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Emerging Microbes & Infections Volume 7, 2018 - Issue 1
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Original Articles

Genetic and evolutionary analysis of emerging H3N2 canine influenza virus

Gairu LiMOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary MedicineNanjing Agricultural UniversityNanjingChina
,
Ruyi WangMOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary MedicineNanjing Agricultural UniversityNanjingChina
,
Cheng ZhangMOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary MedicineNanjing Agricultural UniversityNanjingChina
,
Shilei WangMOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary MedicineNanjing Agricultural UniversityNanjingChina
,
Wanting HeMOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary MedicineNanjing Agricultural UniversityNanjingChina
,
Junyan ZhangMOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary MedicineNanjing Agricultural UniversityNanjingChina
,
Jie LiuMOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary MedicineNanjing Agricultural UniversityNanjingChina
,
Yuchen CaiMOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary MedicineNanjing Agricultural UniversityNanjingChina
,
Jiyong ZhouMOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary MedicineNanjing Agricultural UniversityNanjingChina
&
Shuo SuMOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary MedicineNanjing Agricultural UniversityNanjingChinaCorrespondence[email protected]
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Pages 1-15 | Received 20 Dec 2017, Accepted 20 Mar 2018, Published online: 25 Apr 2018

References

  • LiSAvian-origin H3N2 canine influenza A viruses in Southern ChinaInfect. Genet. Evol.201010 1286 128810.1016/j.meegid.2010.08.0102950248
  • DaesubSExperimental Infection of dogs with avian-origin canine influenza A virus (H3N2)Emerg. Infect. Dis.2009155610.3201/eid1501.080755
  • SunchaiPInfluenza A virus (H3N8) in dogs with respiratory disease, FloridaEmerg. Infect. Dis.20081490210.3201/eid1406.071270
  • IanEHVSpread of canine influenza A(H3N2) virus, United StatesEmerg. Infect. Dis.201723195010.3201/eid2312.170246
  • BunpapongNGenetic characterization of canine influenza A virus (H3N2) in ThailandVirus Genes201448566310.1007/s11262-013-0978-z
  • DaesubSTransmission of avian influenza virus (H3N2) to dogsEmerg. Infect. Dis.20081474110.3201/eid1405.071471
  • LeeIWComparison of the virulence and transmissibility of canine H3N2 influenza viruses and characterization of their canine adaptation factorsEmerg. Microbes Infect.2018710.1038/s41426-017-0013-x5841232
  • BrettASInfluenza a pandemic (H1N1) 2009 virus infection in domestic catEmerg. Infect. Dis.20101653410.3201/eid1603.091737
  • FranzoGTucciaroneCMCecchinatoMDrigoMCanine parvovirus type 2 (CPV-2) and Feline panleukopenia virus (FPV) codon bias analysis reveals a progressive adaptation to the new niche after the host jumpMol. Phylogen. Evol.2017114829210.1016/j.ympev.2017.05.019
  • ButtAMNasrullahIQamarRTongYEvolution of codon usage in Zika virus genomes is host and vector specificEmerg. Microbes Infect.2016510.1038/emi.2016.1065117728
  • AnhlanDGrundmannNMakalowskiWLudwigSScholtissekCOrigin of the 1918 pandemic H1N1 influenza A virus as studied by codon usage patterns and phylogenetic analysisRNA201117647310.1261/rna.23952113004067
  • Behura SusantaKSeverson DavidWCodon usage bias: causative factors, quantification methods and genome‐wide patterns: with emphasis on insect genomesBiol. Rev. Camb. Philos. Soc.201288496110.1111/j.1469-185X.2012.00242.x
  • PepinKMDomsicJMcKennaRGenomic evolution in a virus under specific selection for host recognitionInfect. Genet. Evol.2008882583410.1016/j.meegid.2008.08.008
  • ChenHSunSNorenburgJLSundbergPMutation and selection cause codon usage and bias in mitochondrial genomes of ribbon worms (Nemertea)PLoS ONE20149e8563110.1371/journal.pone.00856313893253
  • GranthamRGautierCGouyMMercierRPavéACodon catalog usage and the genome hypothesisNucleic Acids Res.1980819719710.1093/nar/8.1.197-c
  • Parmley JoannaLHurst LaurenceDHow do synonymous mutations affect fitness?Bioessays20072951551910.1002/bies.20592
  • HussainSRasoolSTAnalysis of synonymous codon usage in Zika virusActa Trop.201717313614610.1016/j.actatropica.2017.06.006
  • van HemertFvan der KuylACBerkhoutBImpact of the biased nucleotide composition of viral RNA genomes on RNA structure and codon usageJ. Gen. Virol.2016972608261910.1099/jgv.0.000579
  • CristinaJMorenoPMoratorioGMustoHGenome-wide analysis of codon usage bias in EbolavirusVirus Res.2015196879310.1016/j.virusres.2014.11.005
  • SinghNKTyagiAKaurRVermaRGuptaPKCharacterization of codon usage pattern and influencing factors in Japanese encephalitis virusVirus Res.2016221586510.1016/j.virusres.2016.05.008
  • GoñiNPandemic influenza A virus codon usage revisited: biases, adaptation and implications for vaccine strain developmentVirol. J.2012926310.1186/1743-422X-9-2633543350
  • ZhouTGuWMaJSunXLuZAnalysis of synonymous codon usage in H5N1 virus and other influenza A virusesBioSyst200581778610.1016/j.biosystems.2005.03.002
  • KumarNRevelation of influencing factors in overall codon usage bias of equine influenza virusesPLoS ONE201611e015437610.1371/journal.pone.01543764847779
  • LiuXWuCChenAYHCodon usage bias and recombination events for neuraminidase and hemagglutinin genes in Chinese isolates of influenza A virus subtype H9N2Arch. Virol.201015568569310.1007/s00705-010-0631-2
  • MoonHH3N2 canine influenza virus with the matrix gene from the pandemic A/H1N1 virus: infection dynamics in dogs and ferretsEpidemiol. Infect.201414377278010.1017/S0950268814001617
  • ZhuHHughesJMurciaPROrigins and evolutionary dynamics of H3N2 canine influenza virusJ. Virol.2015895406541810.1128/JVI.03395-144442499
  • YangGMutation tryptophan to leucine at position 222 of haemagglutinin could facilitate H3N2 influenza A virus infection in dogsJ. Gen. Virol.2013942599260810.1099/vir.0.054692-04093785
  • BeraBCGenetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolutionBMC Genomics20171810.1186/s12864-017-4063-15568313
  • LiuXsZhangYgFangYzWangYlPatterns and influencing factor of synonymous codon usage in porcine circovirusVirol. J.201296810.1186/1743-422X-9-683341187
  • MuellerSPapamichailDColemanJRSkienaSWimmerEReduction of the rate of poliovirus protein synthesis through large-scale codon deoptimization causes attenuation of viral virulence by lowering specific infectivityJ. Virol.2006809687969610.1128/JVI.00738-061617239
  • SánchezGBoschAPintóRMGenome variability and capsid structural constraints of hepatitis A virusJ. Virol.20037745245910.1128/JVI.77.1.452-459.2003140588
  • HuJsThe characteristic of codon usage pattern and its evolution of hepatitis C virusInfect. Genet. Evol.2011112098210210.1016/j.meegid.2011.08.025
  • SharpPMLiWHThe codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applicationsNucleic Acids Res.1987151281129510.1093/nar/15.3.1281340524
  • AtanaskaMPAvian influenza A(H7N2) virus in human exposed to sick cats, New York, USA, 2016Emerg. Infect. Dis.2017232046
  • HorimotoTKawaokaYInfluenza: lessons from past pandemics, warnings from current incidentsNat. Rev. Microbiol.2005359110.1038/nrmicro1208
  • DornAKippenbergerSClinical application of CpG-, non-CpG-, and antisense oligodeoxynucleotides as immunomodulatorsCurr. Opin. Mol. Ther.2008101020
  • ChenYChenYFExtensive homologous recombination in classical swine fever virus: a re-evaluation of homologous recombination events in the strain AF407339Saudi J. Biol. Sci.20142131131610.1016/j.sjbs.2013.12.0044150228
  • MaraisGMouchiroudDDuretLDoes recombination improve selection on codon usage? Lessons from nematode and fly complete genomesProc. Natl Acad. Sci. USA200198568810.1073/pnas.09142769833274
  • SalterLAThe phylogenetic handbook: a practical approach to DNA and protein phylogenyAm. J. Hum. Biol.20041635435510.1002/ajhb.20017
  • HuelsenbeckJPRonquistFMRBAYES: Bayesian inference of phylogenetic treesBioinformatics20011775475510.1093/bioinformatics/17.8.754
  • FranzoGCorteyMSegalésJHughesJDrigoMPhylodynamic analysis of porcine circovirus type 2 reveals global waves of emerging genotypes and the circulation of recombinant formsMol. Phylogen. Evol.201610026928010.1016/j.ympev.2016.04.028
  • StamatakisARAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogeniesBioinformatics2014301312131310.1093/bioinformatics/btu0333998144
  • RicePLongdenIBleasbyAEMBOSS: the European Molecular Biology Open Software SuiteTrends Genet.20001627627710.1016/S0168-9525(00)02024-2
  • ComeronJMAguadéMAn evaluation of measures of synonymous codon usage biasJ. Mol. Evol.19984726827410.1007/PL00006384
  • WongEHMSmithDKRabadanRPeirisMPoonLLMCodon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza VirusBMC Evol. Biol.20101025310.1186/1471-2148-10-2532933640
  • SueokaNDirectional mutation pressure and neutral molecular evolutionProc. Natl Acad. Sci. USA198885265310.1073/pnas.85.8.2653280056
  • PuigbòPBravoIGGarcia-VallveSCAIcal: a combined set of tools to assess codon usage adaptationBiol. Direct2008310.1186/1745-6150-3-382553769
  • PuigbòPAragonèsLGarcia-VallvéSRCDI/eRCDI: a web-server to estimate codon usage deoptimizationBMC Res. Notes2010310.1186/1756-0500-3-872853550
  • SueokaNIntrastrand parity rules of DNA base composition and usage biases of synonymous codonsJ. Mol. Evol.19954031832510.1007/BF00163236
  • SueokaNTranslation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon positionGene1999238535810.1016/S0378-1119(99)00320-0
  • NasrullahIButtAMTahirSIdreesMTongYGenomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolutionBMC Evol. Biol.20151517410.1186/s12862-015-0456-44550055

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