Isolation and complete nucleotide sequence of a Batai virus strain in Inner Mongolia, China

Abstract

Background: Batai virus (BATV) is a member of the Orthobunyavirus genus of the family Bunyaviridae, and a vector-borne pathogen. Genomic variations of BATV exist in different regions of the world, due to genetic reassortment. Whole-genome sequencing of any isolate is necessary for a phylogenetic analysis. In 1998, a BATV strain was isolated from an Anopheles philippines mosquito in Yunnan Province, China. This strain has not been found to infect any other host. We investigated BATV infection in cattle in Inner Mongolia, China and performed deep sequencing of the genome of the BATV isolate.

Findings: Ninety-five blood samples were collected from cattle in Inner Mongolia, China in 2012. The BATV infection rate was 2.1%. Previously, BATV strain NM/12 was isolated from two cattle in Inner Mongolia, China, and the whole genomic sequence of the strain has been available. We determined the complete genomic nucleotide sequences of the small (S), medium (M), and large (L) genome segments using bovine blood obtained in 2012, and the nucleotide homologies of these segments with those from GenBank were 88.7%-97%, 84%-95.4%, and 72.6%-95.8%, respectively. The deduced amino acid identities were 87.2-99.7%, 64.2-96.8%, and 81.1-98.6%. Phylogenetic analyses based on full-length genomic sequences indicated that the M and L segments, and a portion of the S segment, of NM/12 are most closely related to the BATV strains isolated in Asia. The S and M segments of NM/12 were independent of phylogenetic lineages. The L segment was the most closely related to Chittoor/IG-20217 (isolated in India), and distantly related to isolated strains in Italy. Nucleotide substitution rates in the nucleotide sequences that code for the nucleocapsid, envelope glycoprotein, and polymerase protein of NM/12 strain were 2.56%, 4.69%, and 4.21%, respectively, relative to the original strain of MM2222.

Conclusion: A novel BATV NM/12 strain from bovine serum collected in Inner Mongolia was isolated from cattle in China for the first time. Our findings elucidate the evolutionary status of the BATV NM/12 strain among different orthobunyavirus strains and may provide some clues to prevent the emergence of BATV infection in cattle and humans.

Figure 1

Amplification of the M gene from BATV by RT-PCR with P1 and P2 primers. BATV RNA was used as template and specific primers targeting the virus M gene were used in an RT-PCR assay. (Lanes: M, Trans 2K DNA Marker; Lanes: 1–2, blood samples of cattle; Lanes: 3, cytopathic effect of Vero cell; Lanes: 4, Death of the Challenged Mice; Lanes: 5, negative control).

Figure 2

Electron microscopy of negative-stained Batai virus particles from cattle. Scale bar indicates 100 nm.

Figure 3

Phylogenies of the S, M and L segments of the genus Orthobunyavirus. The genome of BATV N and NSs genes of partial S segment (a; length =911 nucleotides), M (b; length = 4405 nucleotides), and the partial L segment (c; length = 580 nucleotides) representative Orthobunyavirus for the aligned sequence and phylogenetic tree.The phylogenetic tree was constructed by the neighbor-joining method using 1000 bootstrapping replicates.