Metavirome Analysis Reveals a High Prevalence of Porcine Hemagglutination Encephalomyelitis Virus in Clinically Healthy Pigs in China

Six swine coronaviruses (SCoVs), which include porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine hemagglutination encephalomyelitis virus (PHEV), porcine respiratory coronavirus (PRCV), swine acute diarrhea syndrome coronavirus (SADS-CoV), and porcine delta coronavirus (PDCoV), have been reported as infecting and causing serious diseases in pigs. To investigate the genetic diversity and spatial distribution of SCoVs in clinically healthy pigs in China, we collected 6400 nasal swabs and 1245 serum samples from clinically healthy pigs at slaughterhouses in 13 provinces in 2017 and pooled them into 17 libraries by type and region for next-generation sequencing (NGS) and metavirome analyses. In total, we identified five species of SCoVs, including PEDV, PDCoV, PHEV, PRCV, and TGEV. Strikingly, PHEV was detected from all the samples in high abundance and its genome sequences accounted for 75.28% of all coronaviruses, while those belonging to TGEV (including PRCV), PEDV, and PDCoV were 20.4%, 2.66%, and 2.37%, respectively. The phylogenetic analysis showed that two lineages of PHEV have been circulating in pig populations in China. We also recognized two PRCVs which lack 672 nucleotides at the N-terminus of the S gene compared with that of TGEV. Together, we disclose preliminarily the genetic diversities of SCoVs in clinically healthy pigs in China and provide new insights into two SCoVs, PHEV and PRCV, that have been somewhat overlooked in previous studies in China.

[1]  H. Ouyang,et al.  Transmissible Gastroenteritis Virus: An Update Review and Perspective , 2023, Viruses.

[2]  Danna Zhou,et al.  Epidemic and Evolutionary Characteristics of Swine Enteric Viruses in South-Central China from 2018 to 2021 , 2022, Viruses.

[3]  R. Tiwari,et al.  Swine coronaviruses (SCoVs) and their emerging threats to swine population, inter-species transmission, exploring the susceptibility of pigs for SARS-CoV-2 and zoonotic concerns , 2022, The veterinary quarterly.

[4]  Xiuyu Wang,et al.  Porcine Epidemic Diarrhea Virus Infection Disrupts the Nasal Endothelial Barrier To Favor Viral Dissemination , 2022, Journal of virology.

[5]  Changcheng Wu,et al.  Genetic Characteristics of Porcine Hemagglutinating Encephalomyelitis Coronavirus: Identification of Naturally Occurring Mutations Between 1970 and 2015 , 2022, Frontiers in Microbiology.

[6]  P. Woo,et al.  Interspecies Jumping of Bat Coronaviruses , 2021, Viruses.

[7]  Enhui Cui,et al.  Porcine deltacoronavirus and its prevalence in China: a review of epidemiology, evolution, and vaccine development , 2021, Archives of Virology.

[8]  Qiang Liu,et al.  Porcine enteric coronaviruses: an updated overview of the pathogenesis, prevalence, and diagnosis , 2021, Veterinary Research Communications.

[9]  Younjung Kim,et al.  Transmission Dynamics of African Swine Fever Virus, South Korea, 2019 , 2021, Emerging infectious diseases.

[10]  M. Pomorska-Mól,et al.  Porcine Coronaviruses: Overview of the State of the Art , 2021, Virologica Sinica.

[11]  Jianguo Dong,et al.  Molecular Characteristics and Pathogenicity of Porcine Epidemic Diarrhea Virus Isolated in Some Areas of China in 2015–2018 , 2020, Frontiers in Veterinary Science.

[12]  Y. Rehman,et al.  Potential role of viral metagenomics as a surveillance tool for the early detection of emerging novel pathogens , 2020, Archives of Microbiology.

[13]  Qiuhong Wang,et al.  Porcine epidemic diarrhea virus (PEDV): An update on etiology, transmission, pathogenesis, and prevention and control , 2020, Virus Research.

[14]  Jingfei Wang,et al.  Fur Seal Feces-Associated Circular DNA Virus Identified in Pigs in Anhui, China , 2020, Virologica Sinica.

[15]  L. Giménez-Lirola,et al.  Detecting and Monitoring Porcine Hemagglutinating Encephalomyelitis Virus, an Underresearched Betacoronavirus , 2020, mSphere.

[16]  Kai Zhao,et al.  A pneumonia outbreak associated with a new coronavirus of probable bat origin , 2020, Nature.

[17]  M. Koopmans,et al.  Virus Metagenomics in Farm Animals: A Systematic Review , 2020, Viruses.

[18]  Zili Li,et al.  Isolation and Identification of Porcine Deltacoronavirus and Alteration of Immunoglobulin Transport Receptors in the Intestinal Mucosa of PDCoV-Infected Piglets , 2020, Viruses.

[19]  N. Pastor,et al.  A Review on Viral Metagenomics in Extreme Environments , 2019, Front. Microbiol..

[20]  Zhen Ding,et al.  Prevalence and phylogenetic analyses of porcine diarrhea associated viruses in Southern China from 2012 to 2018 , 2019 .

[21]  Yingbo Luo,et al.  The re‐emerging of SADS‐CoV infection in pig herds in Southern China , 2019, Transboundary and emerging diseases.

[22]  J. Zimmerman,et al.  Evaluation of the Serologic Cross-Reactivity between Transmissible Gastroenteritis Coronavirus and Porcine Respiratory Coronavirus Using Commercial Blocking Enzyme-Linked Immunosorbent Assay Kits , 2019, mSphere.

[23]  L. Saif,et al.  Decline of transmissible gastroenteritis virus and its complex evolutionary relationship with porcine respiratory coronavirus in the United States , 2019, Scientific Reports.

[24]  J. Zimmerman,et al.  Porcine Hemagglutinating Encephalomyelitis Virus: A Review , 2019, Front. Vet. Sci..

[25]  A. Vlasova,et al.  Emerging and re-emerging coronaviruses in pigs , 2019, Current Opinion in Virology.

[26]  S. Xiao,et al.  Evolutionary and genotypic analyses of global porcine epidemic diarrhea virus strains , 2018, Transboundary and emerging diseases.

[27]  Jialu Wang,et al.  An alternative pathway of enteric PEDV dissemination from nasal cavity to intestinal mucosa in swine , 2018, Nature Communications.

[28]  F. Gao,et al.  Genomic characterization and pathogenicity of a porcine hemagglutinating encephalomyelitis virus strain isolated in China , 2018, Virus Genes.

[29]  P. Gauger,et al.  Metagenomic analysis of the RNA fraction of the fecal virome indicates high diversity in pigs infected by porcine endemic diarrhea virus in the United States , 2018, Virology Journal.

[30]  Yao-Wei Huang,et al.  Discovery of a novel swine enteric alphacoronavirus (SeACoV) in southern China , 2017, Veterinary Microbiology.

[31]  L. Wang,et al.  Genomic Characterization of a New PRCV Variant, United States, 2014. , 2017, Transboundary and emerging diseases.

[32]  C. Sánchez,et al.  Virulence factors in porcine coronaviruses and vaccine design , 2016, Virus Research.

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

[34]  G. Gao,et al.  Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses , 2016, Trends in Microbiology.

[35]  David K. Smith,et al.  Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia , 2016, Science.

[36]  T. Huang,et al.  Newly Emerged Porcine Deltacoronavirus Associated With Diarrhoea in Swine in China: Identification, Prevalence and Full‐Length Genome Sequence Analysis , 2015, Transboundary and emerging diseases.

[37]  Chengping Lu,et al.  Genomic and Epidemiological Characteristics Provide New Insights into the Phylogeographical and Spatiotemporal Spread of Porcine Epidemic Diarrhea Virus in Asia , 2015, Journal of Clinical Microbiology.

[38]  Kunihiko Sadakane,et al.  MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph , 2014, Bioinform..

[39]  Changhee Lee,et al.  Complete Genome Characterization of Korean Porcine Deltacoronavirus Strain KOR/KNU14-04/2014 , 2014, Genome Announcements.

[40]  A. Vlasova,et al.  Distinct Characteristics and Complex Evolution of PEDV Strains, North America, May 2013–February 2014 , 2014, Emerging infectious diseases.

[41]  Jiyong Zhou,et al.  Evidence of Recombinant Strains of Porcine Epidemic Diarrhea Virus, United States, 2013 , 2014, Emerging infectious diseases.

[42]  Yin Jiang,et al.  Rapid Detection, Complete Genome Sequencing, and Phylogenetic Analysis of Porcine Deltacoronavirus , 2014, Emerging infectious diseases.

[43]  Leyi Wang,et al.  Detection and Genetic Characterization of Deltacoronavirus in Pigs, Ohio, USA, 2014 , 2014, Emerging infectious diseases.

[44]  Jian Liu,et al.  Whole-genome analysis of porcine epidemic diarrhea virus (PEDV) from eastern China , 2014, Archives of Virology.

[45]  G. Qi,et al.  Complete genomic sequence of the coronavirus transmissible gastroenteritis virus SHXB isolated in China , 2014, Archives of Virology.

[46]  Koichiro Tamura,et al.  MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. , 2013, Molecular biology and evolution.

[47]  S. Alqasrawi,et al.  Novel coronavirus infections in Jordan, April 2012: epidemiological findings from a retrospective investigation. , 2013, Eastern Mediterranean health journal = La revue de sante de la Mediterranee orientale = al-Majallah al-sihhiyah li-sharq al-mutawassit.

[48]  M. Liao,et al.  Complete Genome Sequence of a Novel Porcine Epidemic Diarrhea Virus in South China , 2012, Journal of Virology.

[49]  M. Liao,et al.  Complete Genome Sequence of a Highly Prevalent Isolate of Porcine Epidemic Diarrhea Virus in South China , 2012, Journal of Virology.

[50]  Qigai He,et al.  New Variants of Porcine Epidemic Diarrhea Virus, China, 2011 , 2012, Emerging infectious diseases.

[51]  Q. Xie,et al.  Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in south China , 2012, Virus Genes.

[52]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[53]  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.

[54]  B. Martínez-López,et al.  African swine fever: an epidemiological update. , 2012, Transboundary and emerging diseases.

[55]  P. Simmonds,et al.  The Fecal Virome of Pigs on a High-Density Farm , 2011, Journal of Virology.

[56]  F. Gao,et al.  Vomiting and wasting disease associated with hemagglutinating encephalomyelitis viruses infection in piglets in jilin, china , 2011, Virology Journal.

[57]  W. Basso,et al.  Hemagglutinating Encephalomyelitis Coronavirus Infection in Pigs, Argentina , 2008, Emerging infectious diseases.

[58]  P. Woo,et al.  Comparative Analysis of 22 Coronavirus HKU1 Genomes Reveals a Novel Genotype and Evidence of Natural Recombination in Coronavirus HKU1 , 2006, Journal of Virology.

[59]  K. Katoh,et al.  MAFFT version 5: improvement in accuracy of multiple sequence alignment , 2005, Nucleic acids research.

[60]  M. Pensaert,et al.  A new coronavirus-like particle associated with diarrhea in swine , 2005, Archives of Virology.

[61]  J. Peiris,et al.  Epidemiology and cause of severe acute respiratory syndrome (SARS) in Guangdong, People's Republic of China, in February, 2003 , 2003, The Lancet.

[62]  A. Parwani,et al.  Molecular characterization and pathogenesis of transmissible gastroenteritis coronavirus (TGEV) and porcine respiratory coronavirus (PRCV) field isolates co-circulating in a swine herd , 2000, Archives of Virology.

[63]  K. Lole,et al.  Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination , 1999, Journal of Virology.

[64]  N. Hirano,et al.  A serological survey of human coronavirus in pigs of the Tohoku District of Japan. , 1998, Advances in experimental medicine and biology.

[65]  G. Herrler,et al.  Point mutations in the S protein connect the sialic acid binding activity with the enteropathogenicity of transmissible gastroenteritis coronavirus , 1997, Journal of virology.

[66]  Joaquín Dopazo,et al.  Genetic evolution and tropism of transmissible gastroenteritis coronaviruses , 1992, Virology.

[67]  A. Look,et al.  Human aminopeptidase N is a receptor for human coronavirus 229E , 1992, Nature.

[68]  B. Delmas,et al.  Aminopeptidase N is a major receptor for the enteropathogenic coronavirus TGEV , 1992, Nature.

[69]  D. Ochs,et al.  Immunodeficiency in young pigs. , 1989, American journal of veterinary research.

[70]  A. Pospischil,et al.  [Current aspects in the etiology of viral diarrheas of swine: occurrence of infections with the epizootic viral diarrhea (EVD) virus]. , 1980, Berliner und Munchener tierarztliche Wochenschrift.

[71]  E. N. Wood.  An apparently new syndrome of porcine epidemic diarrhoea , 1977, Veterinary Record.

[72]  W. Mengeling,et al.  Pathogenicity of field isolants of hemagglutinating encephalomyelitis virus for neonatal pigs. , 1976, Journal of the American Veterinary Medical Association.