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

• Published in: Infection, genetics and evolution Vol. 115; p. 105499
• Main Authors: Chen, Qian, Ma, Jiangtao, Gao, Lei, Xian, Ran, Wei, Kaixin, Shi, Anqi, Yuan, Fang, Cao, Min, Zhao, Yu, Jin, Miao, Kuai, Wenhe
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.11.2023
• Subjects: GII.6[P7]; Norovirus; Recombination; System dynamics analysis; Whole genome; System dynamics analysis; Whole genome; Recombination; Norovirus; GII.6[P7]
• ISSN: 1567-1348; 1567-7257
• DOI: 10.1016/j.meegid.2023.105499

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. •Recombination between GII.6a and GII.6c and recombination within GII.6a in this area.•The evolutionary rates of GII.P7 RdRp region is 2.91 × 10−3 substitutions/site/year.•The evolutionary rates of GII.6 VP1 region is 2.61 × 10−3 substitutions/site/year.•The GII.6a group strains only bind to the type of GII.P7 RdRp region.•There were variations in aa131 and aa354 of GII.6a VP1 region from 1976 to 2020.