Detection and genetic analysis of a novel atypical porcine pestivirus
from piglets with congenital tremor in Japan
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 analyzed 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% to
99.7% sequence identity among the genotype 3 strains, while Anna/2020
showed 87.0% to 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.