 LTPGDSSSGWTAG 6 278 287 10 KYNENGTITD 7 314 325 12 QTSNFRVQPTES 8 407 428 22 VRQIAPGQTGKIADYNYKLPDD 9 437 450 14 NSNNLDSKVGGNYN 10 461 485 25 LKPFERDISTEIYQAGSTPCNGVEG 11 493 506 14 QSYGFQPTNGVGYQ 12 521 533 13 PATVCGPKKSTNL 13 567 581 15 RDIADTTDAVRDPQT 14 597 607 11 VITPGTNTSNQ 15 625 648 24 HADQLTPTWRVYSTGSNVFQTRAG 16 654 661 8 EHVNNSYE 17 673 691 19 SYQTQTNSPRRARSVASQS 18 700 713 16 GAENSVAYSNNSIA 19 768 780 13 TGIAVEQDKNTQE 20 788 799 14 IYKTPPIKDFGG 21 805 816 12 ILPDPSKPSKRS 22 1134 1150 17 NNTVYDPLQPELDSFKE 23 1153 1171 19 DKYFKNHTSPDVDLGDISG 24 1255 1267 13 KFDEDDSEPVLKG


id: cord-318625-hf7fgtnp
type: ORG
entity:
  Structure Function and Evolution of Coronavirus Spike Proteins Peptide Vaccine Progress and Challenges Peptide


id: cord-259925-g28sx9qu
type: PROTEIN
entity:
  interleukins IL 1β IL1RA IL2 IL4 IL5 IL6 IL7 IL8 IL9 IL10 IL12p70 IL13 IL15 IL17A eotaxin basic fibroblast growth factor FGF2 granulocyte colony stimulating factor GCSF granulocytemacrophage colony stimulating factor GMCSF Interferon gamma IFNγ IFN


id: cord-259925-g28sx9qu
type: DNA
entity:
  protein 16 IL 1βInterleukin 1β ACE2Angiotensin converting enzyme 2 FGF2Basic fibroblast growth factor 2


id: cord-259925-g28sx9qu
type: GGP
entity:
  interleukins IL 1β IL1RA IL2 IL4 IL5 IL6 IL7 IL8 IL9 IL10 IL12p70 IL13 IL15 IL17A eotaxin basic fibroblast growth factor FGF2 granulocyte


id: cord-299989-p59u6qa0
type: CELL_LINE
entity:
  CESC cervical squamous cell carcinoma and endocervical adenocarcinoma COAD colon adenocarcinoma ESCA esophageal carcinoma HNSC head and neck squamous cell carcinoma LIHC liver hepatocellular carcinoma READ rectum adenocarcinoma STAD stomach adenocarcinoma


id: cord-279202-iyteg4h9
type: DNA
entity:
  F1F 5 0 ATT CAT ATG GCA CGA ATC CTA AAC C 3 0 and F1R 5 0 ATT AAG CTT ACC CAA ATT GCG TGA CCT GC 3 0


id: cord-268480-fd5xi4q1
type: GGP
entity:
  P 26 VP6 I 21 VP1 R 19 VP2 C 19 VP3 M 30 NSP1 A 21 NSP2 N 21 NSP3 T 27 NSP4 E and 21 NSP5 6 H genotypes


id: cord-268968-0s6e6y8s
type: TAXON
entity:
  virus human rhinovirus adenovirus human coronavirus human bocavirus human enterovirus parainfluenza virus


id: cord-271897-9oqzsd70
type: DNA
entity:
  Swedish National Veterinary Institute SVA Uppsala Sweden four subsequent virus strains 80 1989 162 1997 255 1997 and G225 2017


id: cord-278465-tjjkz16y
type: WORK_OF_ART
entity:
  A Language and Environment for Statistical Computing R Foundtation for Statistical Computing Genetic


id: cord-278465-tjjkz16y
type: DISEASE
entity:
  zoonotic Woolhouse and Gowtage Sequeria 2005 and it is in environments where humans are in close proximity


id: cord-299827-lxyo3z3u
type: DNA
entity:
  grant Calicivirus nei carnivori e nell uomo caratterizzazione molecolare epidemiologia implicazioni zoonosiche PRIN 2008 20084F4P7X_003


id: cord-302679-wytog9cv
type: GGP
entity:
  HIV HCV HBV SARS coronaviruses 17 18 27 After a successful clinical trial the siRNA based drug Onpatrro


id: cord-302679-wytog9cv
type: WORK_OF_ART
entity:
  Adenovirus Epidemiology Global Spread of Novel Serotypes and Advances in Treatment and Prevention Genomic


id: cord-318577-04jsj9sb
type: CHEMICAL
entity:
  Norwalk like virus genes in the caecum contents of pigs Pet dogs a transmission route for human noroviruses Molecular characterization and pathogenicity of a genogroup GVI feline norovirus Complete genome sequences of novel canine


id: cord-339259-4oi7slk9
type: ORG
entity:
  the National Laboratory for Veterinary Quality Control on Poultry Production NLQP Ministry of Agriculture


id: cord-279495-zxerb7de
type: CELL_LINE
entity:
  China High frequency RNA recombination of murine coronaviruses The molecular biology of coronaviruses Isolation and characterization of a novel antigenic subtype of infectious bronchitis virus serotype DE072 Stem loop III


id: cord-279495-zxerb7de
type: ORG
entity:
  the International Committee on Taxonomy of Viruses International Union of Microbiological Societies Virology Division Molecular


id: cord-262592-0rdiosxd
type: DNA
entity:
  KU253323 KU253349 stool sample 3142 region 1 KU253350 KU253362 stool sample 3210 region 2 KU253363 KU253375 stool sample 3213 region 1


id: cord-262592-0rdiosxd
type: DISEASE
entity:
  acutely infected with NoV GII 4 to amplify by RT PCR a 386 base region encompassing nucleotides 1 to 386 of the VP1 gene reference sequence GenBank JX459908


id: cord-325679-4lfpy84d
type: CHEMICAL
entity:
  Aichivirus D kagovirus 1 Aichivirus E rabbit kobuvirus and Aichivirus F bat kobuvirus respectively Adams


id: cord-311144-tumtzad8
type: GGP
entity:
  Evol DOI 10 1016 j meegid 2020 104557 sha f450f1ed036685aef5a2de67cdbf11a8b3caa429 doc_id 311144 cord_uid tumtzad8 SARS CoV 2


id: cord-265329-bsypo08l
type: DNA
entity:
  sixth 1899 1923 and seventh El Tor cholera pandemic 1961 1962 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975


# bib

id: cord-252441-190jmgcq
author: Liu, Yong-sheng
date: 2011-03-05
txt: ./txt/cord-252441-190jmgcq.txt
cache: ./cache/cord-252441-190jmgcq.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1567134811000608
doi: 10.1016/j.meegid.2011.02.018
summary:
  To give a new perspective on the evolutionary characteristics shaping the genetic diversity of enterovirus 71 (EV71) and the effects of natural selection from its host on the codon usage pattern of the virus, the relative synonymous codon usage (RSCU) values, codon usage bias (CUB) values, effective number of codons (ENCs) values and nucleotide contents were calculated to implement a comparative analysis to evaluate the dynamics of the virus evolution. Although it is known that compositional constraints and translation selection are the more generally accepted mechanisms accounting for codon usage bias (Coleman To give a new perspective on the evolutionary characteristics shaping the genetic diversity of enterovirus 71 (EV71) and the effects of natural selection from its host on the codon usage pattern of the virus, the relative synonymous codon usage (RSCU) values, codon usage bias (CUB) values, effective number of codons (ENCs) values and nucleotide contents were calculated to implement a comparative analysis to evaluate the dynamics of the virus evolution.

title:
  The characteristics of the synonymous codon usage in enterovirus 71 virus and the effects of host on the virus in codon usage pattern

abstract:
  To give a new perspective on the evolutionary characteristics shaping the genetic diversity of enterovirus 71 (EV71) and the effects of natural selection from its host on the codon usage pattern of the virus, the relative synonymous codon usage (RSCU) values, codon usage bias (CUB) values, effective number of codons (ENCs) values and nucleotide contents were calculated to implement a comparative analysis to evaluate the dynamics of the virus evolution. The characteristics of the synonymous codon usage patterns and nucleotide contents of EV71 and the comparison between ENC values for the whole coding sequence of EV71 and that of coding sequences for viral proteins of EV71 all indicate that the interaction between mutation pressure from virus and natural selection from host exists in the processes of evolution of EV71. The synonymous codon usage pattern of EV71 is a mixture of coincidence and antagonism to that of host cell. In addition, the genetic diversity of EV71 strains and the preferential selection of some synonymous codons in EV71 strains based on the different epidemic areas were observed, suggesting that geographic and social factors may play roles in influencing the evolution of this virus.


id: cord-253090-kllrqoxi
title: Codon adaptation biases among sylvatic and urban genotypes of Dengue virus type 2
author: dos Passos Cunha, Marielton
date: 2018-05-21
txt: ./txt/cord-253090-kllrqoxi.txt
cache: ./cache/cord-253090-kllrqoxi.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29792991/
doi: 10.1016/j.meegid.2018.05.017
summary:
  Dengue virus (DENV) emerged from the sylvatic environment and colonized urban settings, being sustained in a human-Aedes-human transmission chain, mainly by the bites of females of the anthropophilic species Aedes aegypti. In this context, as previous analyses have suggested (Moncayo et al., 2004) , our findings support the notion that for the sylvatic strains to effectively colonize the urban environment, the virus needs a number of silent, adaptive nucleotide substitutions to optimize the codon usage to invertebrate host cells, while maintaining a compositional base balance suitable for efficient alternate spread among both human and insect hosts. In conclusion, our findings provide a comprehensive assessment of the codon adaptation of DENV-2 in different habitats (i.e. urban and sylvatic settings) and host systems (i.e. Homo sapiens and the mosquito vector Aedes aegypti). In this context, although the virus replicates in both human and mosquitoes, our analysis suggested that DENV-2 codon usage is better adapted to humans than to the main cosmopolitan vector (Ae. aegypti).

abstract:
  Dengue virus (DENV) emerged from the sylvatic environment and colonized urban settings, being sustained in a human-Aedes-human transmission chain, mainly by the bites of females of the anthropophilic species Aedes aegypti. Herein, we sought evidence for fine-tuning in viral codon usage, possibly due to viral adaptation to human transmission. We compared the codon adaptation of DENV serotype 2 (DENV-2) genotypes from urban and sylvatic habitats and tried to correlate the findings with key evolutionary determinants. We found that DENV-2 codons of urban and sylvatic genotypes had a higher CAI to humans than to Ae. aegypti. Remarkably, we found no significant differences in codon adaptation to human between urban American/Asian and sylvatic DENV-2 genotypes. Moreover, CAI values were significantly different, when comparing all genotypes to Ae. aegypti codon preferences, with lower values for sylvatic than urban genotypes. In summary, our findings suggest the presence of a molecular signature among the genotypes that circulate in sylvatic and urban environments, and may help explain the trafficking of DENV-2 strains to an urban cycle.


id: cord-253245-433mg0ke
author: Gao, Zhiru
date: 2020-08-05
txt: ./txt/cord-253245-433mg0ke.txt
cache: ./cache/cord-253245-433mg0ke.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.meegid.2020.104494
doi: 10.1016/j.meegid.2020.104494
summary:
  A recent study reported that four medical workers aged 30-36 years who had re-detectable positive (RP) for SARS-CoV-2 within 5-13 days after being cured and discharged, indicating that some of the recovered patients may still be virus carriers, which caused widespread concern (Lan et al., 2020). Although the results of the three nucleic acid tests were negative for the patient, there were viral residue in the lungs, so even if the patient was discharged, we supposed that virus would transfer positive again after a period of time (Yao et al., 2020) . In addition, initial studies reported that the SARS-CoV-2 RNA could be detected in the feces of 81.8% recovered patients (54/66), even in those with negative throat swabs (Ling et al., 2020) . In other words, even if sometimes the virus nucleic acid tested by RT-PCR is positive in the recovery phase of COVID-19, it will not cause a more serious condition, and antiviral therapy may not be required in most patients.

title:
  A systematic review of re-detectable positive virus nucleic acid among COVID-19 patients in recovery phase

abstract:
  A large number of coronavirus disease 2019 (COVID-19) patients have been cured and discharged due to timely and effective treatments. While some discharged patients have been found re-positive nucleic acid again in the recovery phase. Until now, there is still a great challenge to its infectivity and the specific potential mechanism which need further discussion. However, more intensive attention should be paid to the prognosis of the recovered patients. In this review, we mainly focus on the characteristics, potential reasons, infectivity, and outcomes of re-detectable positive patients, thereby providing some novel insights into the cognition of COVID-19.


id: cord-255141-55ho9av4
title: Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus
author: Abolnik, Celia
date: 2015-04-03
txt: ./txt/cord-255141-55ho9av4.txt
cache: ./cache/cord-255141-55ho9av4.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1567134815001185
doi: 10.1016/j.meegid.2015.03.033
summary:
  A QX-like strain was analysed by high-throughput Illumina sequencing and genetic variation across the entire viral genome was explored at the sub-consensus level by single nucleotide polymorphism (SNP) analysis. The E and 3b protein products play key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 5′UTR did not alter the predicted secondary structure. Coronavirus accessory proteins are generally dispensable for virus replication, but they play vital roles in virulence and pathogenesis by affecting host innate immune responses, encoding pro-or anti-apoptotic activities, or by effecting other signalling pathways that influence disease outcomes (Susan & Julian, 2011) . Mapping of the receptor-binding domain and amino acids critical for attachment in the spike protein of avian coronavirus infectious bronchitis virus Analysis of a QX-like avian infectious bronchitis virus genome identified recombination in the region containing the ORF 5a, ORF 5b, and nucleocapsid protein gene sequences

abstract:
  Infectious bronchitis virus (IBV) is a Gammacoronavirus that causes a highly contagious respiratory disease in chickens. A QX-like strain was analysed by high-throughput Illumina sequencing and genetic variation across the entire viral genome was explored at the sub-consensus level by single nucleotide polymorphism (SNP) analysis. Thirteen open reading frames (ORFs) in the order 5′-UTR-1a-1ab-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3′UTR were predicted. The relative frequencies of missense: silent SNPs were calculated to obtain a comparative measure of variability in specific genes. The most variable ORFs in descending order were E, 3b, 5′UTR, N, 1a, S, 1ab, M, 4c, 5a, 6b. The E and 3b protein products play key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 5′UTR did not alter the predicted secondary structure. The frequency of SNPs in the Spike (S) protein ORF of 0.67% was below the genomic average of 0.76%. Only three SNPS were identified in the S1 subunit, none of which were located in hypervariable region (HVR) 1 or HVR2. The S2 subunit was considerably more variable containing 87% of the polymorphisms detected across the entire S protein. The S2 subunit also contained a previously unreported multi-A insertion site and a stretch of four consecutive mutated amino acids, which mapped to the stalk region of the spike protein. Template-based protein structure modelling produced the first theoretical model of the IBV spike monomer. Given the lack of diversity observed at the sub-consensus level, the tenet that the HVRs in the S1 subunit are very tolerant of amino acid changes produced by genetic drift is questioned.


id: cord-257584-v38tjof3
author: Fahmi, Muhamad
date: 2020-03-03
txt: ./txt/cord-257584-v38tjof3.txt
cache: ./cache/cord-257584-v38tjof3.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.meegid.2020.104272
doi: 10.1016/j.meegid.2020.104272
summary:
  Two of six Clade 2 nonstructural proteins, NS7b and NS8, were exclusively conserved among 2019-nCoV, BetaCoV_RaTG, and BatSARS-like Cov. NS7b and NS8 have previously been shown to affect immune response signaling in the SARS-CoV experimental model. This was done using a combination of the phylogenetic tree constructed from the genome sequences and the cluster tree developed from the profiles retrieved from the presence and absence of homologs of ten 2019-nCoV proteins. The phylogenetic analysis using complete genome sequences showed that 2019-nCoV was the most closely related to BatCoV RaTG13 and belonged to the Sarbecovirus subgenus of Betacoronavirus, together with SARS coronavirus and Bat-SARS-like coronavirus (BAT-SL-CoVZXC21 and BAT-SL-CoVZC45) with the full support of reliability (Fig. 1) . Two (NS7b and NS8) of five nonstructural proteins were specific for 2019-nCoV and its closely related species, BatCoV RaTG13 and Bat-SARS-like coronavirus (BAT-SL-CoVZXC21 and BAT-SL-CoVZC45).

title:
  Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV

abstract:
  The seventh novel human infecting Betacoronavirus that causes pneumonia (2019 novel coronavirus, 2019-nCoV) originated in Wuhan, China. The evolutionary relationship between 2019-nCoV and the other human respiratory illness-causing coronavirus is not closely related. We sought to characterize the relationship of the translated proteins of 2019-nCoV with other species of Orthocoronavirinae. A phylogenetic tree was constructed from the genome sequences. A cluster tree was developed from the profiles retrieved from the presence and absence of homologs of ten 2019-nCoV proteins. The combined data were used to characterize the relationship of the translated proteins of 2019-nCoV to other species of Orthocoronavirinae. Our analysis reliably suggests that 2019-nCoV is most closely related to BatCoV RaTG13 and belongs to subgenus Sarbecovirus of Betacoronavirus, together with SARS coronavirus and Bat-SARS-like coronavirus. The phylogenetic profiling cluster of homolog proteins of one annotated 2019-nCoV protein against other genome sequences revealed two clades of ten 2019-nCoV proteins. Clade 1 consisted of a group of conserved proteins in Orthocoronavirinae comprising Orf1ab polyprotein, Nucleocapsid protein, Spike glycoprotein, and Membrane protein. Clade 2 comprised six proteins exclusive to Sarbecovirus and Hibecovirus. Two of six Clade 2 nonstructural proteins, NS7b and NS8, were exclusively conserved among 2019-nCoV, BetaCoV_RaTG, and BatSARS-like Cov. NS7b and NS8 have previously been shown to affect immune response signaling in the SARS-CoV experimental model. Thus, we speculated that knowledge of the functional changes in the NS7b and NS8 proteins during evolution may provide important information to explore the human infective property of 2019-nCoV.


id: cord-259925-g28sx9qu
author: Saleemi, Mansab Ali
date: 2020-10-06
txt: ./txt/cord-259925-g28sx9qu.txt
cache: ./cache/cord-259925-g28sx9qu.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1567134820304147?v=s5
doi: 10.1016/j.meegid.2020.104583
summary:
  The World Health Organization (WHO) has named the disease caused by the virus as COVID-19 and the virus which is the culprit was renamed from the initial novel respiratory 2019 coronavirus to SARS-CoV-2. To identify the etiological source of a novel human pathogen is a dynamic process that needs comprehensive and extensive scientific validations, such as observed in the Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS), and human immunodeficiency virus (HIV) cases. Up to date, it is unclear how SARS-CoV-2 interacts with the host antiviral immunity, hence lessons can be learned from previous studies of other members of the coronavirus family and also human pathogenic viruses, such as human immunodeficiency viruses and severe acute respiratory syndrome (SARS) CoV known as human CoVs (HCoVs) due to their ability to cause human infections (Andersen et al., 2020) .

title:
  Emergence and molecular mechanisms of SARS-CoV-2 and HIV to target host cells and potential therapeutics

abstract:
  The emergence of a new coronavirus, in around late December 2019 which had first been reported in Wuhan, China has now developed into a massive threat to global public health. The World Health Organization (WHO) has named the disease caused by the virus as COVID-19 and the virus which is the culprit was renamed from the initial novel respiratory 2019 coronavirus to SARS-CoV-2. The person-to-person transmission of this virus is ongoing despite drastic public health mitigation measures such as social distancing and movement restrictions implemented in most countries. Understanding the source of such an infectious pathogen is crucial to develop a means of avoiding transmission and further to develop therapeutic drugs and vaccines. To identify the etiological source of a novel human pathogen is a dynamic process that needs comprehensive and extensive scientific validations, such as observed in the Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS), and human immunodeficiency virus (HIV) cases. In this context, this review is devoted to understanding the taxonomic characteristics of SARS-CoV-2 and HIV. Herein, we discuss the emergence and molecular mechanisms of both viral infections. Nevertheless, no vaccine or therapeutic drug is yet to be approved for the treatment of SARS-CoV-2, although it is highly likely that new effective medications that target the virus specifically will take years to establish. Therefore, this review reflects the latest repurpose of existing antiviral therapeutic drug choices available to combat SARS-CoV-2.


id: cord-260644-5moccf8c
title: Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2
author: Hashemi, Seyed Ahmad
date: 2020-11-07
txt: ./txt/cord-260644-5moccf8c.txt
cache: ./cache/cord-260644-5moccf8c.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1567134820304561
doi: 10.1016/j.meegid.2020.104625
summary:
  title: Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2 Regarding the high price and low availability of sequencing techniques in developing countries, here we describe a rapid and inexpensive method for the detection of D614G mutation in SARS-CoV-2. Some researchers evaluated and compared the whole genome sequence of SARS-CoV-2 isolated in various parts of the world and identified some mutations. The high-frequency mutations of the SARS-CoV-2 genome were seen in nsp6, RNA polymerase, helicase, membrane glycoprotein, RNA primase, nucleocapsid phosphoprotein, and spike protein genes (Yin, 2020) . In the first step, we used the sequence of S protein of SARS-CoV-2, published in Gene bank with accession number MT252819.1, for appropriate restriction endonuclease selection and primer design. The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity

abstract:
  In late 2019, an outbreak of respiratory disease named COVID-19 started in the world. To date, thousands of cases of infection are reported worldwide. Most researchers focused on epidemiology and clinical features of COVID-19, and a small part of studies was performed to evaluate the genetic characteristics of this virus. Regarding the high price and low availability of sequencing techniques in developing countries, here we describe a rapid and inexpensive method for the detection of D614G mutation in SARS-CoV-2. Using bioinformatics databases and software, we designed the PCR-RFLP method for D614G mutation detection. We evaluated 144 SARS-CoV-2 positive samples isolated in six months in Northeastern Iran. Our results showed that the prevalent type is S-D in our isolates, and a small number of isolated belongs to the S-G type. Of 144 samples, 127 (88.2%) samples have belonged to type S-D, and 13 (9%) samples typed S-G. The first S-G type was detected on 2020 June 10. We have little information about the prevalence of D614G mutation, and it seems that the reason is the lack of cheap and fast methods. We hope that this method will provide more information on the prevalence and epidemiology of D614G mutations worldwide.


id: cord-261547-8tfbhmzo
title: Genetic diversity of bats coronaviruses in the Atlantic Forest hotspot biome, Brazil
author: Góes, Luiz Gustavo Bentim
date: 2016-07-26
txt: ./txt/cord-261547-8tfbhmzo.txt
cache: ./cache/cord-261547-8tfbhmzo.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1567134816303240
doi: 10.1016/j.meegid.2016.07.034
summary:
  In this report, we identified and characterized previously unknown and diverse genetic clusters of bat coronaviruses in the Atlantic Forest Biome, Brazil. Recently, a number of novel bats CoVs have been identified, primarily from African, Asian and European bats (Calisher et al., 2006; Chu et al., 2006; Drexler et al., 2014) , as well as from South American countries including Costa Rica, Panama, Ecuador, Mexico and Brazil (Corman et al., 2013; Goes et al., 2013) . Coronaviruses were detected in 15 bat intestines samples from eight bat species with distinct diet habit, demonstrating a marked potential of CoVs distribution among bat species in AFB that harbours 9% of world''s bat diversity. α-CoV sequences obtained from bats of same genus presented high nucleotide sequence similarity (e.g. Artibeus, Glossophaga, Carollia, Molossus, Myotis and Sturnira) (Fig. 1D and Supplementary table), even with sequences detected in other studies from bats of geographically distant regions. It is indispensable in future to investigate the evolutionary events in genetically diverse bats CoVs using complete genome sequences, and their possible transmission potentials to human being.

abstract:
  Bats are notorious reservoirs of genetically-diverse and high-profile pathogens, and are playing crucial roles in the emergence and re-emergence of viruses, both in human and in animals. In this report, we identified and characterized previously unknown and diverse genetic clusters of bat coronaviruses in the Atlantic Forest Biome, Brazil. These results highlight the virus richness of bats and their possible roles in the public health.


id: cord-261914-qfim8nu5
author: Oem, Jae-Ku
date: 2019-06-04
txt: ./txt/cord-261914-qfim8nu5.txt
cache: ./cache/cord-261914-qfim8nu5.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.meegid.2019.06.003
doi: 10.1016/j.meegid.2019.06.003
summary:
  This study aimed to analyze the complete genome sequence, i.e., 11 genome segments of the lapine rotavirus (LRV) identified in the intestine of a dead rabbit in the Republic of Korea (ROK) and to describe the genetic relationships between this lapine isolate [RVA/Rabbit-wt/KOR/Rab1404/2014/G3P[22] (Rab1404)] and other lapine isolates/strains. Additionally, the genome segments VP6 (I2), NSP1 (N2), and NSP5 (H3) of Rab1404 were closely related to those of bovine RVAs. This is the first report describing the complete genome sequence of an LRV detected in the ROK. The objective of this study was to analyze an LRV isolated from the intestine of a dead rabbit in 2014 in the ROK by performing a complete genomic sequence analysis of the 11 genome segments and to characterize the phylogenetic relationships between our isolate and other lapine isolates/strains.

title:
  Genetic characteristics and analysis of a novel rotavirus G3P[22] identified in diarrheic feces of Korean rabbit

abstract:
  Group A rotaviruses (RVAs) are important gastroenteric pathogens that infect humans and animals. This study aimed to analyze the complete genome sequence, i.e., 11 genome segments of the lapine rotavirus (LRV) identified in the intestine of a dead rabbit in the Republic of Korea (ROK) and to describe the genetic relationships between this lapine isolate [RVA/Rabbit-wt/KOR/Rab1404/2014/G3P[22] (Rab1404)] and other lapine isolates/strains. Rab1404 possessed the following genotype constellation: G3-P[22]-I2-R3-C3-M3-A9-N2-T3-E3-H3. The P[22] genotype was found to originate from rabbits and was for the first time identified in the ROK. Phylogenetic analysis showed that Rab1404 possessed VP1-3 and VP7 genes, which were closely related to those of the bat strain LZHP2; NSP1-4 genes, which were closely related to those of the simian strain RRV; and VP4, VP6, and NSP5 genes, which were closely related to the genes obtained from other rabbits. Interestingly, a close relationship between Rab1404 and simian RVA strain RVA/Simian-tc/USA/RRV/1975/G3P[3] for 8 gene segments was observed. RRV is believed to be a reassortant between bovine-like RVA strain and canine/feline RVA strains. Rab1404 and canine/feline RVAs shared the genes encoding VP1, VP3, VP7, NSP3, and NSP4. Additionally, the genome segments VP6 (I2), NSP1 (N2), and NSP5 (H3) of Rab1404 were closely related to those of bovine RVAs. This is the first report describing the complete genome sequence of an LRV detected in the ROK. These results indicate that Rab1404 could be a result of interspecies transmission, possibly through multiple reassortment events in the strains of various animal species and the subsequent transmission of the virus to a rabbit. Additional studies are required to determine the evolutionary source and to identify possible reservoirs of RVAs in nature.


id: cord-262592-0rdiosxd
title: Human norovirus hyper-mutation revealed by ultra-deep sequencing
author: Cuevas, José M.
date: 2016-04-17
txt: ./txt/cord-262592-0rdiosxd.txt
cache: ./cache/cord-262592-0rdiosxd.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1567134816301435
doi: 10.1016/j.meegid.2016.04.017
summary:
  This revealed the presence of low-frequency sequences carrying large numbers of U-to-C or A-to-G base transitions, suggesting a role for hyper-mutation in NoV diversity. Based on the sequence context of the observed changes, we propose that NoV hypermutation might be driven by ADAR-mediated editing of the viral genomic RNA of either polarity during replication. We used 16 stool samples from patients acutely infected with NoV GII.4 to amplify by RT-PCR a 386-base region encompassing nucleotides 1 to 386 of the VP1 gene (reference sequence: GenBank JX459908; Fig. 1A ). After 48 h incubation, total RNA was extracted from cells, residual DNA was removed with DNAse I, a specific primer annealing to the minus-strand of the VP1 capsid gene was used for reverse transcription, and high-fidelity PCR amplification of a region encompassing positions 19 to 323 of the VP1 gene (305 bases, although only the 266 bases excluding primer regions Fig. 1 .

abstract:
  Human noroviruses (NoVs) are a major cause of gastroenteritis worldwide. It is thought that, similar to other RNA viruses, high mutation rates allow NoVs to evolve fast and to undergo rapid immune escape at the population level. However, the rate and spectrum of spontaneous mutations of human NoVs have not been quantified previously. Here, we analyzed the intra-patient diversity of the NoV capsid by carrying out RT-PCR and ultra-deep sequencing with 100,000-fold coverage of 16 stool samples from symptomatic patients. This revealed the presence of low-frequency sequences carrying large numbers of U-to-C or A-to-G base transitions, suggesting a role for hyper-mutation in NoV diversity. To more directly test for hyper-mutation, we performed transfection assays in which the production of mutations was restricted to a single cell infection cycle. This confirmed the presence of sequences with multiple U-to-C/A-to-G transitions, and suggested that hyper-mutation contributed a large fraction of the total NoV spontaneous mutation rate. The type of changes produced and their sequence context are compatible with ADAR-mediated editing of the viral RNA.


id: cord-263476-ju7xqwa7
author: Xia, Jing
date: 2016-08-13
txt: ./txt/cord-263476-ju7xqwa7.txt
cache: ./cache/cord-263476-ju7xqwa7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27530216/
doi: 10.1016/j.meegid.2016.08.011
summary:
  The aim of this study was to decipher the molecular epidemiological and antigenic characteristics of infectious bronchitis virus strains (IBVs) isolated in recent years in southwestern China. The antigenicity of ten IBVs, including seven field strains and commonly used vaccine strains, were assayed with a viral cross-neutralization assay in chicken embryonated kidney cells (CEK). To determine the antigenic relatedness between the field IBV isolates and the vaccine viral strains, double-direction viral cross-neutralization (VN) tests were performed in chicken embryo kidney (CEK) cells using constant viral titers and diluted serum. The tested strains came from six different genotypes and included seven IBV field isolates (Sczy3, cK/CH/SCDY/141030, cK/CH/SCLS/140104, cK/CH/CQKX/ 150203, cK/CH/SCYB/140913, cK/CH/SCMY/10I, cK/CH/SCYB/141102) and the three most commonly used vaccine viral strains (H120, M41, and 4/91). Ten IBVs, including seven field strains from different genotype backgrounds and three commonly used vaccine strains (H120, 4/91, and M41), were analyzed and grouped into four serotypes: Massachusetts (Mass hereafter), 793B, Sczy3, and SCYB.

title:
  Phylogenetic and antigenic analysis of avian infectious bronchitis virus in southwestern China, 2012–2016

abstract:
  The aim of this study was to decipher the molecular epidemiological and antigenic characteristics of infectious bronchitis virus strains (IBVs) isolated in recent years in southwestern China. A total of 24 field strains were isolated from diseased chickens between 2012 and 2016. Phylogenetic analysis based on S1 nucleotide sequences showed that 16 of the 24 isolates were clustered into four distinct genotypes: QX (37.5%), TW (16.7%, TWI and TWII), Mass (8.3%), and J2 (4.2%). The QX genotype was still the prevalent genotype in southwestern China. Recombination analysis of the S1 subunit gene showed that eight of the 24 field strains were recombinant variants that originated from field strains and vaccine strains. A new potential recombination hotspot [ATTTT(T/A)] was identified, implying that recombination events may become more and more common. The antigenicity of ten IBVs, including seven field strains and commonly used vaccine strains, were assayed with a viral cross-neutralization assay in chicken embryonated kidney cells (CEK). The results showed that the ten IBVs could be divided into four serotypes (Massachusetts, 793B, Sczy3, and SCYB). Sczy3 and 793B were the predominant serotypes. Six of the seven field isolates (all except for cK/CH/SCYB/140913) cross-reacted well with anti-sera against other field strains. In conclusion, the genetic and antigenic features of IBVs from southwestern China in recent years have changed when compared to the previous reports. The results could provide a reference for vaccine development and the prevention of infectious bronchitis in southwestern China.


id: cord-263481-w5ytp1q7
author: Lokman, Syed Mohammad
date: 2020-06-02
txt: ./txt/cord-263481-w5ytp1q7.txt
cache: ./cache/cord-263481-w5ytp1q7.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1567134820302203?v=s5
doi: 10.1016/j.meegid.2020.104389
summary:
  MERS-CoV uses dipeptidyl peptidase-4 (DPP4) as entry receptor [11] whereas SARS-CoV and SARS-CoV-2 utilize ACE-2 (angiotensin converting enzyme-2) [12] , abundantly available in lung alveolar epithelial cells and enterocytes, suggesting S glycoprotein as a potential drug target to halt the entry of SARS-with remarkable properties like glutamine-rich 42 aa long exclusive molecular signature (DSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIE) in position 983-1024 of polyprotein 1ab (pp1ab) [16] , diversified receptor-binding domain (RBD), unique furin cleavage site (PRRAR↓SV) at S1/S2 boundary in S glycoprotein which could play roles in viral pathogenesis, diagnosis and treatment [17] . There is growing evidence that spike protein, a 1273 amino acid long glycoprotein having multiple domains, possibly plays a major role in SARS-CoV-2 pathogenesis. In this study, we have analyzed 320 genomic sequences of SARS-CoV-2 to identify mutations between the available genomes followed by the amino acid variations in the glycoprotein S to foresee their impact on the viral entry to host cell from structural biology viewpoint.

title:
  Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach

abstract:
  The newly identified SARS-CoV-2 has now been reported from around 185 countries with more than a million confirmed human cases including more than 120,000 deaths. The genomes of SARS-COV-2 strains isolated from different parts of the world are now available and the unique features of constituent genes and proteins need to be explored to understand the biology of the virus. Spike glycoprotein is one of the major targets to be explored because of its role during the entry of coronaviruses into host cells. We analyzed 320 whole-genome sequences and 320 spike protein sequences of SARS-CoV-2 using multiple sequence alignment. In this study, 483 unique variations have been identified among the genomes of SARS-CoV-2 including 25 nonsynonymous mutations and one deletion in the spike (S) protein. Among the 26 variations detected, 12 variations were located at the N-terminal domain and 6 variations at the receptor-binding domain (RBD) which might alter the interaction of S protein with the host receptor angiotensin converting enzyme-2 (ACE2). Besides, 22 amino acid insertions were identified in the spike protein of SARS-CoV-2 in comparison with that of SARS-CoV. Phylogenetic analyses of spike protein revealed that Bat coronavirus have a close evolutionary relationship with circulating SARS-CoV-2. The genetic variation analysis data presented in this study can help a better understanding of SARS-CoV-2 pathogenesis. Based on results reported herein, potential inhibitors against S protein can be designed by considering these variations and their impact on protein structure.


id: cord-265329-bsypo08l
title: Emergence of genomic diversity and recurrent mutations in SARS-CoV-2
author: van Dorp, Lucy
date: 2020-05-05
txt: ./txt/cord-265329-bsypo08l.txt
cache: ./cache/cord-265329-bsypo08l.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1567134820301829
doi: 10.1016/j.meegid.2020.104351
summary:
  Three sites in Orf1ab in the regions encoding Nsp6, Nsp11, Nsp13, and one in the Spike protein are characterised by a particularly large number of recurrent mutations (>15 events) which may signpost convergent evolution and are of particular interest in the context of adaptation of SARS-CoV-2 to the human host. The extraordinary availability of genomic data during the COVID-19 pandemic has been made possible thanks to a tremendous effort by hundreds of researchers globally depositing SARS-CoV-2 assemblies (Table S1 ) and the proliferation of close to real time data visualisation and analysis tools including NextStrain (https://nextstrain.org) and CoV-GLUE (http://cov-glue.cvr.gla.ac.uk). In this work we use this data to analyse the genomic diversity that has emerged in the global population of SARS-CoV-2 since the beginning of the COVID-19 pandemic, based on a download of 7710 assemblies. The genomic diversity of the global SARS-CoV-2 population being recapitulated in multiple countries points to extensive worldwide transmission of COVID-19, likely from extremely early on in the pandemic.

abstract:
  SARS-CoV-2 is a SARS-like coronavirus of likely zoonotic origin first identified in December 2019 in Wuhan, the capital of China's Hubei province. The virus has since spread globally, resulting in the currently ongoing COVID-19 pandemic. The first whole genome sequence was published on January 52,020, and thousands of genomes have been sequenced since this date. This resource allows unprecedented insights into the past demography of SARS-CoV-2 but also monitoring of how the virus is adapting to its novel human host, providing information to direct drug and vaccine design. We curated a dataset of 7666 public genome assemblies and analysed the emergence of genomic diversity over time. Our results are in line with previous estimates and point to all sequences sharing a common ancestor towards the end of 2019, supporting this as the period when SARS-CoV-2 jumped into its human host. Due to extensive transmission, the genetic diversity of the virus in several countries recapitulates a large fraction of its worldwide genetic diversity. We identify regions of the SARS-CoV-2 genome that have remained largely invariant to date, and others that have already accumulated diversity. By focusing on mutations which have emerged independently multiple times (homoplasies), we identify 198 filtered recurrent mutations in the SARS-CoV-2 genome. Nearly 80% of the recurrent mutations produced non-synonymous changes at the protein level, suggesting possible ongoing adaptation of SARS-CoV-2. Three sites in Orf1ab in the regions encoding Nsp6, Nsp11, Nsp13, and one in the Spike protein are characterised by a particularly large number of recurrent mutations (>15 events) which may signpost convergent evolution and are of particular interest in the context of adaptation of SARS-CoV-2 to the human host. We additionally provide an interactive user-friendly web-application to query the alignment of the 7666 SARS-CoV-2 genomes.


id: cord-266660-0wq77k6y
author: Choi, Jong-Chul
date: 2014-06-19
txt: ./txt/cord-266660-0wq77k6y.txt
cache: ./cache/cord-266660-0wq77k6y.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1567134814002081
doi: 10.1016/j.meegid.2014.06.005
summary:
  title: Comparative genome analysis and molecular epidemiology of the reemerging porcine epidemic diarrhea virus strains isolated in Korea We detected three PEDV strains from ten small intestine samples from piglets with acute diarrhea and we determined the complete genome sequences of the reemerging Korean PEDV field isolates, except for the noncoding regions from both ends. This study aimed to determine the complete genome sequence of the reemerging Korean PEDV strain and to investigate their genetic relationship with other strains using comparative genome analysis and phylogenetic analysis. In addition, all available complete genome sequences of PEDV isolates from Korea were included in the alignment to compare the recent Korean strains with previous endemic Korean PEDV strains. Multiple alignment with other PEDV complete genomes indicated that the reemerging Korean strains possess genome sequences, which are distinct from those of previous Korean field strains (Fig. 1) .

title:
  Comparative genome analysis and molecular epidemiology of the reemerging porcine epidemic diarrhea virus strains isolated in Korea

abstract:
  Porcine epidemic diarrhea virus (PEDV), a member of the Coronaviridae family, is an enveloped, positive-sense, single-stranded RNA virus, which causes severe diarrhea and dehydration in suckling pigs. We detected three PEDV strains from ten small intestine samples from piglets with acute diarrhea and we determined the complete genome sequences of the reemerging Korean PEDV field isolates, except for the noncoding regions from both ends. The complete genome sequences of the strains were identical or almost identical (one synonymous single-nucleotide polymorphism (SNP) in the ORF1a/1b genomic sequence). Interestingly, comparative genome analysis of recent Korean PEDV isolates and other strains revealed that the complete genome sequences of recent Korean strains were almost identical (99.9%) to those of the US PEDV strains isolated in 2013. These results suggest that the three reemerging Korean strains are distinct from previous endemic Korean PEDV strains and has been recently introduced into Korea from oversea with high likelihood.


id: cord-266914-3eatplc2
title: Nsp1 proteins of group I and SARS coronaviruses share structural and functional similarities
author: Wang, Yongjin
date: 2010-06-02
txt: ./txt/cord-266914-3eatplc2.txt
cache: ./cache/cord-266914-3eatplc2.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1567134810001371
doi: 10.1016/j.meegid.2010.05.014
summary:
  The group II coronaviruses severe acute respiratory syndrome coronavirus (SARS-CoV) and mouse hepatitis coronavirus (MHV) encode a number of proteins that antagonize host innate immunity. Innate immune signal transduction was stimulated by NDV infection in cells transfected with plasmids-expressing nsp1 from HCoV-229E, HCoV-NL63 or SARS-CoV, or with a control plasmid. Luciferase reporter assays showed that synthesis of the innate immune promoter IFN-band ISG15-driven genes was suppressed by 5-20-folds in HCoV-229E and HCoV-NL63 nsp1-expressing 293 cells (Fig. 4A) . Synthesis of non-immune promoter-driven genes, including for SV40, HSV-TK and CMV promoters, was inhibited to a similar extent by the two group I coronavirus nsp1 proteins (Fig. 4B) . These results indicate that group I coronaviruses have evolved a mechanism strikingly similar to SARS-CoV for antagonizing host cell proliferation and innate immunity using nsp1. Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells

abstract:
  The nsp1 protein of the highly pathogenic SARS coronavirus suppresses host protein synthesis, including genes involved in the innate immune system. A bioinformatic analysis revealed that the nsp1 proteins of group I and SARS coronaviruses have similar structures. Nsp1 proteins of group I coronaviruses interacted with host ribosomal 40S subunit and did not inhibit IRF-3 activation. However, synthesis of host immune and non-immune proteins was inhibited by nsp1 proteins at both transcriptional and translational levels, similar to SARS coronavirus nsp1. These results indicate that different coronaviruses might employ the same nsp1 mechanism to antagonize host innate immunity and cell proliferation. However, nsp1 may not be the key determinant of viral pathogenicity, or the factor used by the SARS coronavirus to evade host innate immunity.


id: cord-267136-1abp6oom
author: Lan, Yu-Ching
date: 2004-12-07
txt: ./txt/cord-267136-1abp6oom.txt
cache: ./cache/cord-267136-1abp6oom.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1567134804001224
doi: 10.1016/j.meegid.2004.08.005
summary:
  Taiwan experienced a large number of severe acute respiratory syndrome (SARS) viral infections between March and July 2003; by September of that year, 346 SARS cases were confirmed by RT-PCR or serological tests. In order to better understand evolutionary relationships among SARS coronaviruses (SCoVs) from different international regions, we performed phylogenetic comparisons of full-length genomic and protein sequences from 45 human SCoVs (including 12 from Taiwan) and two civet SCoVs. All the Taiwanese SARS-CoV strains which associated with nosocomial infection formed a monophyletic clade within the late phase of the SARS epidemic. To better understand evolutionary relationships between SCoVs isolated in Taiwan and those isolated in other parts of the world, we constructed phylogenetic trees with two different methods using full-length genomic sequences from 45 human (12 Taiwanese) and two civet SCoVs. Tree topologies were consistent for the NJ (Fig. 1a) and Pars (Fig. 1b) methods. Pairwise comparison methods were used to analyze nucleotide sequence variation within the full-length genomes of 20 human SCoVs (7 from early epidemic and 13 from late epidemic) (Fig. 2) .

title:
  Phylogenetic analysis and sequence comparisons of structural and non-structural SARS coronavirus proteins in Taiwan

abstract:
  Taiwan experienced a large number of severe acute respiratory syndrome (SARS) viral infections between March and July 2003; by September of that year, 346 SARS cases were confirmed by RT-PCR or serological tests. In order to better understand evolutionary relationships among SARS coronaviruses (SCoVs) from different international regions, we performed phylogenetic comparisons of full-length genomic and protein sequences from 45 human SCoVs (including 12 from Taiwan) and two civet SCoVs. All the Taiwanese SARS-CoV strains which associated with nosocomial infection formed a monophyletic clade within the late phase of the SARS epidemic. This Taiwanese clade could be further divided into two epidemic waves. Taiwan SCoVs in the first wave clustered with three isolates from the Amoy Gardens housing complex in Hong Kong indicating their possible origin. Of the 45 human SCoVs, one isolate from Guangdong province, China, exhibited an extra 29-nucleotide fragment between Orf 10 and Orf 11—similar to the civet SCoV genome. Nucleotide and protein sequence comparisons suggested that all SCoVs of late epidemic came from human-to-human transmission, while certain SCoVs of early epidemic might have originated in animals.


id: cord-267168-qjktnnn6
title: Evolutionary genetics of canine respiratory coronavirus and recent introduction into Swedish dogs
author: Wille, Michelle
date: 2020-03-20
txt: ./txt/cord-267168-qjktnnn6.txt
cache: ./cache/cord-267168-qjktnnn6.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1567134820301210
doi: 10.1016/j.meegid.2020.104290
summary:
  In this study, Swedish privately-owned dogs with characteristic signs of canine infectious respiratory disease (n = 88) were screened for CRCoV and 13 positive samples (14.7%, 8.4–23.7% [95% confidence interval (CI)]) were further sequenced. To assess recombination, a concatenated sequence was generated including the viruses from which there were sequences from the partial Non-structural protein 2a (NS), and full length HE, S, envelope (E), and M, resulting in 6541 bp for analysis and the genes were placed in genomic order. Assessment of the S, E, M, NS2 and HE genes generated using Sanger and high-throughput sequencing (Table A1 ) demonstrated high genetic similarity of viruses detected in Swedish dogs, despite sampling from numerous clinics across Sweden and an over a period of 3 years. In this study, we aimed to reveal the epidemiology and evolutionary genetics of CRCoV, one of the causative agents of canine infectious respiratory disease (CIRD), in Sweden.

abstract:
  Canine respiratory coronavirus (CRCoV) has been identified as a causative agent of canine infectious respiratory disease, an upper respiratory infection affecting dogs. The epidemiology is currently opaque, with an unclear understanding of global prevalence, pathology, and genetic characteristics. In this study, Swedish privately-owned dogs with characteristic signs of canine infectious respiratory disease (n = 88) were screened for CRCoV and 13 positive samples (14.7%, 8.4–23.7% [95% confidence interval (CI)]) were further sequenced. Sequenced Swedish CRCoV isolates were highly similar despite being isolated from dogs living in geographically distant locations and sampled across 3 years (2013–2015). This is due to a single introduction into Swedish dogs in approximately 2010, as inferred by time structured phylogeny. Unlike other CRCoVs, there was no evidence of recombination in Swedish CRCoV isolates, further supporting a single introduction. Finally, there were low levels of polymorphisms, in the spike genes. Overall, we demonstrate that there is little diversity of CRCoV which is endemic in Swedish dogs.


id: cord-268480-fd5xi4q1
title: Identification of two novel Rotavirus A genotypes, G35 and P[50], from Peruvian alpaca faeces
author: Rojas, Miguel A.
date: 2017-09-01
txt: ./txt/cord-268480-fd5xi4q1.txt
cache: ./cache/cord-268480-fd5xi4q1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28866138/
doi: 10.1016/j.meegid.2017.08.019
summary:
  Rotavirus A (RVA) Alp11B was detected from a neonatal Peruvian alpaca presenting with diarrhea, and the Alp11B VP7, VP4, VP6, NSP4, and NSP5 genes were sequenced. Once RVA was detected, the sample was subjected to additional RT-PCR amplifications to identify the VP4, VP7, VP6, NSP4, and NSP5 genotypes using specific primers (Appendix) that were previously published or designed based on RVA sequences available in GenBank. Sequences of Alp11B strain were aligned and compared to that of each corresponding gene of RVA strains obtained from GenBank, by using MegAlign, which are available in the Lasergene software package (DNASTAR, Madison, WI). The nucleotide sequences of the VP4 and VP7 genes from Alp11B were not related to any RVA strain available in GenBank (Fig. 2) . The vicuña strain possesses the unique NSP4-E16 genotype, but the NSP5 gene was not characterized. Infection, Genetics and Evolution 55 (2017) 71-74 E16-H6 with high identity to camelid, bat, and human-like RVA strains.

abstract:
  Rotavirus A (RVA) Alp11B was detected from a neonatal Peruvian alpaca presenting with diarrhea, and the Alp11B VP7, VP4, VP6, NSP4, and NSP5 genes were sequenced. The partial genotype constellation of this strain, RVA/Alpaca-wt/PER/Alp11B/2010, was determined to be G35-P[50]-I13-E16-H6.


id: cord-268968-0s6e6y8s
author: Kim, You-Jin
date: 2014-05-10
txt: ./txt/cord-268968-0s6e6y8s.txt
cache: ./cache/cord-268968-0s6e6y8s.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/24820343/
doi: 10.1016/j.meegid.2014.05.007
summary:
  The mean evolutionary rate of G protein was calculated as 3.275 × 10(−3) nucleotide substitution/site/year and several positively selected sites for amino acid substitutions were located in the predicted epitope region. Positive selection results in frequent reversible amino acid replacements in the G protein gene of human respiratory syncytial virus Genetic variability of human respiratory syncytial virus A strains circulating in Ontario: a novel genotype with a 72 nucleotide G gene duplication Complete genome sequence of human respiratory syncytial virus genotype A with a 72-nucleotide duplication in the attachment protein G gene Ten years of global evolution of the human respiratory syncytial virus BA genotype with a 60-nucleotide duplication in the G protein gene Genetic analysis of attachment glycoprotein (G) gene in new genotype ON1 of human respiratory syncytial virus detected in Japan

title:
  Rapid replacement of human respiratory syncytial virus A with the ON1 genotype having 72 nucleotide duplication in G gene

abstract:
  Human respiratory syncytial virus (HRSV) is the main cause of severe respiratory illness in young children and elderly people. We investigated the genetic characteristics of the circulating HRSV subgroup A (HRSV-A) to determine the distribution of genotype ON1, which has a 72-nucleotide duplication in attachment G gene. We obtained 456 HRSV-A positive samples between October 2008 and February 2013, which were subjected to sequence analysis. The first ON1 genotype was discovered in August 2011 and 273 samples were identified as ON1 up to February 2013. The prevalence of the ON1 genotype increased rapidly from 17.4% in 2011–2012 to 94.6% in 2012–2013. The mean evolutionary rate of G protein was calculated as 3.275 × 10(−3) nucleotide substitution/site/year and several positively selected sites for amino acid substitutions were located in the predicted epitope region. This basic and important information may facilitate a better understanding of HRSV epidemiology and evolution.


id: cord-269187-lt0uo7q3
author: Saha, Indrajit
date: 2020-07-11
txt: ./txt/cord-269187-lt0uo7q3.txt
cache: ./cache/cord-269187-lt0uo7q3.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1567134820302884?v=s5
doi: 10.1016/j.meegid.2020.104457
summary:
  Thus it is important for all the nations to perform the genome-wide analysis in order to identify the genetic variation in Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) so that proper vaccine can be designed. Based on this information, they developed an SNP-based PCR assay to show differentiation between To address the above facts, we have analyzed publicly available 566 Indian complete or near complete SARS-CoV-2 genomes in order to find the mutation points as substitution, deletion J o u r n a l P r e -p r o o f and insertion. In this section, we have discussed the source of data or genomic sequence of virus and methods used in systemic way to accomplish this task of finding mutation points as substitution, deletion, insertion as well as SNPs. The genomic sequences of Indian SARS-CoV-2 virus was collected from Global Initiative on Sharing All Influenza Data (GISAID) 1 in fasta format on 11th June 2020.

title:
  Genome-wide analysis of Indian SARS-CoV-2 genomes for the identification of genetic mutation and SNP

abstract:
  The wave of COVID-19 is a big threat to the human population. Presently, the world is going through different phases of lock down in order to stop this wave of pandemic; India being no exception. We have also started the lock down on 23rd March 2020. In this current situation, apart from social distancing only a vaccine can be the proper solution to serve the population of human being. Thus it is important for all the nations to perform the genome-wide analysis in order to identify the genetic variation in Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) so that proper vaccine can be designed. This fast motivated us to analyze publicly available 566 Indian complete or near complete SARS-CoV-2 genomes to find the mutation points as substitution, deletion and insertion. In this regard, we have performed the multiple sequence alignment in presence of reference sequence from NCBI. After the alignment, a consensus sequence is build to analyze each genome in order to identify the mutation points. As a consequence, we have found 933 substitutions, 2449 deletions and 2 insertions, in total 3384 unique mutation points, in 566 genomes across 29.9 K bp. Further, it has been classified into three groups as 100 clusters of mutations (mostly deletions), 1609 point mutations as substitution, deletion and insertion and 64 SNPs. These outcomes are visualized using BioCircos and bar plots as well as plotting entropy value of each genomic location. Moreover, phylogenetic analysis has also been performed to see the evolution of SARS-CoV-2 virus in India. It also shows the wide variation in tree which indeed vivid in genomic analysis. Finally, these SNPs can be the useful target for virus classification, designing and defining the effective dose of vaccine for the heterogeneous population.


id: cord-269283-jm18lj5t
author: Uddin, Md Bashir
date: 2020-07-01
txt: ./txt/cord-269283-jm18lj5t.txt
cache: ./cache/cord-269283-jm18lj5t.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1567134820302719?v=s5
doi: 10.1016/j.meegid.2020.104440
summary:
  Bioinformatics analysis, satellite derived imaging data and epidemiological attributes were employed to investigate origin, immunogenic resemblance and global threat of newly pandemic SARS-CoV-2 including Bangladesh perspective. The study also prioritized the temperature comparison through satellite imaging alongside compiling and analyzing the epidemiological outbreak information on the 2019 novel coronavirus based on several open datasets on COVID-19 (SARS-CoV-2) and discussed possible threats to Bangladesh. As the outbreak of the 2019 novel coronavirus (COVID-19 [SARS-CoV-2]) is expanding rapidly, analysis of epidemiological data of COVID-19 is necessary to explore the measures of burden associated with the disease and to simultaneously gather information on determinants and interventions. Moreover, the conservancy study of immunogenic peptides predicted from the SARS-CoV-2 proteins was also compared against other human coronavirus strains (HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63, HKU1 and MERS-CoV). Cross-checked conservancy analysis of COVID-19 antigenic epitopes with SARS-CoV proteins showed that conservancy when crosschecked with other coronaviruses, including BufCoV-HKU26 of Bangladesh origin, was not significant ( Table 3) .

title:
  Ancestral origin, antigenic resemblance and epidemiological insights of novel coronavirus (SARS-CoV-2): Global burden and Bangladesh perspective

abstract:
  SARS-CoV-2, a new coronavirus strain responsible for COVID-19 has emerged in Wuhan City, China and still continuing its worldwide pandemic nature. Considering the severity of the disease, a number of studies are underway, and full genomic sequences have already been released in the last few weeks to enable the understanding of the evolutionary origin and molecular characteristics of this virus. Bioinformatics analysis, satellite derived imaging data and epidemiological attributes were employed to investigate origin, immunogenic resemblance and global threat of newly pandemic SARS-CoV-2 including Bangladesh perspective. Based on currently available genomic information, a phylogeny study was employed focusing four types of representative viral proteins (spike, membrane, envelope and nucleoprotein) of SARS-CoV-2, HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63, HKU1, MERS-CoV, HKU4, HKU5 and BufCoV-HKU26. The findings clearly demonstrated that SARS-CoV-2 exhibited evolutionary convergent relation with previously reported SARS-CoV. It was also found that SARS-CoV-2 proteins were highly similar and identical to SARS-CoV proteins, though proteins from other coronaviruses showed lower level of similarity and identical patterns. The cross-checked conservancy analysis of SARS-CoV-2 antigenic epitopes showed significant conservancy with antigenic epitopes derived from SARS-CoV. The study also prioritized the temperature comparison through satellite imaging alongside compiling and analyzing the epidemiological outbreak information on the 2019 novel coronavirus based on several open datasets on COVID-19 (SARS-CoV-2) and discussed possible threats to Bangladesh.


id: cord-269353-wgeuh1i2
title: The adaptation of codon usage of +ssRNA viruses to their hosts
author: Tian, Lin
date: 2018-06-02
txt: ./txt/cord-269353-wgeuh1i2.txt
cache: ./cache/cord-269353-wgeuh1i2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29864509/
doi: 10.1016/j.meegid.2018.05.034
summary:
  Consequently, we test the hypothesis that similarity of codon usage preference and the degree of matching between BSTVs and their hosts will be lower than that of NSTVs, which only need to coevolve with few hosts. Our results show that NSTVs have a higher degree of matching to their hosts'' tRNA pools than BSTVs. Further, analysis of the effective number of codons (ENC) infers that codon usage bias of NSTVs is relatively stronger than that of BSTVs. Thus, codon usage of NSTVs tends to better match their host than that of BSTVs. This supports the hypothesis that viruses adapt to the expression system of their host(s). As expected, our analysis show that generally NSTVs are more adapted to their hosts'' codon usage pattern and tRNA pools than BSTVs. This may help the virus to use the host transcript machinery more efficiently and, therefore, replicate faster.

abstract:
  Viruses depend on their host's cellular structure to survive. Most of them do not have tRNAs, their translation relies on hosts' tRNA pools. Over the course of evolution, viruses needed to optimally exploit cellular processes of their host. Thus, codon usage of a virus should coevolve with its host to efficiently and rapidly replicate. Some viruses can invade a broad spectrum of hosts (BSTVs), while others can invade a narrow spectrum only (NSTVs). Consequently, we test the hypothesis that similarity of codon usage preference and the degree of matching between BSTVs and their hosts will be lower than that of NSTVs, which only need to coevolve with few hosts. We compare the patterns of codon usage in 255 virus genomes to test this hypothesis. Our results show that NSTVs have a higher degree of matching to their hosts' tRNA pools than BSTVs. Further, analysis of the effective number of codons (ENC) infers that codon usage bias of NSTVs is relatively stronger than that of BSTVs. Thus, codon usage of NSTVs tends to better match their host than that of BSTVs. This supports the hypothesis that viruses adapt to the expression system of their host(s).


id: cord-271818-bedfwdyt
title: Distribution of bat-borne viruses and environment patterns
author: Afelt, Aneta
date: 2017-12-23
txt: ./txt/cord-271818-bedfwdyt.txt
cache: ./cache/cord-271818-bedfwdyt.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1567134817304355
doi: 10.1016/j.meegid.2017.12.009
summary:
  Viruses associated to synanthropic bat genera, such as Myotis or Scotophilus were associated to highly transformed habitats with human presence while viruses associated to fruit bat genera were correlated with natural environments with dense forest, grassland areas and regions of high elevation. Another conclusion from this analysis is the higher bat biodiversity observed in Cambodia associated to more anthropized environment than in LAO PDR where dense forest was predominant (Fig. 3) . The contributions of the environmental variables to the construction of this axis were the highest for elevation, SDI and grassland which were correlated on the negative side and connectivity, forest fragmentation, cropland cover, water cover, wetland cover and settlement cover which were distributed on the positive side (Fig. 4a) . The principal dimension of variability of the PCA opposed anthropogenic transformed lands on the positive side to more natural environments (i.e. forest, higher elevation areas and grassland areas, with low fragmentation) on the negative side (Fig. 4a) .

abstract:
  Environmental modifications are leading to biodiversity changes, loss and habitat disturbance. This in turn increases contacts between wildlife and hence the risk of transmission and emergence of zoonotic diseases. We analyzed the environment and land use using remote spatial data around the sampling locations of bats positive for coronavirus (21 sites) and astrovirus (11 sites) collected in 43 sites. A clear association between viruses and hosts was observed. Viruses associated to synanthropic bat genera, such as Myotis or Scotophilus were associated to highly transformed habitats with human presence while viruses associated to fruit bat genera were correlated with natural environments with dense forest, grassland areas and regions of high elevation. In particular, group C betacoronavirus were associated with mosaic habitats found in anthropized environments.


id: cord-271897-9oqzsd70
title: Molecular epidemiology of infectious bronchitis virus in Poland from 1980 to 2017
author: Domanska-Blicharz, Katarzyna
date: 2020-01-07
txt: ./txt/cord-271897-9oqzsd70.txt
cache: ./cache/cord-271897-9oqzsd70.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31917362/
doi: 10.1016/j.meegid.2020.104177
summary:
  Additionally, two strains from 1989 and 1997 formed a separate branch of the phylogenetic tree categorized as unique early Polish variants, and one strain was revealed to be the recombinant of these and GI-1 lineage viruses. Irrespective of year of isolation and S1-dependent genotype, the genome sequences of Polish IBV strains showed the presence of six genes and 13 ORFs: 5′UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3′UTR, however their individual genes and putative proteins had different lengths. Genotyping based on phylogenetic analysis of full S1 coding region sequences of 34 Polish IBV strains from the years 1980-2017 grouped (caption on next page) K. Phylogenetic analysis of the full S1 coding region showed that strain 80/ 1989 forms a separate branch on the tree designated as early Polish and was classified as a unique variant of IBV within the GI genotype.

abstract:
  The presence of infectious bronchitis virus (IBV) was identified for the first time in the poultry population in Poland at the end of the 1960s. From this time a few waves of epidemics caused by different IBV variants spread across the country. In order to gain more insight into the molecular epidemiology of IBV in Poland, in the present study the S1 coding region of 34 IBV isolates and nearly whole genome of 10 strains collected over a period of 38 years was characterized. Phylogenetic analysis showed that these strains belonged to five recently established IBV lineages: GI-1, GI-12, GI-13, GI-19 and GI-23. Additionally, two strains from 1989 and 1997 formed a separate branch of the phylogenetic tree categorized as unique early Polish variants, and one strain was revealed to be the recombinant of these and GI-1 lineage viruses. Irrespective of year of isolation and S1-dependent genotype, the genome sequences of Polish IBV strains showed the presence of six genes and 13 ORFs: 5′UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3′UTR, however their individual genes and putative proteins had different lengths. The phylogenetic analyses performed on the genome of ten Polish IBV strains revealed that they cluster into different groups. The Polish GI-1, GI-19 and GI-23 strains cluster with other similar viruses of these lineages, with the exception of the two strains from 1989 and 1997 which are different. It seems that in Poland in the 1980s and 1990s IBV strains with a unique genome backbone circulated in the field, which were then replaced by other strains belonging to other IBV lineages with a genome backbone specific to these lineages. The recombination analysis showed that some Polish strains resulted from a recombination event involving different IBV lineages, most frequently GI-13 and GI-19.


id: cord-276052-gk6n8slx
title: Isolation of Tioman virus from Pteropus giganteus bat in North-East region of India
author: Yadav, Pragya
date: 2016-09-09
txt: ./txt/cord-276052-gk6n8slx.txt
cache: ./cache/cord-276052-gk6n8slx.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1567134816303926
doi: 10.1016/j.meegid.2016.09.010
summary:
  During the survey for Nipah virus among bats at North-East region of India; Tioman virus (TioV), a new member of the Paramyxoviridae family was isolated from tissues of Pteropus giganteus bats for the first time in India. While investigating NiV in urine samples of giant fruit bats of the Pteropus genus on Tioman Island, Malaysia, in 2001, researchers isolated a novel virus which was placed in the Rubulavirus genus of the Paramyxoviridae family. In order to study susceptibility of different vertebrate cells to TioV, the infectious virus titer was determined by estimating 50% tissue culture infective dose (TCID 50 ) using Reed and Muench method (Reed and Muench, 1938) . Negative contrast electron microscopy of the cell supernatant of Vero CCL-81 infected with virus isolate showed the presence of virus particles with the typical paramyxovirus morphology. TioV isolated from kidney tissue homogenate of bat showed a titer of 10 4.61 /100 μL by TCID 50 in Vero CCL-81 cell line.

abstract:
  Bat-borne viral diseases are a major public health concern among newly emerging infectious diseases which includes severe acute respiratory syndrome, Nipah, Marburg and Ebola virus disease. During the survey for Nipah virus among bats at North-East region of India; Tioman virus (TioV), a new member of the Paramyxoviridae family was isolated from tissues of Pteropus giganteus bats for the first time in India. This isolate was identified and confirmed by RT-PCR, sequence analysis and electron microscopy. A range of vertebrate cell lines were shown to be susceptible to Tioman virus. Negative electron microscopy study revealed the “herringbone” morphology of the nucleocapsid filaments and enveloped particles with distinct envelope projections a characteristic of the Paramyxoviridae family. Sequence analysis of Nucleocapsid gene of TioV demonstrated sequence identity of 99.87% and 99.99% nucleotide and amino acid respectively with of TioV strain isolated in Malaysia, 2001. This report demonstrates the first isolation of Tioman virus from a region where Nipah virus activity has been noticed in the past and recent years. Bat-borne viruses have become serious concern world-wide. A Survey of bats for novel viruses in this region would help in recognizing emerging viruses and combating diseases caused by them.


id: cord-278465-tjjkz16y
title: Urbanization and the dynamics of RNA viruses in Mallards (Anas platyrhynchos)
author: Wille, Michelle
date: 2017-03-18
txt: ./txt/cord-278465-tjjkz16y.txt
cache: ./cache/cord-278465-tjjkz16y.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28323070/
doi: 10.1016/j.meegid.2017.03.019
summary:
  Recent studies have been instrumental in starting to describe dynamics and ecology of AMPV-1 and CoV in wild birds; 9-12% of migrating Mallards have CoV infections, compared to a lower prevalence (2%) of AMPV-1 towards the end of the migratory season in Sweden (Tolf et al., 2013b; Wille et al., 2015) . In context of IAV, and to a lesser degree CoV and APMV-1, an assessment of virus prevalence and diversity in an urban population will further allow us to assess if dynamics in wild birds are reflected in an urban setting. In comparing prevalence [Sept-Dec] between our urban dataset and a wild bird dataset from southern Sweden using the same qPCR methods (Wille et al., 2015) , autumnal prevalence for IAV (p b 0.0010) and CoV (p b 0.0010) is significantly different, where prevalence for both these viruses is lower in urban Mallards (Fig. 2) .

abstract:
  Urbanization is intensifying worldwide, and affects the epidemiology of infectious diseases. However, the effect of urbanization on natural host-pathogen systems remains poorly understood. Urban ducks occupy an interesting niche in that they directly interact with both humans and wild migratory birds, and either directly or indirectly with food production birds. Here we have collected samples from Mallards (Anas platyrhynchos) residing in a pond in central Uppsala, Sweden, from January 2013 to January 2014. This artificial pond is kept ice-free during the winter months, and is a popular location where the ducks are fed, resulting in a resident population of ducks year-round. Nine hundred and seventy seven (977) fecal samples were screened for RNA viruses including: influenza A virus (IAV), avian paramyxovirus 1, avian coronavirus (CoV), and avian astrovirus (AstroV). This intra-annual dataset illustrates that these RNA viruses exhibit similar annual patterns to IAV, suggesting similar ecological factors are at play. Furthermore, in comparison to wild ducks, autumnal prevalence of IAV and CoV are lower in this urban population. We also demonstrate that AstroV might be a larger burden to urban ducks than IAV, and should be better assessed to demonstrate the degree to which wild birds contribute to the epidemiology of these viruses. The presence of economically relevant viruses in urban Mallards highlights the importance of elucidating the ecology of wildlife pathogens in urban environments, which will become increasingly important for managing disease risks to wildlife, food production animals, and humans.


id: cord-278973-82n0d1dh
author: Li, Zhijie
date: 2016-05-31
txt: ./txt/cord-278973-82n0d1dh.txt
cache: ./cache/cord-278973-82n0d1dh.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.meegid.2016.05.039
doi: 10.1016/j.meegid.2016.05.039
summary:
  This study describes the isolation, molecular characterization and analysis of pathogenicity of MRV variant B/03 from wild short-nosed fruit bats. BALB/c mice experimentally infected with B/03 virus by intranasal inoculation developed severe respiratory distress with tissue damage and inflammation. MRV isolates were obtained from hosts with or without clinical signs of disease, and the virus can infect a broad range of mammals (Dermody et al., 2013) . In this study, we report the characterization of a novel MRV strain (called "B/03") isolated from healthy, wild shortnosed fruit bats in Guangdong province, China. In this study, one strain of MRV, B/03, was isolated by in vitro cell culture from thirty wild short-nosed fruit bat samples from Shaoguan city of China''s Guangdong province. Based on sequence comparison and phylogenetic analysis, we conclude that the B/03 isolate is a novel type 1 bat orthoreovirus, and it might have originated from gene segment mixing during infection with more than one MRV strain in nature.

title:
  Characterization and pathogenicity of a novel mammalian orthoreovirus from wild short-nosed fruit bats

abstract:
  Mammalian orthoreoviruses (MRVs) have a wide range of geographic distribution and have been isolated from humans and various animals. This study describes the isolation, molecular characterization and analysis of pathogenicity of MRV variant B/03 from wild short-nosed fruit bats. Negative stain electron microscopy illustrated that the B/03 strain is a non-enveloped icosahedral virus with a diameter of 70 nm. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) migration patterns showed that the B/03 viral genome contains 10 segments in a 3:3:4 arrangement. The isolate belongs to MRV serotype 1 based on S1 gene nucleotide sequence data. BALB/c mice experimentally infected with B/03 virus by intranasal inoculation developed severe respiratory distress with tissue damage and inflammation. Lastly, B/03 virus has an increased transmission risk between bats and humans or animals.


id: cord-279202-iyteg4h9
author: Shesheer Kumar, Munpally
date: 2008-01-05
txt: ./txt/cord-279202-iyteg4h9.txt
cache: ./cache/cord-279202-iyteg4h9.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1567134808000038
doi: 10.1016/j.meegid.2007.12.008
summary:
  title: Expression of alternate reading frame protein (F1) of hepatitis C virus in Escherichia coli and detection of antibodies for F1 in Indian patients Apart from the core (21 kD), a novel hepatitis C virus (HCV) frame shift protein (F1) is synthesized from the initiation codon of the polyprotein sequence followed by ribosomal frame shift into the −2/+1 reading frame. Further, results of western blots, carried out with patients sera titrated with purified core protein, confirmed the presence of antibodies specific to F1. The positive signal observed for F1 in western analysis with HCV infected sera suggests that F1 protein is synthesized in the natural course of HCV infection in Indian patients as well. Functional properties of a 16 kDa protein translated from an alternative open reading frame of the core encoding genomic region of hepatitis C virus

title:
  Expression of alternate reading frame protein (F1) of hepatitis C virus in Escherichia coli and detection of antibodies for F1 in Indian patients

abstract:
  Apart from the core (21 kD), a novel hepatitis C virus (HCV) frame shift protein (F1) is synthesized from the initiation codon of the polyprotein sequence followed by ribosomal frame shift into the −2/+1 reading frame. To date, no information is available on F1 protein of Indian isolates, and hence detection of antibodies for F1 protein in Indian patients assumes great relevance. Specific primers have been designed to amplify sequence coding for 120aa of truncated F1 (tF1). The amplified tF1 has been cloned in bacterial expression vector, pET21b for expression in Escherichia coli. Partially purified expressed protein has been subjected to western blot analysis using patients’ sera. Three HCV positive sera employed in western analysis showed positive signals to tF1, while sera from uninfected individuals failed to give any signals. Further, results of western blots, carried out with patients sera titrated with purified core protein, confirmed the presence of antibodies specific to F1. The positive signal observed for F1 in western analysis with HCV infected sera suggests that F1 protein is synthesized in the natural course of HCV infection in Indian patients as well. Presence of antibodies against F1 protein of subtype 1c has been demonstrated, for the first time, in Indian patients.


id: cord-279495-zxerb7de
author: Liu, Xiaoli
date: 2012-11-21
txt: ./txt/cord-279495-zxerb7de.txt
cache: ./cache/cord-279495-zxerb7de.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1567134812003292
doi: 10.1016/j.meegid.2012.09.016
summary:
  Four Massachusetts-type (Mass-type) strains of infectious bronchitis coronavirus (IBV) were compared genetically with the pathogenic M41 and H120 vaccine strains using the complete genomic sequences. Phylogenetic analysis, and pairwise comparison of full-length genomes and the nine genes, identified the occurrence of recombination events in the genome of strain CK/VH/LHLJ/07VII, which suggests that this virus originated from recombination events between M41and H120-like strains at the switch site located at the 3′ end of the nucleocapsid (N) genes. Herein, we sequenced the complete genome of four IBV Mass-type strains that showed S1 gene diversity (Liu et al., 2009; Ma et al., 2012; Sun et al., 2011) , and we present evidence for in-field recombination between pathogenic and vaccinal strains. Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus

title:
  Comparative analysis of four Massachusetts type infectious bronchitis coronavirus genomes reveals a novel Massachusetts type strain and evidence of natural recombination in the genome

abstract:
  Four Massachusetts-type (Mass-type) strains of infectious bronchitis coronavirus (IBV) were compared genetically with the pathogenic M41 and H120 vaccine strains using the complete genomic sequences. The results revealed that strains ck/CH/LNM/091017 and ck/CH/LDL/101212 were closely related to the H120 vaccine, which suggests that they might represent re-isolations of vaccine strains or variants of vaccine strains that have resulted from the accumulated point mutations after several passages in chickens. In contrast, strains ck/CH/LHLJ/07VII and ck/CH/LHLJ/100902 had a close genetic relationship with the pathogenic M41 strain. In addition, molecular markers have been identified that distinguish between field and vaccine (or vaccine-like) Mass-type viruses, which may be able to differentiate between field and vaccine strains for diagnostic purposes. Phylogenetic analysis, and pairwise comparison of full-length genomes and the nine genes, identified the occurrence of recombination events in the genome of strain CK/VH/LHLJ/07VII, which suggests that this virus originated from recombination events between M41- and H120-like strains at the switch site located at the 3′ end of the nucleocapsid (N) genes. To our knowledge, this is the first time that evidence for the evolution and natural recombination under field conditions between Mass-type pathogenic and vaccinal IBV strains has been documented. These findings provide insights into the emergence and evolution of the Mass-type IB coronaviruses and may help to explain the emergence of Mass-type IBV in chicken flocks all over the world.


id: cord-279836-lyvvtwvg
title: Molecular detection and genomic characteristics of bovine kobuvirus from dairy calves in China
author: Li, Huiping
date: 2019-06-24
txt: ./txt/cord-279836-lyvvtwvg.txt
cache: ./cache/cord-279836-lyvvtwvg.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.meegid.2019.103939
doi: 10.1016/j.meegid.2019.103939
summary:
  In this study, 96 diarrheic and 77 non-diarrheic fecal samples from dairy calves were collected from 14 dairy farms in 4 provinces to investigate the molecular prevalence and genomic characteristics of Bovine Kobuvirus (BKoV) in China. Interestingly, three potential novel VP1 lineages were identified from 15 complete VP1 sequences, and a unique triple nucleotide insertion which can result in an aa insertion, was first observed in the 11/12 VP0 fragments with 660 bp long in this study, compared with known BKoV VP0 sequences. Interestingly, phylogenetic tree based on aa sequences of these genomes showed that CHZ/CHINA was clustered into an independent branch, suggesting the strain may represent a novel BKoV strain. Further phylogenetic analysis based on genomic sequences revealed that CHZ/CHINA clusters on an independent branch, with the three VP0, VP3, VP1 protein aa sequences generating the same result (Fig. 3) , showing that CHZ/CHINA displays a larger genetic distance from the other three genomes and indicating that CHZ/CHINA may represent a novel BKoV strain.

abstract:
  In this study, 96 diarrheic and 77 non-diarrheic fecal samples from dairy calves were collected from 14 dairy farms in 4 provinces to investigate the molecular prevalence and genomic characteristics of Bovine Kobuvirus (BKoV) in China. The results showed that the BKoV positive rate for the diarrheic feces (35.42%) was significantly higher than that for the non-diarrheic feces (11.69%, p < 0.001). Interestingly, three potential novel VP1 lineages were identified from 15 complete VP1 sequences, and a unique triple nucleotide insertion which can result in an aa insertion, was first observed in the 11/12 VP0 fragments with 660 bp long in this study, compared with known BKoV VP0 sequences. Moreover, the first Chinese BKoV genome was successfully obtained from a diarrheic fecal sample, named CHZ/CHINA. The open reading frame (ORF) of the genome from strain CHZ/China shares 87.4%–88.3% nucleotide (nt) and 93.7%–96.4% amino acid (aa) identity, compared with the three known genomes of BKoV. Interestingly, phylogenetic tree based on aa sequences of these genomes showed that CHZ/CHINA was clustered into an independent branch, suggesting the strain may represent a novel BKoV strain. The findings contribute to better understanding the molecular characteristics and evolution of BKoV.


id: cord-288687-2dz8bu73
author: Zhai, Bintao
date: 2018-06-26
txt: ./txt/cord-288687-2dz8bu73.txt
cache: ./cache/cord-288687-2dz8bu73.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.meegid.2018.06.028
doi: 10.1016/j.meegid.2018.06.028
summary:
  In this study, a total of 138 blood specimens collected from Bactrian camels from Zhangye City in Gansu Province and Yili and Aksu in Xinjiang Province, China, were examined for the presence of Borrelia spp. Phylogenetic tree of the 5S-23S rRNA gene sequences of Borrelia species obtained in the present study and those deposited in GenBank from different countries; accession numbers are shown after isolate names. Phylogenetic tree of the 5S-23S rRNA gene sequences of Borrelia species obtained in the present study and those deposited in GenBank from different countries; accession numbers are shown after isolate names. Phylogenetic tree of the flaB gene sequences of Borrelia species obtained in the present study and those deposited in GenBank from different countries; accession numbers are shown after isolate names. Phylogenetic tree of the OspA gene sequences of Borrelia species obtained in the present study and those deposited in GenBank from different countries; accession numbers are shown after isolate names.

title:
  First detection and molecular identification of Borrelia species in Bactrian camel (Camelus bactrianus) from Northwest China

abstract:
  Comprehensive epidemiological surveys for Lyme disease have not been conducted for the Bactrian camel in China. In this study, a total of 138 blood specimens collected from Bactrian camels from Zhangye City in Gansu Province and Yili and Aksu in Xinjiang Province, China, were examined for the presence of Borrelia spp. Species-specificity nested PCR based on the 5S-23S rRNA, OspA, flaB and 16S rRNA genes revealed that the total positive rate of Borrelia spp. was 3.6% (5/138, 95% CI = 0.2–17.9). These results were confirmed by sequence analysis of the positive PCR products or positive colonies. This is the first report of Borrelia pathogens in camels in China. Two Borrelia species that cause Lyme disease and one that causes relapsing fever were identified in the camel blood samples by sequencing. The findings of this study indicate that the Bactrian camel may serve as a potential natural host of Lyme disease and/or relapsing fever in China.


id: cord-293588-7pflfznh
title: Analysis of the codon usage of the ORF2 gene of feline calicivirus
author: Zang, Minghui
date: 2017-06-16
txt: ./txt/cord-293588-7pflfznh.txt
cache: ./cache/cord-293588-7pflfznh.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.meegid.2017.06.013
doi: 10.1016/j.meegid.2017.06.013
summary:
  Furthermore, there was a significant correlation between the ENC values and the nucleotide compositions (p b 0.01), which indicates that mutational bias influences the synonymous codon usage pattern of the ORF2 gene of FCV. We found a correlation between the Aroma values and U3 s, G3 s and GC3s (p b 0.05), confirming that natural selection influences the codon usage bias of the FCV ORF2 gene. Thus, natural selection plays a major role in shaping the codon usage bias of ORF2 gene of FCV compared to mutational pressure. Here, we used ENC-Plots (Fig. 1) and PCA (Fig. 3) analysis according to the geographical distribution to investigate the major factors shaping the codon usage bias of the FCV ORF2 gene . Furthermore, analysis of the relationships between nucleotide composition and the codon contents at the third base positions suggested that mutation pressure is one of the factors in shaping the codon usage of FCV ORF2.

abstract:
  Feline calicivirus (FCV) is a highly prevalent pathogen of the domestic cat that causes acute infections of the oral and upper respiratory tract. The E region of the ORF2 protein is responsible for the induction of virus-neutralizing antibodies, thus it is important to understand the codon usage of this gene. Here, analysed 90 coding sequences of ORF2 and show that it undergoes a low codon usage bias. In addition, although mutational bias is one of the factors shaping the codon usage bias of this gene, natural selection plays a more significant role. Our results reveal part of the mechanisms driving FCV evolution, which will lay foundation for the further research of FCV.


id: cord-297530-7zbvgvk8
title: Phylogenetic and epidemic modeling of rapidly evolving infectious diseases
author: Kühnert, Denise
date: 2011-08-31
txt: ./txt/cord-297530-7zbvgvk8.txt
cache: ./cache/cord-297530-7zbvgvk8.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S156713481100284X
doi: 10.1016/j.meegid.2011.08.005
summary:
  By using Kingman''s coalescent as a prior density on trees, Bayesian inference can be used to simultaneously estimate the phylogeny of the viral sequences and the demographic history of the virus population (Drummond et al., 2002 (Drummond et al., , 2005 , see Box 1). A maximum likelihood based method (the single rate dated tips (SRDT) model; Rambaut, 2000) , estimates ancestral divergence times and overall substitution rate on a fixed tree, assuming a strict molecular clock. While the generalized skyline plot is a good tool for data exploration, and to assist in model selection (e.g., Pybus et al., 2003; Lemey et al., 2004) , it infers demographic history based on a single input tree and therefore does not account for sampling error produced by phylogenetic reconstruction nor for the intrinsic stochasticity of the coalescent process.

abstract:
  Epidemic modeling of infectious diseases has a long history in both theoretical and empirical research. However the recent explosion of genetic data has revealed the rapid rate of evolution that many populations of infectious agents undergo and has underscored the need to consider both evolutionary and ecological processes on the same time scale. Mathematical epidemiology has applied dynamical models to study infectious epidemics, but these models have tended not to exploit – or take into account – evolutionary changes and their effect on the ecological processes and population dynamics of the infectious agent. On the other hand, statistical phylogenetics has increasingly been applied to the study of infectious agents. This approach is based on phylogenetics, molecular clocks, genealogy-based population genetics and phylogeography. Bayesian Markov chain Monte Carlo and related computational tools have been the primary source of advances in these statistical phylogenetic approaches. Recently the first tentative steps have been taken to reconcile these two theoretical approaches. We survey the Bayesian phylogenetic approach to epidemic modeling of infection diseases and describe the contrasts it provides to mathematical epidemiology as well as emphasize the significance of the future unification of these two fields.


id: cord-297679-swmb19ty
title: Genetic and phylogenetic analysis of canine bufavirus from Anhui Province, Eastern China
author: Wang, Yong
date: 2020-10-20
txt: ./txt/cord-297679-swmb19ty.txt
cache: ./cache/cord-297679-swmb19ty.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.meegid.2020.104600
doi: 10.1016/j.meegid.2020.104600
summary:
  title: Genetic and phylogenetic analysis of canine bufavirus from Anhui Province, Eastern China Selective pressure analysis of the VP2 region indicated that the canine bufavirus (CBuV) was mainly subject to negative selection during evolution. In 2018, a virus with a close genetic relationship to the human bufavirus (HuBuV) was detected in dogs with either gastroenteric or respiratory disease in Italy; it was named canine bufavirus (CBuV) (Martella et al., 2018) . To this end, fecal samples from different cities in Anhui province, eastern China were collected in this study to explore the molecular and phylogenetic characteristics of CBuV. And the negative selection codons were located on B-cell epitopes, it did not affect the immunogenicity of CBuVs. This study provides a reference for further understanding of the epidemic and molecular characteristics of the virus in China.

abstract:
  Bufavirus is a novel virus associated with canine gastroenteritis. Three strains of bufavirus were first detected in dog feces collected from Anhui province in Eastern China. The near-complete genome sequences were amplified. Sequence alignment showed 98.3–99.5% homology between the three bufavirus strains and reference strains. Phylogenetic analysis showed the distributed viruses forming a cluster of close relationships. Selective pressure analysis of the VP2 region indicated that the canine bufavirus (CBuV) was mainly subject to negative selection during evolution. The negative selection site was located on the residue of B-cell epitopes, indicating minimal change to the virus's immunogenicity. Since this is the first report of CBuV circulating in Anhui Province, this study will provide further understanding of the phylogenetic and molecular characteristics of CBuV and serve as a reference for prevention and vaccine development.


id: cord-299827-lxyo3z3u
title: A novel feline norovirus in diarrheic cats
author: Di Martino, Barbara
date: 2015-12-29
txt: ./txt/cord-299827-lxyo3z3u.txt
cache: ./cache/cord-299827-lxyo3z3u.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1567134815300848
doi: 10.1016/j.meegid.2015.12.019
summary:
  In the full-length ORF2, encoding the VP1 capsid protein, the virus was genetically closest to the canine GVI.2 NoV strains C33/Viseu/2007/PRT and FD53/2007/ITA (81.0–84.0% nt and 93.0–94.0% aa identities), suggesting a recombination nature, with the cross-over site being mapped to the ORF1-ORF2 junction. c o m / l o c a t e / m e e g i d Altogether these findings indicate that diverse NoV strains may infect cats, as observed in dogs, and that the feline and canine host may be infected by the same NoV strains, thus constituting an enlarged host reservoir for these animal NoVs. In order to draw a more complete picture of NoVs molecular epidemiology in cats, in this study a collection of fecal specimens from diarrheic and healthy animals was screened using either broadly-reactive primers for caliciviruses and primers specific for NoVs. A total of 105 stool samples from domestic cats aged 2-12 months were collected from April to July 2013 in three different shelters located in South Italy.

abstract:
  By screening a collection of fecal samples from young cats housed in three different shelters in South Italy, noroviruses (NoVs) were found in 3/48 (6.2%) specimens of animals with enteritis signs while they were not detected in samples collected from healthy cats (0/57). Upon sequence analysis of the short RNA-dependent RNA polymerase (RdRp) region, the three strains displayed the highest nucleotide (nt) and amino acid (aa) identities to the prototype GIV.2 strain lion/Pistoia/387/06/ITA (91.0–93.0% nt and 97.0–98.0% aa). The sequence of ~ 3.4-kb portion at the 3′ end of the genome of a NoV strain, TE/77-13/ITA, was determined. In the full-length ORF2, encoding the VP1 capsid protein, the virus was genetically closest to the canine GVI.2 NoV strains C33/Viseu/2007/PRT and FD53/2007/ITA (81.0–84.0% nt and 93.0–94.0% aa identities), suggesting a recombination nature, with the cross-over site being mapped to the ORF1-ORF2 junction. Based on the full-length VP1 amino acid sequence, we classified the novel feline NoV, together with the canine strains Viseu and FD53, as a genotype 2, within the genogroup GVI. These findings indicate that, as observed for GIV NoV, GVI strains may infect both the canine and feline host. Unrestricted circulation of NoV strains in small carnivores may provide the basis for quick genetic diversification of these viruses by recombination. Interspecies circulation of NoVs in pets must also be considered when facing outbreaks of enteric diseases in these animals.


id: cord-299989-p59u6qa0
author: Zhang, Lei
date: 2020-06-18
txt: ./txt/cord-299989-p59u6qa0.txt
cache: ./cache/cord-299989-p59u6qa0.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.meegid.2020.104428
doi: 10.1016/j.meegid.2020.104428
summary:
  title: Comparative analysis of SARS-CoV-2 receptor ACE2 expression in multiple solid tumors and matched non-diseased tissues Here, we analyze a large data set comprising ACE2 mRNA expression for 7592 tissue samples across 22 types of primary solid tumor and 4461 samples across matched 18 non-diseased tissues. Our results unravel eight normal tissues and 10 primary solid tumors, which might be at high risk of SARS-CoV-2 infection. These findings may provide additional insight into the prevention and treatment of SARS-CoV-2 infection, in particular for patients with these 10 vulnerable cancer types. Interestingly, our finding that ACE2 was highly expressed in breast appears to be in contrast to a retrospective study on nine pregnant women with COVID-19 in the third trimester, in which the colostrum from six patients tested negative for SARS-CoV-2 (H.

title:
  Comparative analysis of SARS-CoV-2 receptor ACE2 expression in multiple solid tumors and matched non-diseased tissues

abstract:
  The emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a global public health emergency. SARS-CoV-2 employs the host cell receptor ACE2 for cellular entry. Nonetheless, the differences in ACE2 expression pattern in lung versus other normal and solid tumor tissues remain incompletely characterized. Here, we analyze a large data set comprising ACE2 mRNA expression for 7592 tissue samples across 22 types of primary solid tumor and 4461 samples across matched 18 non-diseased tissues. Our results unravel eight normal tissues and 10 primary solid tumors, which might be at high risk of SARS-CoV-2 infection. These findings may provide additional insight into the prevention and treatment of SARS-CoV-2 infection, in particular for patients with these 10 vulnerable cancer types.


id: cord-302679-wytog9cv
author: Panda, Somnath
date: 2020-06-23
txt: ./txt/cord-302679-wytog9cv.txt
cache: ./cache/cord-302679-wytog9cv.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.meegid.2020.104439
doi: 10.1016/j.meegid.2020.104439
summary:
  title: Bioinformatics analysis reveals four major hexon variants of human adenovirus type-3 (HAdV-3) as the potential strains for development of vaccine and siRNA-based therapeutics against HAdV-3 respiratory infections Then, we have identified the conserved locations in HVR encoding regions of the hexon gene and fr om those locations we have designed functional siRNAs. Next, we have also designed immunogenic vaccine peptide epitopes from the hexon protein that can be used to design a vaccine. The variations among the HVR encoding regions of the hexon gene of 3Hv-1 to 3Hv-4 were shown by multi-sequence alignment (MSA), in silico RE analysis Numerous tools are available to design functional siRNAs such as MysiRNA-designer [22] , siDirect [23] and siMAX-siRNA Designer (https://eurofinsgenomics.eu/en/dnarna-oligonucleotides/custom-dna-rna-oligos/simax-sirna/) etc. We have designed functional siRNAs from those conserved regions and immunogenic vaccine peptide epitopes from the hexon protein.

title:
  Bioinformatics analysis reveals four major hexon variants of human adenovirus type-3 (HAdV-3) as the potential strains for development of vaccine and siRNA-based therapeutics against HAdV-3 respiratory infections

abstract:
  Human adenovirus type 3 (HAdV-3) encompasses 15–87% of all adenoviral respiratory infections. The significant morbidity and mortality, especially among the neonates and immunosuppressed patients, demand the need for a vaccine or a targeted antiviral against this type. However, due to the existence of multiple hexon variants (3Hv-1 to 3Hv-25), the selection of vaccine strains of HAdV-3 is challenging. This study was designed to evaluate HAdV-3 hexon variants for the selection of potential vaccine candidates and the use of hexon gene as a target for designing siRNA that can be used as a therapy. Based on the data of worldwide distribution, duration of circulation, co-circulation and their percentage among all the variants, 3Hv-1 to 3Hv-4 were categorized as the major hexon variants. Phylogenetic analysis and the percentage of homology in the hypervariable regions followed by multi-sequence alignment, zPicture analysis and restriction enzyme analysis were carried out. In the phylogram, the variants were arranged in different clusters. The HVR encoding regions of hexon of 3Hv-1 to 3Hv-4 showed 16 point mutations resulting in 12 amino acids substitutions. The homology in HVRs was 81.81–100%. Therefore, the major hexon variants are substantially different from each other which justifies their inclusion as the potential vaccine candidates. Interestingly, despite the significant differences in the DNA sequence, there were many conserved areas in the HVRs, and we have designed functional siRNAs form those locations. We have also designed immunogenic vaccine peptide epitopes from the hexon protein using bioinformatics prediction tool. We hope that our developed siRNAs and immunogenic vaccine peptide epitopes could be used in the future development of siRNA-based therapy and designing a vaccine against HAdV-3.


id: cord-311144-tumtzad8
title: Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America
author: Franco-Muñoz, Carlos
date: 2020-09-17
txt: ./txt/cord-311144-tumtzad8.txt
cache: ./cache/cord-311144-tumtzad8.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32950697/
doi: 10.1016/j.meegid.2020.104557
summary:
  A total of 504 amino acid and nucleotide sequences of the S and N proteins of SARS-CoV-2 from seven South American countries (Argentina, Brazil, Chile, Ecuador, Peru, Uruguay, and Colombia), reported as of June 3, and corresponding to samples collected between March and April 2020, were compared through substitution matrices using the Muscle algorithm in MEGA X. Substitution matrices of nucleotides and amino acids of S and N proteins were generated from a multiple sequence alignment with the reference genome against the 43 assembled Colombian SARS-CoV-2 genomes (Table 1) using the Muscle algorithm (Edgar, 2004) in MEGA X (Kumar et al., 2016) . The analysis of substitution frequencies by country shows that D614G substitution in the S protein was frequent in Argentina, Brazil, Chile, Colombia and Peru, with J o u r n a l P r e -p r o o f Journal Pre-proof 80-100% of the reported sequences ( Fig. 2A) .

abstract:
  SARS-CoV-2 is a new member of the genus Betacoronavirus, responsible for the COVID-19 pandemic. The virus crossed the species barrier and established in the human population taking advantage of the spike protein high affinity for the ACE receptor to infect the lower respiratory tract. The Nucleocapsid (N) and Spike (S) are highly immunogenic structural proteins and most commercial COVID-19 diagnostic assays target these proteins. In an unpredictable epidemic, it is essential to know about their genetic variability. The objective of this study was to describe the substitution frequency of the S and N proteins of SARS-CoV-2 in South America. A total of 504 amino acid and nucleotide sequences of the S and N proteins of SARS-CoV-2 from seven South American countries (Argentina, Brazil, Chile, Ecuador, Peru, Uruguay, and Colombia), reported as of June 3, and corresponding to samples collected between March and April 2020, were compared through substitution matrices using the Muscle algorithm in MEGA X. Forty-three sequences from 13 Colombian departments were obtained in this study using the Oxford Nanopore and Illumina MiSeq technologies, following the amplicon-based ARTIC network protocol. The substitutions D614G in S and R203K/G204R in N were the most frequent in South America, observed in 83% and 34% of the sequences respectively. Strikingly, genomes with the conserved position D614 were almost completely replaced by genomes with the G614 substitution between March to April 2020. A similar replacement pattern was observed with R203K/G204R although more marked in Chile, Argentina and Brazil, suggesting similar introduction history and/or control strategies of SARS-CoV-2 in these countries. It is necessary to continue with the genomic surveillance of S and N proteins during the SARS-CoV-2 pandemic as this information can be useful for developing vaccines, therapeutics and diagnostic tests.


id: cord-318577-04jsj9sb
title: Identification of a novel canine norovirus
author: Bodnar, Livia
date: 2017-04-24
txt: ./txt/cord-318577-04jsj9sb.txt
cache: ./cache/cord-318577-04jsj9sb.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.meegid.2017.04.020
doi: 10.1016/j.meegid.2017.04.020
summary:
  By screening a collection of fecal samples from young dogs from different European countries, noroviruses (NoVs) were found in 13/294 (4.4%) animals with signs of enteritis whilst they were not detected in healthy dogs (0/42). Interestingly, significant sequence variation has been found across different canine/feline NoV strains identified to date, allowing the classification of at least 4 genotypes from three distinct genogroups, i.e. GIV.2, GVI.1 and GVI.2 and GVII ( Table 1 ). In order to draw a more complete picture of NoV molecular epidemiology in dogs, in this study a collection of fecal specimens from diarrheic and healthy animals obtained from different European countries was screened using both broadly-reactive primers for caliciviruses and primers specific for NoVs. The sequence of a large portion of the genome at the 3′ end of two canine NoV strains was determined.

abstract:
  By screening a collection of fecal samples from young dogs from different European countries, noroviruses (NoVs) were found in 13/294 (4.4%) animals with signs of enteritis whilst they were not detected in healthy dogs (0/42). An informative portion of the genome (3.4 kb at the 3′ end) was generated for four NoV strains. In the capsid protein VP1 region, strains 63.15/2015/ITA and FD53/2007/ITA were genetically related to the canine GVI.2 strain C33/Viseu/2007/PRT (97.4–98.6% nt and 90.3–98.6% aa). Strain FD210/2007/ITA displayed the highest identity to the GVI.1 canine strain Bari/91/2007/ITA (88.0% nt and 95.0% aa). Strain 5010/2009/ITA displayed only 66.6–67.6% nt and 75.5–81.6% aa identities to the GVI.1 canine strains FD210/2007/ITA and Bari/91/2007/ITA and the GVI feline strain M49-1/2012/JPN. Identity to the other canine/feline NoVs strains in the VP1 was lower than 67.6% nt and 62.7% aa. Based on the full-length VP1 amino acid sequence and the criteria proposed for distinction of NoV genotypes, the canine NoV 5010/2009/ITA could represent the prototype of a third GVI genotype, thus providing further evidence for the genetic heterogeneity of NoVs in carnivores.


id: cord-318625-hf7fgtnp
author: Vashi, Yoya
date: 2020-05-27
txt: ./txt/cord-318625-hf7fgtnp.txt
cache: ./cache/cord-318625-hf7fgtnp.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1567134820302136
doi: 10.1016/j.meegid.2020.104382
summary:
  The present study followed computational approaches to identify Band T-cell epitopes for the spike (S) glycoprotein of SARS-CoV-2 by its interactions with the human leukocyte antigen alleles. The work could be useful for understanding the immunodominant regions in the surface protein of SARS-CoV-2 and could potentially help in designing some peptide-based diagnostics. The potential epitope regions were predicted using the sequence of the S protein of SARS-CoV-2 that showed the least variability (GenBank accession number NC_045512). We identified 18 linear epitopes, predicted by ElliPro (IEDB), which contained regions from 19 of our selected peptides (highlighted in red in Table 2 ). The study could help us to use the predicted peptide as an immunogen for the development of diagnostics and vaccines against SARS-CoV-2. In the present study, peptide segments were identified on S proteins for the development of diagnostics and vaccines against SARS-CoV-2.

title:
  Understanding the B and T cell epitopes of spike protein of severe acute respiratory syndrome coronavirus-2: A computational way to predict the immunogens

abstract:
  The 2019 novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak has caused a large number of deaths, with thousands of confirmed cases worldwide. The present study followed computational approaches to identify B- and T-cell epitopes for the spike (S) glycoprotein of SARS-CoV-2 by its interactions with the human leukocyte antigen alleles. We identified 24 peptide stretches on the SARS-CoV-2 S protein that are well conserved among the reported strains. The S protein structure further validated the presence of predicted peptides on the surface, of which 20 are surface exposed and predicted to have reasonable epitope binding efficiency. The work could be useful for understanding the immunodominant regions in the surface protein of SARS-CoV-2 and could potentially help in designing some peptide-based diagnostics. Also, identified T-cell epitopes might be considered for incorporation in vaccine designs.


id: cord-319399-r5hgfsxz
author: Chakraborty, Supriyo
date: 2019-11-06
txt: ./txt/cord-319399-r5hgfsxz.txt
cache: ./cache/cord-319399-r5hgfsxz.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.meegid.2019.104106
doi: 10.1016/j.meegid.2019.104106
summary:
  title: Japanese encephalitis virus: A multi-epitope loaded peptide vaccine formulation using reverse vaccinology approach The predicted epitopes identified in five proteins selected in this study could be promising for formulating a peptide vaccine against JEV and hence, could prevent the spread of JEV in affected individuals. In this study, the potential epitopes for peptide vaccine formulation were identified in five proteins of JEV namely E, prM, NS1, NS3 and NS5. In a study, the probable epitopes were identified from E6 protein of hrHPVs and these epitopes were reported to possess competence in preparing successful peptide vaccine against hrHPVs. Based on in silico approach, it was suggested Table 2a Immunogenicity (Ig) and number of aliphatic amino acids in T-cell epitopes of JEV (Hopp & Woods approach, 1981 The present study suggested that a multi-epitope-based peptide vaccine against JEV could be developed by combining the promising Bcell and T-cell epitopes found in E, prM, NS1, NS3 and NS5 proteins.

title:
  Japanese encephalitis virus: A multi-epitope loaded peptide vaccine formulation using reverse vaccinology approach

abstract:
  Japanese encephalitis (JE) is a serious leading health complication emerging expansively that has severely affected the survival rate of human beings. This fatal disease is caused by JE Virus (JEV). The current study was carried out for designing a multi-epitope loaded peptide vaccine to prevent JEV. Based on reverse vaccinology and in silico approaches, octapeptide B-cell and hexapeptide T-cell epitopes belonging to five proteins, viz. E, prM, NS1, NS3 and NS5 of JEV were determined. Hydrophilicity, antigenicity, immunogenicity and aliphatic amino acids of the epitopes were estimated. Further, the epitopes were analyzed for different physicochemical parameters, e.g. total net charges, amino acid composition and Boman index. Out of all the epitopes, a total of four T-cell epitopes namely KRADSS, KRSRRS, SKRSRR and KECPDE and one B-cell epitope i.e. PKPCSKGD were found to have potential for raising immunity in human against the pathogen. Taking into account the outcome of this study, the pharmaceutical industries could initiate efforts to combine the identified epitopes together with adjuvant or carrier protein to develop a multi-epitope-loaded peptide vaccine against JEV. The peptide vaccine, being cost effective, could be administered as a prophylactic measure and in JEV infected individuals to combat the spread of this virus in human population. However, prior to administration into human beings, the vaccine must pass through several clinical trials.


id: cord-325679-4lfpy84d
author: Niu, Ting-Jiang
date: 2018-12-06
txt: ./txt/cord-325679-4lfpy84d.txt
cache: ./cache/cord-325679-4lfpy84d.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1567134818309547
doi: 10.1016/j.meegid.2018.12.010
summary:
  To investigate the presence and genetic variability of FeKoV in northeast China, 197 fecal samples were collected from 105 cats with obvious diarrhea and 92 asymptomatic cats in Shenyang, Jinzhou, Changchun, Jilin and Harbin regions, Northeast China, and viruses were detected by RT-PCR with universal primers targeting all kobuviruses. By genetic analysis based on partial 3D gene, all kobuvirus-positive samples were more closely related to previous FeKoV strains with high identities of 90.5%–97.8% and 96.6%–100% at the nucleotide and amino acid levels. Additionally, phylogenetic analysis based on the complete VP1 gene indicated that all FeKoV strains identified in this study were placed into a cluster, which separated from other reference strains previously reported, and three identical amino acid substitutions were present at the C-terminal of the VP1 protein for these FeKoV strains. The genetic analysis based on the partial RdRp gene indicated that FeKoV strains shared higher nucleotide (81.2%-82.1%) and amino acid identities (91.4%-92.1%) with CaKoV strains previously reported (Kapoor et al.

title:
  Detection and genetic characterization of kobuvirus in cats: The first molecular evidence from Northeast China

abstract:
  Feline kobuvirus (FeKoV), a novel picornavirus of the genus kobuvirus, was initially identified in the feces of cats with diarrhea in South Korea in 2013. To date, there is only one report of the circulation of kobuvirus in cats in southern China. To investigate the presence and genetic variability of FeKoV in northeast China, 197 fecal samples were collected from 105 cats with obvious diarrhea and 92 asymptomatic cats in Shenyang, Jinzhou, Changchun, Jilin and Harbin regions, Northeast China, and viruses were detected by RT-PCR with universal primers targeting all kobuviruses. Kobuvirus was identified in 28 fecal samples with an overall prevalence of 14.2% (28/197) of which 20 samples were co-infected with feline parvovirus (FPV) and/or feline bocavirus (FBoV). Diarrhoeic cats had a higher kobuvirus prevalence (19.1%, 20/105) than asymptomatic cats (8.7%, 8/92). By genetic analysis based on partial 3D gene, all kobuvirus-positive samples were more closely related to previous FeKoV strains with high identities of 90.5%–97.8% and 96.6%–100% at the nucleotide and amino acid levels. Additionally, phylogenetic analysis based on the complete VP1 gene indicated that all FeKoV strains identified in this study were placed into a cluster, which separated from other reference strains previously reported, and three identical amino acid substitutions were present at the C-terminal of the VP1 protein for these FeKoV strains. Furthermore, two complete FeKoV polyprotein genomes were successfully obtained from two positive samples and designated 16JZ0605 and 17CC0811, respectively. The two strains shared 92.9%–94.9% nucleotide identities and 96.8%–98.4% amino acid identities to FeKoV prototype strains. Phylogenetic analysis indicated that FeKoVs were clustered according to their geographical regions, albeit with limited sequences support. This study provides the first molecular evidence that FeKoV circulates in cats in northeast China, and these FeKoVs exhibit genetic diversity and unique evolutionary trend.


id: cord-331237-t3z1hbox
author: Ogawa, Hirohito
date: 2015-03-16
txt: ./txt/cord-331237-t3z1hbox.txt
cache: ./cache/cord-331237-t3z1hbox.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1567134815000982
doi: 10.1016/j.meegid.2015.03.013
summary:
  helvum samples and previously reported sequences, revealed that 12 of the fragments grouped with Leptospira borgpetersenii and Leptospira kirschneri; however, the remaining 58 flaB fragments appeared not to be associated with any reported species. Additionally, the 16S ribosomal RNA gene (rrs) amplified from 27 randomly chosen flaB-positive samples was compared with previously reported sequences, including bat-derived Leptospira spp. A nested PCR based on the flagellin B gene (flaB) sequence was used to amplify the extracted DNA samples (n = 529) to detect the flaB gene of pathogenic Leptospira spp. Six flaB fragments (ZFB08-62, ZFB09-25, ZFB09-32, ZFB12-05, ZFB12-107 and ZFB12-110) in the FC5 cluster were related to the corresponding gene sequences, all of which were identical to Leptospira borgpetersenii strains including Jules, De 10, Arborea, Poi, and Veldrat Batavia 46. The phylogenetic analyses of flaB and rrs infer that genes from potentially pathogenic Leptospira spp.

title:
  Molecular epidemiology of pathogenic Leptospira spp. in the straw-colored fruit bat (Eidolon helvum) migrating to Zambia from the Democratic Republic of Congo

abstract:
  The role played by bats as a potential source of transmission of Leptospira spp. to humans is poorly understood, despite various pathogenic Leptospira spp. being identified in these mammals. Here, we investigated the prevalence and diversity of pathogenic Leptospira spp. that infect the straw-colored fruit bat (Eidolon helvum). We captured this bat species, which is widely distributed in Africa, in Zambia during 2008–2013. We detected the flagellin B gene (flaB) from pathogenic Leptospira spp. in kidney samples from 79 of 529 E. helvum (14.9%) bats. Phylogenetic analysis of 70 flaB fragments amplified from E. helvum samples and previously reported sequences, revealed that 12 of the fragments grouped with Leptospira borgpetersenii and Leptospira kirschneri; however, the remaining 58 flaB fragments appeared not to be associated with any reported species. Additionally, the 16S ribosomal RNA gene (rrs) amplified from 27 randomly chosen flaB-positive samples was compared with previously reported sequences, including bat-derived Leptospira spp. All 27 rrs fragments clustered into a pathogenic group. Eight fragments were located in unique branches, the other 19 fragments were closely related to Leptospira spp. detected in bats. These results show that rrs sequences in bats are genetically related to each other without regional variation, suggesting that Leptospira are evolutionarily well-adapted to bats and have uniquely evolved in the bat population. Our study indicates that pathogenic Leptospira spp. in E. helvum in Zambia have unique genotypes.


id: cord-331503-whw2pq1f
title: Role of the IFNG +874T/A polymorphism in Chagas disease in a Colombian population
author: Torres, Orlando A.
date: 2010-03-30
txt: ./txt/cord-331503-whw2pq1f.txt
cache: ./cache/cord-331503-whw2pq1f.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/20359550/
doi: 10.1016/j.meegid.2010.03.009
summary:
  The human IFNG IFN-g Chagas disease Single nucleotide polymorphism (SNP) Genetics Association study A B S T R A C T Genetic susceptibility to Trypanosoma cruzi infection and the development of cardiomyopathy is complex, heterogeneous, and likely involves several genes. Here we investigated the association between the interferon-gamma gene (IFNG) +874T/A polymorphism and Chagas disease, focusing on susceptibility and severity. Here we investigated the association between the interferon-gamma gene (IFNG) +874T/A polymorphism and Chagas disease, focusing on susceptibility and severity. Due to this, we selected the +874T/A polymorphism of IFNG to assess the potential association of this SNP in the susceptibility and/or clinical features of Chagas disease in a Colombian population from an endemic area. We found a statistically significant difference in the distribution of the A/A genotype (low production of IFN-g) and the A allele at the IFNG polymorphism between Chagas patient and control groups.

abstract:
  Genetic susceptibility to Trypanosoma cruzi infection and the development of cardiomyopathy is complex, heterogeneous, and likely involves several genes. Previous studies have implicated cytokine and chemokine genes in susceptibility to Chagas disease. Here we investigated the association between the interferon-gamma gene (IFNG) +874T/A polymorphism and Chagas disease, focusing on susceptibility and severity. This study included 236 chagasic patients (asymptomatic, n = 116; cardiomyopathic, n = 120) and 282 healthy controls from a Colombian population where T. cruzi is highly endemic. Individuals were genotyped for functional single nucleotide polymorphism (SNP; rs2430561; A/T) of the IFNG gene by amplification refractory mutational system PCR (ARMS-PCR). Moreover, clinical manifestations of Chagas in patients were analyzed. We found a significant difference in the distribution of the IFNG +874 “A” allele between patients and healthy controls (P = 0.003; OR = 1.46, 95% CI, 1.13–1.89). The frequency of the IFNG +874 genotype A/A, which is associated with reduced production of interferon-gamma, was increased in the patients relative to controls (38.1% vs. 26.6%). We compared the frequencies of IFNG alleles and genotypes between asymptomatic patients and those with chagasic cardiomyopathy and found no significant difference. Our data suggest that the IFNG +874T/A genetic polymorphism may be involved in susceptibility but not in the progression of Chagas disease in this Colombian population.


id: cord-333712-sdtxi8xw
title: Geographical structure of bat SARS-related coronaviruses
author: Yu, Ping
date: 2019-02-06
txt: ./txt/cord-333712-sdtxi8xw.txt
cache: ./cache/cord-333712-sdtxi8xw.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S156713481830902X
doi: 10.1016/j.meegid.2019.02.001
summary:
  In 2005, the discovery of novel CoVs related to human SARS-CoVs in Chinese horseshoe bats (genus Rhinolophus), named SARS-related coronaviruses (SARSr-CoVs), provided new clue that bats may be the natural host for SARS-CoV (Lau et al., 2005; Li et al., 2005) . SARS-CoV and SARSr-CoVs belong to lineage B of genus Betacoronavirus in the family Coronaviridae and share the same genomic organization with other coronaviruses, including genes coding for 16 nonstructural proteins (nsp, in ORF1ab domain), the structural proteins like spike protein (S), envelope (E), membrane (M), nucleocapsid (N) and other several genes (Perlman and Netland, 2009; Woo et al., 2009) . Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences Identification of diverse alphacoronaviruses and genomic characterization of a novel severe acute respiratory syndrome-like coronavirus from bats in China

abstract:
  Bats are the natural reservoirs of severe acute respiratory syndrome coronavirus (SARS-CoV) which caused the outbreak of human SARS in 2002–2003. We introduce the genetic diversity of SARS-related coronaviruses (SARSr-CoVs) discovered in bats and provide insights on the bat origin of human SARS. We also analyze the viral geographical structure that may improve our understanding of the evolution of bat SARSr-CoVs.


id: cord-338723-3vm23fgy
author: Lee, In-Hee
date: 2020-08-26
txt: ./txt/cord-338723-3vm23fgy.txt
cache: ./cache/cord-338723-3vm23fgy.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.meegid.2020.104507
doi: 10.1016/j.meegid.2020.104507
summary:
  title: A survey of genetic variants in SARS-CoV-2 interacting domains of ACE2, TMPRSS2 and TLR3/7/8 across populations Nonetheless, a systematic mutagenesis study on the receptor binding domain of ACE2 is required to understand the difference in host-viral interaction across populations. SARS-CoV-2 is an enveloped and positive single-stranded RNA (ssRNA) virus and initiates human cell entry by binding of spike (S) protein present on the viral envelope to angiotensin converting enzyme 2 (ACE2) receptor on the host cells (Zhou et al., 2020b) . Here we surveyed the genetic variants in functional residues of ACE2, TMPRSS2, CTSB/L (CatB/L), and TLR3/7/8 to investigate the difference in the genetic predisposition to the susceptibly of SARS-CoV-2 infection and the initiation of innate immune response. The list of reported genetic variants in the genes and their allele frequencies (AFs) were ACE2 is highly conserved with few nonsynonymous variants in the interacting domain with the SARS-CoV-2 RBM (Lan et al., 2020) .

title:
  A survey of genetic variants in SARS-CoV-2 interacting domains of ACE2, TMPRSS2 and TLR3/7/8 across populations

abstract:
  The COVID-19 pandemic highlighted healthcare disparities in multiple countries. As such morbidity and mortality vary significantly around the globe between populations and ethnic groups. Underlying medical conditions and environmental factors contribute higher incidence in some populations and a genetic predisposition may play a role for severe cases with respiratory failure. Here we investigated whether genetic variation in the key genes for viral entry to host cells—ACE2 and TMPRSS2—and sensing of viral genomic RNAs (i.e., TLR3/7/8) could explain the variation in incidence across diverse ethnic groups. Overall, these genes are under strong selection pressure and have very few nonsynonymous variants in all populations. Genetic determinant for the binding affinity between SARS-CoV-2 and ACE2 does not show significant difference between populations. Non-genetic factors are likely to contribute differential population characteristics affected by COVID-19. Nonetheless, a systematic mutagenesis study on the receptor binding domain of ACE2 is required to understand the difference in host-viral interaction across populations.


id: cord-339120-38rsfs0d
title: Genome analysis of a G9P[23] group A rotavirus isolated from a dog with diarrhea in China
author: Yan, Nan
date: 2019-02-20
txt: ./txt/cord-339120-38rsfs0d.txt
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url: https://www.ncbi.nlm.nih.gov/pubmed/30796978/
doi: 10.1016/j.meegid.2019.02.020
summary:
  authors: Yan, Nan; Tang, Cheng; Kan, Ruici; Feng, Fan; Yue, Hua. title: Genome analysis of a G9P[23] group A rotavirus isolated from a dog with diarrhea in China In this study, an RVA strain designated RVA/Dog-tc/CHN/SCCD-A/2017/G9P[23] was isolated in cell culture from a pet dog stool sample with acute diarrhea, and its whole genome was sequenced. The sequence closest to the NSP4 gene of RVA/Dog-tc/ CHN/SCCD-A/2017/G9P [23] was that of human strain R479 which was previously shown to be of porcine rotavirus origin (Wang et al., 2010) . On the other hand, the sequence closest to the VP1 gene of SCCD-A was that of strain LL3354 which was reported to be the result of a porcine rotavirus having transmitted to a human, but the phylogenetic tree for the VP1 genes showed that strains SCCD-A and LL3354 clustered together in an independent group that was distinct from any of the previously established lineages (Fig. 1) .

abstract:
  Genotype G9 is an emerging genotype among species A rotavirus (RVA) circulating in humans and pigs worldwide. In this study, an RVA strain designated RVA/Dog-tc/CHN/SCCD-A/2017/G9P[23] was isolated in cell culture from a pet dog stool sample with acute diarrhea, and its whole genome was sequenced. The genotype constellation of SCCD-A was G9-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1. All genome segments except the VP1 gene were closely related to the genes from porcine RVA strains or porcine-like human RVA strains. On the other hand, the VP1 gene clustered in a distinct lineage only with that of a G5P[6] porcine-like human RVA, preventing the identification of the exact host species origin, but very unlikely to be originated from human RVA. In addition, phylogenetic analysis showed that the G9 VP7 gene of SCCD-A clustered into a novel sublineage within the lineage III of G9. This first isolation of a G9P[23] RVA from a pet dog may justify the exploration of the role dogs play in the interaction of RVA circulating in pigs and humans.


id: cord-339259-4oi7slk9
author: Naguib, Mahmoud M.
date: 2016-10-26
txt: ./txt/cord-339259-4oi7slk9.txt
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url: https://doi.org/10.1016/j.meegid.2016.10.017
doi: 10.1016/j.meegid.2016.10.017
summary:
  title: Full genome sequence analysis of a newly emerged QX-like infectious bronchitis virus from Sudan reveals distinct spots of recombination By phylogenetic analysis based on the whole S1-gene according to (Valastro et al., 2016) it appeared that the IBV/Ck/Sudan/AR251-15/2014 is closely related to ITA/90254/ 2005 and the previously reported recombinant strains detected in South Africa (Ck/ZA/3665/11) and Sweden (Ck/SWE/0658946/10) which are clustered together within GI-19 lineage (Fig. 3) . The results showed that the Sudanese isolate was a recombinant virus which probably emerged from at least three different genotypes, including the 4/91 genotype as a major parent and the H120 vaccine strain as well as Italy/90254/2005-like viruses as minor parents (Fig. 4) . Characterization and analysis of the full-length genome of a strain of the european qx-like genotype of infectious bronchitis virus Complete genomic sequence analysis of infectious bronchitis virus ark dpi strain and its evolution by recombination

title:
  Full genome sequence analysis of a newly emerged QX-like infectious bronchitis virus from Sudan reveals distinct spots of recombination

abstract:
  Infectious bronchitis virus (IBV) infection continues to cause economically important diseases in poultry while different geno- and serotypes continue to circulate globally. Two infectious bronchitis viruses (IBV) were isolated from chickens with respiratory disease in Sudan. Sequence analysis of the hypervariable regions of the S1 gene revealed a close relation to the QX-like genotype which has not been detected in Sudan before. Whole genome analysis of IBV/Ck/Sudan/AR251–15/2014 isolate by next generation sequencing revealed a genome size of 27,646 nucleotides harbouring 13 open reading frames: 5′-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3′. Highest nucleotide sequence identity of 93% for the whole genome was found with the Chinese IBV strain Ck/CH/LHLJ/140906, the Italian IBV isolate ITA/90254/2005 and the 4/91 vaccine strain. Phylogenetic analysis of the S1 gene revealed that the IBV/Ck/Sudan/AR251–15/2014 isolate clustered together with viruses of the GI-19 lineage. Recombination analysis gave evidence for distinct patterns of origin of RNA in the Sudanese isolate in multiple genes. Several sites of recombination were scattered throughout the genome suggesting that the Sudan-QX-like strain emerged as a unique recombinant from multiple recombination events of parental viruses from 4/91, H120 and ITA/90254/2005 genotypes. The Sudanese QX-like isolate is plausibly genetically different from IBV strains previously reported in Africa and elsewhere.


