Characterizationof complete genome sequence of a rat coronavirus
10.3969/j.issn.1002-2694.2023.00.121
- VernacularTitle:一株鼠冠状病毒的全基因组序列特征分析
- Author:
Jing ZHAO
1
;
Xiao-Hua MA
;
Xiao-Wei NAN
;
Sa-Sa CHAI
;
Li-Li LI
;
Zhao-Jun DUAN
Author Information
1. 甘肃中医药大学公共卫生学院,兰州 730000
- Keywords:
rat coronavirus;
complete genome;
phylogenetic analysis
- From:
Chinese Journal of Zoonoses
2023;39(11):1037-1043
- CountryChina
- Language:Chinese
-
Abstract:
This study determined the whole genome sequence and phylogenetic characteristics of a rat coronavirus.Nucleic acids were extracted from rat intestinal tissues collected in Inner Mongolia,and high-throughput sequencing was performed.A novel alphacoronavirus was present in the samples.The complete genome was amplified with PCR and RACE.Multiple se-quence alignment and a phylogenetic tree were constructed in MEGA.The whole genome of the rat coronavirus,denoted NMR-13,was 27 674 bp and included two non-coding regions and eight open reading frames,successively 5'UTR-ORF1ab-S-ORF3-E-M-ORF6-N-ORF8-3'UTR.Sequence identity analysis indicated that NMR-13 was most closely related to alphacoronavirus,which shared 91.3％nt identity with strain FiCoV/UMN2020.NMR-13h shared the next highest-sequence identitywiththe strains Lucheng/Lijiang-170,Lucheng/Ruian-83 and Lucheng/Lijiang-71 found in Zhejiang Province,China(79.49％,80.6％and 81.0％,respectively).Phylogeneticanalysis indicated that NMR-13 clustered with FiCoV/UMN2020.Recombination analy-sis indicated no recombination phenomenon.A rat coronavirus was isolated in this study,thus enriching the diversity of known alphacoronaviruses,and providing a reference for understanding the molecular genetic characteristics and molecular evolution of mouse coronaviruses in China.
