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.

Mammalian orthoreovirus (MRV) is a non-enveloped double-stranded RNA virus with a broad host range. MRVs are prevalent worldwide and have been isolated from various hosts, including humans, dogs, cats, wild boars, sewage, and pigs, in Japan. However, Japanese porcine MRV has not been genetically characterized yet. While investigating porcine enteric viruses including MRV, five MRVs were isolated from the feces of Japanese pigs using the MA104 cell culture. Genetic analysis of the S1 gene revealed that the Japanese porcine MRV strain isolates could be classified as MRV-2 and MRV-3.Whole genome analysis showed that Japanese porcine MRVs exhibited genetic diversity, although they shared homology with porcine MRV sequences deposited in the DDBJ/EMBL/GenBank database. Several potential intra-genetic reassortment events among MRV strains from pigs, sewage, and humans have been detected in Japan, suggesting zoonotic transmission. Furthermore, homologous recombination events were identified in the M1 and S1 genes of Japanese porcine MRV. These findings imply that different strains of Japanese porcine MRVs share a porcine MRV genomic backbone and have evolved through intra-genetic reassortment and homologous recombination events. Fig. 1C. Fukase et al. LC613213.1 Mammalian orthoreovirus 2 THK0325 MN639758.1 Mammalian orthoreovirus strain 19/242 MN788298.1 Mammalian orthoreovirus strain HLJYC2017 JX486061.1 Mammalian orthoreovirus 3 isolate GD-1 KY419124.1 Mammalian orthoreovirus 3 isolate ZJ2013 KT224508.1 Mammalian orthoreovirus 3 strain SD-14 MK092968.1 Mammalian orthoreovirus 2 isolate OV204 Orthoreovirus Ebina9-2021 M2MARC145 Orthoreovirus Ebina11-2021 M2MARC145 KT444556.1 Mammalian orthoreovirus isolate WIV7 mu-1 gene complete cds KT444536.1 Mammalian orthoreovirus isolate WIV4 mu-1 gene complete cds KC462153.1 Mammalian orthoreovirus isolate HB-A LC121914 Panthera leo KX263311.1 Mammalian orthoreovirus 1 isolate B/03 MG457102.1 Mammalian orthoreovirus isolate SI-MRV04 KU194670.1 Mammalian orthoreovirus 2 isolate T3/Pipistrellus kuhlii/Italy/5515-3/2012 GQ468269.1 Mammalian orthoreovirus 3 isolate MPC/04 LC476919.1 Mammalian orthoreovirus 2 Osaka2014 GU196310.1 Mammalian orthoreovirus 2 MRV2Tou05 LC476899.1 Mammalian orthoreovirus 2 Osaka1994 DQ482462.1 Mammalian orthoreovirus isolate SC-A TY14-M2 LC476909.1 Mammalian orthoreovirus 2 Osaka2005 gene for mu-1 protein complete cds MK408599.1 Mammalian orthoreovirus isolate MRV-3 chamois 84407 Italy 2009 KT444546.1 Mammalian orthoreovirus isolate WIV5 KU194662.1 Mammalian orthoreovirus 3 T3/Pipistrellus kuhlii/Italy/5515-2/2012 JQ412759.1 Mammalian Orthoreovirus strain T3/Bat/Germany/342/08 KX932033.1 Mammalian orthoreovirus isolate mew716 MRV-3 MG457082.1 Mammalian orthoreovirus isolate SI-MRV02 KF154728.1 Mammalian orthoreovirus isolate SI-MRV01 JX415471.1 Porcine reovirus SHR-A M20161.1 Reovirus type 3 Dearing U24260.1 Reovirus type 3 Abmey MN022935.1 Mammalian orthoreovirus strain AP-151/BR KX384850.1 Mammalian orthoreovirus strain MORV/47Ma/06 MG457112.1 Mammalian o...

Rotavirus C (RVC) is a major cause of diarrhoea in swine, cattle, and humans worldwide. RVC exhibits sequence diversity in all 11 genes, especially in VP4 and VP7, and all segment-based genotyping has been performed similar to rotavirus A. To date, recombination events have been reported in rotavirus A and B. However, there are no reports describing gene recombination of RVC, except for recombination in NSP3 between RVC and rotavirus H. In this study, nine porcine RVC strains identified in Japanese pigs were completely sequenced and analysed together with RVC sequences from the GenBank database. The analyses showed that sequences of the VP4, VP2, and NSP1 of several porcine RVC strains did not branch with any of those of the RVC strains in the GenBank database, suggesting new genotypes. Several homologous recombination events, between or within genotypes, were identified in the VP4, VP7, VP2, NSP1, and NSP3 genes. Of these, nine, one, and one intergenotypic recombination events in the VP4, VP2, and NSP3 genes, respectively, were supported with sufficient statistical values. Although these findings suggest occurrences of the intragenic recombination events in the RVC genome, potential sequence errors and poor sequence assemblies in the databases should be watched with care. The results in this study present data about the important recombination events of the RVCs, which influence evolution of the virus by aiding them to gain genetic diversity and plasticity, although further sequence data will be necessary to obtain more comprehensive understanding of such mechanisms.

A novel picornavirus was isolated from the faeces of a diarrhoeic cow using MA-104 cells at the third blind passage. This virus, named Den1/2021/JPN, was completely sequenced using total RNA from the cell culture supernatant by deep sequencing. The genome of Den1/2021/JPN had a standard picornavirus genome organisation with conserved picornaviral motifs. The 5′ untranslated region harboured a type-II internal ribosomal entry site. Den1/2021/JPN was most closely related to a bovine parechovirus (Bo_ParV) named cow/2018/4, which has been recently identified in publicly available databases. Phylogenetic analyses and pairwise sequence comparison revealed that Den1/2021/JPN and Bo_ParV cow/2018/4 clustered with parechoviruses and were most closely related to Parechovirus E identified in birds of prey, exhibiting nucleotide sequence similarity of 64.2–64.5 %, 58.6–59.7 % and 66.3–66.4 % in the polyprotein, P1 and 2C+3 CD coding regions, respectively. This study presents the first report on the isolation of Bo_ParV. Den1/2021/JPN and Bo_ParV cow/2018/4, which are candidates for a novel species in the genus Parechovirus.

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.

Mammalian orthoreovirus (MRV) is a non-enveloped double-stranded RNA virus with a broad host range. MRVs are prevalent worldwide and have been isolated from various hosts, including humans, dogs, cats, wild boars, sewage, and pigs, in Japan. However, Japanese porcine MRV has not been genetically characterized yet. While investigating porcine enteric viruses including MRV, five MRVs were isolated from the feces of Japanese pigs using the MA104 cell culture. Genetic analysis of the S1 gene revealed that the Japanese porcine MRV strain isolates could be classified as MRV-2 and MRV-3. Whole genome analysis showed that Japanese porcine MRVs exhibited genetic diversity, although they shared homology with porcine MRV sequences deposited in the DDBJ/EMBL/GenBank database. Several potential intra-genetic reassortment events among MRV strains from pigs, sewage, and humans have been detected in Japan, suggesting zoonotic transmission. Furthermore, homologous recombination events were identified in the M1 and S1 genes of Japanese porcine MRV. These findings imply that different strains of Japanese porcine MRVs share a porcine MRV genomic backbone and have evolved through intra-genetic reassortment and homologous recombination events.