1 INTRODUCTION
Congenital tremor (CT) in neonatal piglets, also known as “dancing piglet”, was described for the first time in 1922 (Kinsley, 1922). At present, CT is divided into types A and B. Type A is associated with visible histological lesions in the central nervous system (CNS) while type B does not show any apparent lesions. Type A is further divided into types A-I to A-V based on the causative agent, e.g., classical swine fever virus infection (A-I), genetic defect in the Landrace (A-III) and Saddleback (A-IV) pig breeds, and metrifonate intoxication (A-V) (Done, 1976); however, the causal factor of type A-II CT remained unknown for a long time. Recently, several viruses have been proposed to cause type A-II CT, including atypical porcine pestivirus (APPV), and only APPV has been proven to induce CT through the injection of pregnant sows with sera containing APPV (Arruda et al., 2016; de Groof et al., 2016).
APPV belongs to the genus Pestivirus within the familyFlaviviridae . Recently, pestiviruses were categorized into 11 different species based on phylogenetic analysis, and a new host-independent taxonomy system for Pestivirus species was proposed using the format Pestivirus X . APPV was categorized asPestivirus K (Smith et al., 2017). Pestivirus is a small enveloped virus that has a single-stranded positive-sense RNA genome and contains a large open reading frame (ORF), which encodes nearly 4,000 amino acids (aa) and is preceded by a 5′ untranslated region (UTR) and followed by a 3′ UTR. The polyprotein is processed into four structural proteins (C, Erns, E1, and E2) and eight non-structural proteins (Npro, p7, NS2, NS3, NS4A, NS4B, NS5A, and NS5B), and the gene order is 5′-Npro-C-Erns-E1-E2-p7-NS2-3(NS2-NS3)-NS4A-NS4B-NS5A-NS5B-3′ (Tautz et al., 2015).
APPV was first discovered from the serum of a pig without clinical symptoms in the United States (Hause et al., 2015). Since then, APPVs have been found from pigs and wild boars with or without CT worldwide on four continents, and genomic sequence diversity among APPVs has been reported (Beer et al., 2017; Cagatay et al., 2018; Chen et al., 2019; Choe et al., 2020; Colom-Cadena et al., 2018; de Groof et al., 2016; Dénes et al., 2018; Dessureault et al., 2018; Gatto et al., 2018; Mósena et al., 2018; Muñoz‐González et al., 2017; Pan et al., 2019b; Possatti et al., 2018; Postel et al., 2016, 2017; Schwarz et al., 2017; Shen et al., 2018; Sozzi et al., 2019; Stenberg et al., 2020; Xie et al., 2019; Yan et al., 2019; Yuan et al., 2017; Zhang et al., 2017; Zhang et al., 2019; Zhou et al., 2019). However, genome sequence data of APPV have not been reported from Japan.
In the present study, we identified the APPV genome sequence in piglets showing CT on a Japanese pig farm, and we analyzed and compared the complete genome sequences obtained from Japanese pigs with sequences from the DDBJ/EMBL/GenBank databases. Furthermore, a retrospective study to detect APPV was conducted using a total of 399 porcine samples collected from 2005 to 2020 in Japan.