Detection and genetic analysis of a novel atypical porcine pestivirus from piglets with congenital tremor in Japan

Abstract

Atypical porcine pestivirus (APPV), which has been confirmed to be associated with congenital tremor (CT) in pigs, is a newly discovered porcine virus that has been found in the Americas, Europe and Asia; however, no report of APPV in Japan has been published. We identified an APPV in the central nervous system of Japanese piglets with CT and firstly determined and analysed the complete genome sequence. Phylogenetic analysis using the complete genome nucleotide sequence of the Japanese APPV, named Anna/2020, and those of APPVs from the NCBI database showed that APPVs were divided into three genotypes (genotypes 1 to 3), and that Anna/2020 clustered with the genotype 3 APPV strains, but distantly branched from these strains. Pairwise complete coding region nucleotide sequence comparisons revealed that there was 94.0%-99.7% sequence identity among the genotype 3 strains, while Anna/2020 showed 87.0%-89.3% identity to those genotype 3 strains, suggesting that Anna/2020 represents a novel APPV lineage within genotype 3.Retrospective examinations using RT-PCR revealed one genotype 1 and two novel genotype 3 APPVs from pigs without CT, and that novel genotype 3 APPVs have been prevalent in Japan since at least 2007.

The Diversity and Spatiotemporally Evolutionary Dynamic of Atypical Porcine Pestivirus in China

“…We found a strong association between phylogeny and geographic trait (Table 1), revealing geography-driven adaptation as an important factor for the diversification of APPV. Actually, this scenario has been supposed in a recent study from Japan, in which APPVs may independently evolve in the Japanese pig population (Kasahara-Kamiie et al, 2021). In addition, we failed to find recombination signals in the E2 region in our study, although previous works have revealed the presence of recombination events in the non-structural gene regions (Guo et al, 2020).…”

Complete Genome Sequence of a Genotype 3 Atypical Porcine Pestivirus Strain (OKN/2021) from Okinawa Prefecture, Japan

“…APPV has been found in North America, South America, Europe, and Asia thus far ( 6 ). Furthermore, it has been classified into three genotypes, i.e., genotype 1, genotype 2, and genotype 3 ( 7 ). APPV strains classified as genotype 3 were mostly detected in China ( 7 ).…”

“…Furthermore, it has been classified into three genotypes, i.e., genotype 1, genotype 2, and genotype 3 ( 7 ). APPV strains classified as genotype 3 were mostly detected in China ( 7 ). Kasahara-Kamiie et al recently reported a novel APPV strain belonging to genotype 3, speculating that it might have evolved uniquely in the Japanese pig population ( 7 ).…”

“…APPV strains classified as genotype 3 were mostly detected in China ( 7 ). Kasahara-Kamiie et al recently reported a novel APPV strain belonging to genotype 3, speculating that it might have evolved uniquely in the Japanese pig population ( 7 ). The complete genome sequence of another APPV strain, known as OKN/2021, which was derived from the serum of a sucking piglet with CT collected in Nanjo City, Okinawa Prefecture, Japan, in February 2021, is presented here.…”

“…Sanger sequencing of the amplified products was performed using an ABI 3500 system (Thermo Fisher Scientific, Waltham, MA), and the data were assembled using GENETYX v.15 software (Genetyx, Tokyo, Japan) to determine the whole-genome sequence of the OKN/2021 strain. Phylogenetic analysis of 62 full genomes, including strain OKN/2021, was performed with Molecular Evolutionary Genetics Analysis (MEGA) v.11 as described previously ( 7 ).…”