Identification of genetic diversity of porcine Norovirus and Sapovirus in Korea

Abstract

It is well known that Norovirus (NoV) and Sapovirus (SaV) identified in humans and pigs have heterogeneous genome sequences. In this study, a total of three strains of NoV and 37 strains of SaV were detected in 567 porcine fecal samples by RT-PCR, corresponding detection rates of 0.5 and 6.5%, respectively. Phylogenetic analyses were conducted using amino acid sequences of the partial RNA-dependent RNA polymerase (RdRp) and complete capsid proteins of both viruses to determine their genogroups. Analysis with the RdRp sequences indicated that all three NoV strains HW41, DG32, and DO35 detected in this study were classified into genogroup II (GII). A further analysis with the complete capsid sequence demonstrated that the DO35 strain belonged to subgenotype b in GII-21 (GII-21b) along with the SW918 strain. A total of 26 strains out of 27 strains that were selected from the 37 porcine SaVs were classified into genogroup III when they were analyzed with the RdRp sequences. The remaining strain (DO19) was not clustered with any of the previously classified SaV strains, thereby suggesting the advent of a new genogroup virus. Additional analyses with the amino acid sequence of the capsid and the nucleotide sequence of the RdRp and capsid junction region supported the notion that the DO19 strain belonged to a novel genogroup of SaV. To the best of our knowledge, this is the first report to describe a novel porcine SaV belonging to an unknown genogroup in Korea.

Occurrence of Norovirus in pig faecal samples in the Eastern Cape, South Africa

“…were high compared to results obtained from other studies in which the occurrence rates detected were 0.5% in Korean pigs [24], 1.2%…”

Prevalence of Porcine Noroviruses, Molecular Characterization of Emerging Porcine Sapoviruses from Finisher Swine in the United States, and Unified Classification Scheme for Sapoviruses

“…and GXIV?, respectively. Our analysis placed previously unclassified porcine strains Po/ F2-4, Po/F8-9, Po/DO19, and Po/2014P2 into GVII (20,22), which formed at least 3 distinct genetic clusters in the capsid phylogenetic tree (Fig. 1), including the prototypical GVII SaVs (Po/ K7, Po/F2-4, and Po/DO19, respectively).…”

“…Even though different ages of pigs were tested, NoVs were detected only in finisher pigs (7). A Canadian study reported 25% prevalence (41), and many other studies found lower prevalence rates: 2% to 4.6% in Europe (5, 42), 9% in New Zealand (43), 8% in Brazil (44), and Ͻ1% to 15% in Asia (8,15,22). These differences could be due to different geographical locations, different ages of pigs sampled, or the use of different detection methods and primers with various specificities.…”

“…Recently, at least three more SaV genogroups (GVI, GVII, and GVIII) have been proposed based on complete capsid sequences, and several porcine strains are not yet classified (19)(20)(21)(22)(23)(24). One study found porcine SaVs genetically closely related to human GV SaVs (15).…”

“…In addition to infecting humans and pigs, SaVs, possibly representing distinct genogroups, have also been detected in mink, dogs, sea lions, and bats (28)(29)(30)(31); however, no unified classification scheme has been applied to both human and animal SaVs, except for the porcine GIII SaVs. The unclassified porcine strains fall between the interand intragenogroup cutoff distances proposed previously (19,20,22), necessitating a SaV classification scheme based on both human and recently identified animal strains. Both intra-and intergenogroup recombination can occur among SaVs (23,26), making surveillance of these emerging viruses imperative.…”