Coronavirus HKU15 in respiratory tract of pigs and first discovery of coronavirus quasispecies in 5′-untranslated region

References

• de Groot RJ, Baker SC, Baric Ret al. Family—Coronaviridae. In: Adams MJ, Carstens EB, Lefkowitz EJ (eds). Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses, International Union of Microbiological Societies, Virology Division. San Diego, CA: Elsevier, 2012: 806–828.
   Google Scholar
• Woo PCY, Lau SKP, Lam CSFet al.Comparative analysis of complete genome sequences of three avian coronaviruses reveals a novel group 3c coronavirus. J Virol 2009;83: 908–917.
   PubMed Web of Science ®Google Scholar
• Woo PCY, Lau SKP, Lam CSFet al.Discovery of seven novel mammalian and avian coronaviruses in the genus Deltacoronavirus supports bat coronaviruses as the gene source of Alphacoronavirus and Betacoronavirus and avian coronaviruses as the gene source of Gammacoronavirus and Deltacoronavirus. J Virol 2012;86: 3995–4008.
   PubMed Web of Science ®Google Scholar
• International Committee on Taxonomy of Viruses (ICTV). Create 12 new species in the family Coronaviridae. Glasgow: ICTV; 2015. Available at https://talk.ictvonline.org/files/ictv_official_taxonomy_updates_since_the_8th_report/m/animal-ssrna-viruses/5879 (accessed 13 December 2016).
   Google Scholar
• Lee S, Lee C.Complete genome characterization of Korean porcine deltacoronavirus strain KOR/KNU14-04/2014. Genome Announc 2014;2: e01191-14.
   PubMedGoogle Scholar
• Li G, Chen Q, Harmon KMet al.Full-length genome sequence of porcine deltacoronavirus strain USA/IA/2014/8734. Genome Announc 2014;2: e00278-14.
   PubMedGoogle Scholar
• Marthaler D, Raymond L, Jiang Y, Collins J, Rossow K, Rovira A.Rapid detection, complete genome sequencing, and phylogenetic analysis of porcine deltacoronavirus. Emerg Infect Dis 2014;20: 1347–1350.
   PubMed Web of Science ®Google Scholar
• Marthaler D, Jiang Y, Collins J, Rossow K.Complete genome sequence of strain SDCV/USA/Illinois121/2014, a porcine deltacoronavirus from the United States. Genome Announc 2014;2: e00218-14.
   PubMedGoogle Scholar
• Wang L, Byrum B, Zhang Y.Detection and genetic characterization of deltacoronavirus in pigs, Ohio, USA, 2014. Emerg Infect Dis 2014;20: 1227–1230.
   PubMed Web of Science ®Google Scholar
• Wang L, Byrum B, Zhang Y.Porcine coronavirus HKU15 detected in 9 US states, 2014. Emerg Infect Dis 2014;20: 1594–1595.
   PubMed Web of Science ®Google Scholar
• Wang L, Zhang Y, Byrum B.Complete genome sequence of porcine coronavirus HKU15 strain IN2847 from the United States. Genome Announc 2014;2: e00291-14.
   PubMedGoogle Scholar
• Chen F, Zhu Y, Wu M, Ku X, Yao L, He Q.Full-length genome characterization of chinese porcine deltacoronavirus strain CH/SXD1/2015. Genome Announc 2015;3: e01284-15.
   PubMedGoogle Scholar
• Dong N, Fang L, Zeng S, Sun Q, Chen H, Xiao S.Porcine deltacoronavirus in mainland China. Emerg Infect Dis 2015;21: 2254–2255.
   PubMed Web of Science ®Google Scholar
• Hu H, Jung K, Vlasova ANet al.Isolation and characterization of porcine deltacoronavirus from pigs with diarrhea in the United States. J Clin Microbiol 2015;53: 1537–1548.
   PubMed Web of Science ®Google Scholar
• Ma Y, Zhang Y, Liang Xet al.Origin, evolution, and virulence of porcine deltacoronaviruses in the United States. MBio 2015;6: e00064-15.
   PubMed Web of Science ®Google Scholar
• Song D, Zhou X, Peng Qet al.Newly emerged porcine deltacoronavirus associated with diarrhoea in swine in China: identification, prevalence and full-length genome sequence analysis. Transbound Emerg Dis 2015;62: 575–580.
   PubMed Web of Science ®Google Scholar
• Wang Y-W, Yue H, Fang W, Huang Y-W.Complete genome sequence of porcine deltacoronavirus strain CH/Sichuan/S27/2012 from mainland China. Genome Announc 2015;3: e00945-15.
   PubMedGoogle Scholar
• Wang L, Hayes J, Sarver C, Byrum B, Zhang Y.Porcine deltacoronavirus: histological lesions and genetic characterization. Arch Virol 2015;161: 171–175.
   PubMed Web of Science ®Google Scholar
• Homwong N, Jarvis MC, Lam HCet al.Characterization and evolution of porcine deltacoronavirus in the United States. Prev Vet Med 2016;123: 168–174.
   PubMed Web of Science ®Google Scholar
• Janetanakit T, Lumyai M, Bunpapong Net al.Porcine deltacoronavirus, Thailand, 2015. Emerg Infect Dis 2016;20: 757–759.
   Web of Science ®Google Scholar
• Lee JH, Chung HC, Nguyen VGet al.Detection and phylogenetic analysis of porcine deltacoronavirus in Korean swine farms, 2015. Transbound Emerg Dis 2016;63: 248–252.
   PubMed Web of Science ®Google Scholar
• Lorsirigool A, Saeng-chuto K, Temeeyasen Get al.The first detection and full-length genome sequence of porcine deltacoronavirus isolated in Lao PDR. Arch Virol 2016;161: 2909–2911.
   PubMed Web of Science ®Google Scholar
• Saeng-chuto K, Lorsirigool A, Temeeyasen Get al.Different lineage of porcine deltacoronavirus in Thailand, Vietnam and Lao PDR in 2015. Transbound Emerg Dis 2017;64: 3–10.
   PubMed Web of Science ®Google Scholar
• Reynolds DJ, Debney TG, Hall GA, Thomas LH, Parsons KR.Studies on the relationship between coronaviruses from the intestinal and respiratory tracts of calves. Arch Virol 1985;85: 71–83.
   PubMed Web of Science ®Google Scholar
• Laude H, Van Reeth K, Pensaert M.Porcine respiratory coronavirus: molecular features and virus-host interactions. Vet Res 1993;24: 125–150.
   PubMed Web of Science ®Google Scholar
• Lau SKP, Woo PCY, Li KSMet al.Discovery of a novel coronavirus, China Rattus coronavirus HKU24, from Norway rats supports the murine origin of Betacoronavirus 1 and has implications for the ancestor of Betacoronavirus lineage A. J Virol 2015;89: 3076–3092.
   PubMed Web of Science ®Google Scholar
• Woo PCY, Lau SKP, Lam CSFet al.Discovery of a novel bottlenose dolphin coronavirus reveals a distinct species of marine mammal coronavirus in Gammacoronavirus. J Virol 2014;88: 1318–1331.
   PubMed Web of Science ®Google Scholar
• Zhao Y, Tsang C-C, Xiao Met al.Intra-genomic internal transcribed spacer region sequence heterogeneity and molecular diagnosis in clinical microbiology. Int J Mol Sci 2015;16: 25067–25079.
   PubMed Web of Science ®Google Scholar
• Hall TA.BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999;41: 95–98.
   Google Scholar
• Li W, Cowley A, Uludag Met al.The EMBL-EBI bioinformatics web and programmatic tools framework. Nucleic Acids Res 2015;43: W580–W584.
   PubMed Web of Science ®Google Scholar
• Edgar RC.MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32: 1792–1797.
   PubMed Web of Science ®Google Scholar
• Tamura K, Stecher G, Peterson D, Filipski A, Kumar S.MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30: 2725–2729.
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Suchard MA, Xie D, Rambaut A.Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 2012;29: 1969–1973.
   PubMed Web of Science ®Google Scholar
• Costantini V, Lewis P, Alsop J, Templeton C, Saif LJ.Respiratory and fecal shedding of Porcine respiratory coronavirus (PRCV) in sentinel weaned pigs and sequence of the partial S-gene of the PRCV isolates. Arch Virol 2004;149: 957–974.
   PubMed Web of Science ®Google Scholar
• Xu D, Zhang Z, Wang F-S.SARS-associated coronavirus quasispecies in individual patients. N Engl J Med 2004;350: 1366–1367.
   PubMed Web of Science ®Google Scholar
• Zhang X, Hasoksuz M, Spiro Det al.Quasispecies of bovine enteric and respiratory coronaviruses based on complete genome sequences and genetic changes after tissue culture adaptation. Virology 2007;363: 1–10.
   PubMed Web of Science ®Google Scholar
• Briese T, Mishra N, Jain Ket al.Middle East respiratory syndrome coronavirus quasispecies that include homologues of human isolates revealed through whole-genome analysis and virus cultured from dromedary camels in Saudi Arabia. MBio 2014;5: e01146-14.
   PubMed Web of Science ®Google Scholar
• Borucki MK, Lao V, Hwang Met al.Middle East respiratory syndrome coronavirus intra-host populations are characterized by numerous high frequency variants. PLoS ONE 2016;11: e0146251.
   PubMed Web of Science ®Google Scholar
• Woo PCY, Lau SKP, Yip CCYet al.Comparative analysis of 22 coronavirus HKU1 genomes reveals a novel genotype and evidence of natural recombination in coronavirus HKU1. J Virol 2006;80: 7136–7145.
   PubMed Web of Science ®Google Scholar