Determination and analysis of whole genome sequence of recombinant GII.6[P7] norovirus in Ningxia, China

Qian Chen; Jiangtao Ma; Lei Gao; Ran Xian; Kaixin Wei; Anqi Shi; Fang Yuan; Min Cao; Yu Zhao; Miao Jin; Wenhe Kuai

doi:10.1016/j.meegid.2023.105499

Determination and analysis of whole genome sequence of recombinant GII.6[P7] norovirus in Ningxia, China

Infect Genet Evol. 2023 Nov:115:105499. doi: 10.1016/j.meegid.2023.105499. Epub 2023 Sep 19.

Authors

Qian Chen¹, Jiangtao Ma², Lei Gao¹, Ran Xian¹, Kaixin Wei¹, Anqi Shi¹, Fang Yuan³, Min Cao³, Yu Zhao⁴, Miao Jin⁵, Wenhe Kuai³

Affiliations

¹ Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China; School of Public Health, Ningxia Medical University, Yinchuan 750001, China.
² Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China. Electronic address: nxcdcmjt@sina.com.
³ Ningxia Center for Disease Prevention and Control, Yinchuan 750004, China.
⁴ School of Public Health, Ningxia Medical University, Yinchuan 750001, China.
⁵ National Institute for Viral Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102211, China.

PMID: 37734510
DOI: 10.1016/j.meegid.2023.105499

Abstract

While the GII.4 norovirus was the predominant genotype, non-GII.4 genotype was increasingly focused since the non-GII.4 genotype caused regional epidemics. In this study, the detection rate was16.51% (183/1108) in Ningxia from January to December 2020. Among identified genotypes, GII.4[P31] and GII.4[P16] were the dominant genotypes (n = 20 and 18, respectively) while GII.6[P7] was the main type (n = 6) in non-GII.4 strains which was mainly detected in from May to July. The whole genome sequences of the norovirus diarrhea samples identified as GII.6 [P7] with Ct ≤ 30 collected in 2020 were determined. In this study, the complete genome sequences of norovirus strains PL20-044 and QTX20-071 were identified and analyzed phylogenetically. Phylogenetic analysis of the ORF1and ORF2 regions showed that these strains evolved from the GII·P7-GII.6 strains detected in recent years from different country. The results showed that PL20-044 had intra-type recombination with GII·P7-GII.6c and GII·P7-GII.6a, while QTX20-071 had intre-type recombination within GII·P7-GII.6a. The evolutionary rates of the RdRp gene region of the GII·P7 genotype and the VP1 gene region of the GII.6 genotype were 2.91 × 10^-3 (95%HPDs2.32-3.51 × 10^-3) and 2.61 × 10^-3 (95%HPDs2.14-3.11 × 10^-3) substitutions/site/year, respectively. Comparative analysis of the amino acid mutation sites in VP1 with the GII·P7-GII.6a strains before 1997, the later detected strains have changed in aa131 and aa354. Moreover, PL20-044 strains showed special mutations at aa316 and aa395. These results help to understand the norovirus genotype circulating in the human population in Ningxia, and discover the evolutionary characteristics of the GII·P7-GII.6 strain.

Keywords: GII.6[P7]; Norovirus; Recombination; System dynamics analysis; Whole genome.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Caliciviridae Infections* / epidemiology
China / epidemiology
Gastroenteritis* / epidemiology
Genotype
Humans
Norovirus* / genetics
Phylogeny