Intraspecific variation of the hedgehog arteriviruses, which may constitute a new genus in the subfamily Heroarterivirinae of the family Arteriviridae

We recently discovered a novel member of the family Arteriviridae, hedgehog arterivirus 1 (HhAV-1), in the brains of hedgehogs with fatal encephalitis. In this study, we classified this virus and investigated its intrahost genomic diversity using next-generation sequencing. We sequenced HhAV-1 genomes from specimens from seven hedgehogs (two males and five females) with signs of encephalitis that were collected in Buckinghamshire, Gloucestershire, and Cambridgeshire, England, and had died or been euthanised between 2013 and 2024. Analysis of the intrahost populations of these seven HhAV-1 isolates and a previously described isolate revealed the presence of single-nucleotide polymorphisms (SNPs), which were most frequent in open reading frames 5, 6, and 7, encoding glycoprotein 5, the membrane protein, and the nucleocapsid protein. Pairwise comparisons of the eight HhAV-1 variants showed that the nucleotide sequence identity values in their combined complete coding sequences ranged from 76.2% to 100%. The eight HhAV-1 variants also shared at least 82.8% amino acid sequence identity in five domains that are involved in replication and are used for the classification of nidoviruses: 3CLpro, NiRAN, RdRp, ZBD, and HEL1. In a replicase-based phylogenetic tree of members of the family Arteriviridae, the HhAV-1 variants formed a sister cluster to African pouched rat arterivirus. A DEmARC-based pairwise distance analysis indicated that these viruses may comprise a new species, for which we propose the name "Xiarterivirus erinaceid", in a new genus in the subfamily Heroarterivirinae.