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

Abstract

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.

Simultaneous Detection of Porcine Respiratory Coronavirus, Porcine Reproductive and Respiratory Syndrome Virus, Swine Influenza Virus, and Pseudorabies Virus via Quadruplex One-Step RT-qPCR

“…To the best of our knowledge, this is the first report to design specific primers/probes targeting the deletion region of the PRCoV S gene, which can specifically detect PRCoV. Even with the high homology between PRCoV and TGEV, the S gene exhibits a deletion region in PRCoV compared to TGEV [ 2 , 8 , 9 , 11 ], which can thus be used as the targeted region for the differentiation of these two pathogens. Therefore, the PRCoV S gene sequences obtained in Guangxi Province were compared with sequences downloaded from the NCBI GenBank ( (accessed on 15 April 2022)) from other Chinese provinces and other countries around the world, and the deletion region of the S gene was selected when designing the specific primers and probe.…”

“…PRCoV was first reported in Belgium in 1984, and since then, it has been widely prevalent in Europe and North America [ 2 , 7 ]. PRCoV has also been reported in China [ 8 ], but until now, no research has reported the epidemic situations of PRCoV in China. PRCoV is thought to have originated from transmissible gastroenteritis virus (TGEV) [ 9 , 10 ], and there is a 621–681 nucleotide deletion at the N-terminal end of the S gene compared with TGEV, which is usually used to distinguish PRCoV from TGEV [ 8 , 11 ].…”

“…PRCoV has also been reported in China [ 8 ], but until now, no research has reported the epidemic situations of PRCoV in China. PRCoV is thought to have originated from transmissible gastroenteritis virus (TGEV) [ 9 , 10 ], and there is a 621–681 nucleotide deletion at the N-terminal end of the S gene compared with TGEV, which is usually used to distinguish PRCoV from TGEV [ 8 , 11 ]. Currently, the number of published PRCoV strains is still limited, and the hazard of PRCoV to pig herds requires further evaluation.…”

Development of a quadruplex real-time quantitative RT-PCR for detection and differentiation of PHEV, PRV, CSFV, and JEV

“…Overall, PHEV, PRV, CSFV, and JEV are still popular in many countries around the world, and cause different degrees of damages to the pig industry (5,6,13,14,20,21,28,29,57). In China, some provinces have recently reported the prevalence of PHEV, PRV, CSFV, and JEV (41,47,51,(58)(59)(60)(61)(62)(63)(64)(65). The nasal cavity or throat swabs from 1-to 3-week-old piglets in Jilin province in 2010 showed a positivity rate of 44.23% (207/468) for PHEV (58).…”

“…The nasal cavity or throat swabs from 1-to 3-week-old piglets in Jilin province in 2010 showed a positivity rate of 44.23% (207/468) for PHEV (58). The PHEV genome sequences accounted for 75.28% of the identified five coronaviruses of PEDV, PDCoV, PHEV, PRCV, and TGEV in the nasal swabs and serum samples from slaughterhouses in 13 provinces of China in 2017 (59)…”