Emergence of Thailand‐like strains of porcine deltacoronavirus in Guangxi Province, China

Abstract Porcine deltacoronavirus (PDCoV) has been detected sporadically in China since its first description in 2012. In our study, 62 faecal and intestinal samples from pigs with diarrhoea were collected in Guangxi Province, China, during 2017 and 2018. Twelve samples (19.4%, 12/62) were positive for PDCoV. Five complete genomes of PDCoV were then determined, and sequence alignment revealed that the five strains had discontinuous deletions at 400–401 aa in non‐structural protein 2 (NSP2) and 758–760 aa in non‐structural protein 3 (NSP3) compared with the respective proteins in the HKU15‐44 strain. Notably, the CHN‐GX81‐2018 strain contained two insertions in the S gene and 3′‐UTR. Multiple sequence alignment and phylogenetic analysis showed that four strains shared 98.2%–98.4% nucleotide identity with CHN‐AH‐2004 and were classified into a new cluster of China lineage strains, whereas the CHN‐GX81‐2018 strain shared 98.7% nucleotide identity with Vietnam/Binh21/2015 and belonged to the Vietnam/Laos/Thailand lineage. Recombination analyses revealed that four strains were the result of recombination between CHN‐HB‐2014 and Vietnam/Binh21/2015 strains. This study demonstrated the co‐existence of multiple lineages of PDCoV in China, and our findings will aid the reorganization and evolution of the virus.

[1]  Huijun Lu,et al.  Genetic characterization and phylogenetic analysis of porcine deltacoronavirus (PDCoV) in Shandong Province, China , 2020, Virus Research.

[2]  D. Nilubol,et al.  Retrospective study, full‐length genome characterization and evaluation of viral infectivity and pathogenicity of chimeric porcine deltacoronavirus detected in Vietnam , 2019, Transboundary and emerging diseases.

[3]  Y. Zhang,et al.  Detection and spike gene characterization in porcine deltacoronavirus in China during 2016–2018 , 2019, Infection, Genetics and Evolution.

[4]  Susana E Mendoza-Elvira,et al.  First report and phylogenetic analysis of porcine deltacoronavirus in Mexico , 2019, Transboundary and emerging diseases.

[5]  Hui Hu,et al.  Prevalence, phylogenetic and evolutionary analysis of porcine deltacoronavirus in Henan province, China , 2019, Preventive Veterinary Medicine.

[6]  Yun Zhang,et al.  Isolation and characterization of a highly pathogenic strain of Porcine enteric alphacoronavirus causing watery diarrhoea and high mortality in newborn piglets , 2018, Transboundary and emerging diseases.

[7]  A. Jongkaewwattana,et al.  Genomic characterization and pathogenicity of porcine deltacoronavirus strain CHN-HG-2017 from China , 2018, Archives of Virology.

[8]  J. Novotný,et al.  First outbreak with chimeric swine enteric coronavirus (SeCoV) on pig farms in Slovakia - lessons to learn. , 2018, Acta veterinaria Hungarica.

[9]  Chinling Wang,et al.  Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan , 2018, Archives of Virology.

[10]  Heng Wang,et al.  Newly emerged porcine enteric alphacoronavirus in southern China: Identification, origin and evolutionary history analysis , 2018, Infection, Genetics and Evolution.

[11]  G. Gao,et al.  Bat-Origin Coronaviruses Expand Their Host Range to Pigs , 2018, Trends in Microbiology.

[12]  P. Daszak,et al.  Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin , 2018, Nature.

[13]  Tohru Suzuki,et al.  Genetic characterization and pathogenicity of Japanese porcine deltacoronavirus , 2018, Infection, Genetics and Evolution.

[14]  Z. Poljak,et al.  Herd‐level prevalence and incidence of porcine epidemic diarrhoea virus (PEDV) and porcine deltacoronavirus (PDCoV) in swine herds in Ontario, Canada , 2018, Transboundary and emerging diseases.

[15]  F. Zhong,et al.  Isolation and phylogenetic analysis of porcine deltacoronavirus from pigs with diarrhoea in Hebei province, China , 2018, Transboundary and emerging diseases.

[16]  Y. Pan,et al.  Detection and genetic characterization of porcine deltacoronavirus in Tibetan pigs surrounding the Qinghai–Tibet Plateau of China , 2018, Transboundary and emerging diseases.

[17]  Jingyun Ma,et al.  Complete Genome Sequences of Two Porcine Deltacoronavirus Strains, CHN-GD16-03 and CHN-GD16-05, Isolated in Southern China, 2016 , 2018, Genome Announcements.

[18]  Yun Zhang,et al.  A Highly Pathogenic Strain of Porcine Deltacoronavirus Caused Watery Diarrhea in Newborn Piglets , 2017, Virologica Sinica.

[19]  Jingyun Ma,et al.  The detection and phylogenetic analysis of porcine deltacoronavirus from Guangdong Province in Southern China , 2017, Transboundary and emerging diseases.

[20]  C. Lee,et al.  Prevalence, complete genome sequencing and phylogenetic analysis of porcine deltacoronavirus in South Korea, 2014–2016 , 2017, Transboundary and emerging diseases.

[21]  S. Xiao,et al.  Isolation, genomic characterization, and pathogenicity of a Chinese porcine deltacoronavirus strain CHN-HN-2014 , 2016, Veterinary Microbiology.

[22]  Dan Wang,et al.  Occurrence and sequence analysis of porcine deltacoronaviruses in southern China , 2016, Virology Journal.

[23]  D. Nilubol,et al.  The first detection and full-length genome sequence of porcine deltacoronavirus isolated in Lao PDR , 2016, Archives of Virology.

[24]  Bin Yang,et al.  Molecular Epidemiological Investigation of Porcine kobuvirus and Its Coinfection Rate with PEDV and SaV in Northwest China , 2016, BioMed research international.

[25]  Linda J. Saif,et al.  Porcine deltacoronavirus infection: Etiology, cell culture for virus isolation and propagation, molecular epidemiology and pathogenesis , 2016, Virus Research.

[26]  A. Amonsin,et al.  Porcine Deltacoronavirus, Thailand, 2015 , 2016, Emerging infectious diseases.

[27]  M. Nelson,et al.  Characterization and evolution of porcine deltacoronavirus in the United States , 2015, Preventive Veterinary Medicine.

[28]  S. Xiao,et al.  Porcine Deltacoronavirus in Mainland China , 2015, Emerging infectious diseases.

[29]  Joseph T. Thomas,et al.  Pathogenicity and pathogenesis of a United States porcine deltacoronavirus cell culture isolate in 5-day-old neonatal piglets , 2015, Virology.

[30]  A. Vlasova,et al.  Isolation and Characterization of Porcine Deltacoronavirus from Pigs with Diarrhea in the United States , 2015, Journal of Clinical Microbiology.

[31]  Leyi Wang,et al.  Porcine Coronavirus HKU15 Detected in 9 US States, 2014 , 2014, Emerging infectious diseases.

[32]  Qi Chen,et al.  Full-Length Genome Sequence of Porcine Deltacoronavirus Strain USA/IA/2014/8734 , 2014, Genome Announcements.

[33]  Sergei L. Kosakovsky Pond,et al.  A Case for the Ancient Origin of Coronaviruses , 2013, Journal of Virology.

[34]  Kwok-Hung Chan,et 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 , 2012, Journal of Virology.

[35]  P. Halbur,et al.  In situ hybridization technique for the detection of swine enteric and respiratory coronaviruses, transmissible gastroenteritis virus (TGEV) and porcine respiratory coronavirus (PRCV), in formalin-fixed paraffin-embedded tissues , 1996, Journal of Virological Methods.