Viral Metagenomics Identifies a Novel Recombinant Murine Astrovirus from Rattus norvegicus in Jiangsu, China

Abstract Murine astrovirus (MuAstV) is widespread infection among wild and laboratory rats (Rattus norvegicus) and mice (Mus musculus). In this study, using viral metagenomics method, a near-complete genome of astrovirus isolate, named TZ-AST, was identified from Rattus norvegicus in mainland of China for the first time. Phylogenetic analysis showed that isolate TZ-AST and representative Murine astrovirus isolates cluster into one group and the isolate shares 90.2% nucleotide sequence of ORF1a similarity with a USA isolate SJ001 (Genbank Accession No.: MK395165), while sharing 94.9% nucleotide sequence of ORF2 similarity with another USA isolate MAV1 (Genbank Accession No. MF175075). This indicated that TZ-AST might be a recombinant. Complete genome sequences of MuAstV, together with that of TZ-AST were peformed recombination analysis using RDP 5.0. Results showed that TZ-AST with higher sequence similarity to the major parent MuAstV (MK395165), in the region of 494–2028 nt, while in the region of 5010–6259 nt, TZ-AST displayed higher sequence similarity to minor parent MuAstV (MF175075). Phylogenetic trees based on the genome region of 494–2028 nt and 5010–6259 nt were constructed respectively and comfirmed that TZ-AST is a novel Recombinant. Epidemiologic study showed that the prevalence rate of astrovirus was 17.4% in Rattus norvegicus in Taizhou, China.