Sequencing and analysis of the whole genome of a strain of rabies virus transmitted by hog badger in Sichuan province
10.3760/cma.j.cn112866-20240304-00033
- VernacularTitle:四川省1株猪獾传播狂犬病病毒全基因组序列测定及分析
- Author:
Hongrong ZHONG
1
;
Mingfeng JIANG
;
Yuliang FENG
;
Xingyu ZHOU
;
Wei LI
Author Information
1. 四川省疾病预防控制中心，成都 610041
- Keywords:
Rabies virus;
Hog badger;
Whole genome;
Sequence analysis
- From:
Chinese Journal of Experimental and Clinical Virology
2024;38(3):286-293
- CountryChina
- Language:Chinese
-
Abstract:
Objective:The objective of this study is to sequence whole genome of the rabies virus in the saliva specimen of a suspected rabies case with onset of rabies from a wildlife (hog badger) bite wound in Sichuan province, where the genetic variation characteristics of the virus was analyzed at the molecular level, so as to understand the prevalence and mutation of wildlife rabies virus in Sichuan province.Methods:Total viral RNA was extracted from the saliva specimen of the suspected rabies case. Then, rabies virus sequences were amplified using PCR with specific primers; the gene fragments obtained were sequenced, and the sequences obtained were spliced using biological software to obtain the whole genome sequence of the rabies virus strain. The genetic variation characteristics of the whole genome were analyzed.Results:The whole genome nucleotide sequence of a strain of rabies virus of hog badger origin (hereinafter referred to as SCR23-052) was obtained by sequencing, and NCBI online BLAST and comparison with several reference sequences showed that the composition and structure of the whole genome sequence of SCR23-052 conformed to the characteristics of the Lyssavirus under the Rhabdoviridae; the highest similarity in nucleotide and amino acid sequences in various gene regions was observed between SCR23-052 and the strains of Ningxia (J) and Chongqing (CQ92, 02050CHI). The sequence variability of SCR23-052 genome was significantly lower at the amino acid level than that at the nucleotide level, which indicated that most of the nucleotide variants in the protein-coding genes belonged to synonymous mutations. Phylogenetic analysis showed that SCR23-052 belonged to genotype V, which did not show any obvious mutation in the major antigenic site of the glycoprotein, underwent amino acid glycosylation at positions 56 and 338 by the online site prediction, and showed the least amino acid difference compared with the signal peptide sequence of the vaccine strain CTN181. The virus in this study has an A→T mutation at position 332 in the nucleoprotein major antigenic site with all reference vaccine strains, and an L→V mutation at position 379 in the B-cell epitope with the CTN181 vaccine strain. SCR23-052 was consistent with both genotype V reference strains at the nucleoprotein study site.Conclusions:The whole genome sequence of a wildlife strain of genotype V rabies virus of hog badger origin was obtained, which was different from that of the genotype I strain of rabies virus of dog origin that previously reported to be prevalent in Sichuan. The genome sequence of SCR23-052 differed from that of the reference vaccine strains to a varying degree, but the main virulence characteristics remained unaltered.
