Genome characteristics and molecular evolution of the human sapovirus variant GII.8

• Published in: Infection, genetics and evolution Vol. 73; no. C; pp. 362 - 367
• Main Authors: Xue, Liang, Cai, Weicheng, Gao, Junshan, Jiang, Yueting, Wu, Haoming, Zhang, Le, Zuo, Yueting, Dong, Ruimin, Pang, Rui, Zeng, Haiyan, Wu, Shi, Wang, Juan, Zhang, Jumei, Wu, Qingping
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01-09-2019; Elsevier
• Subjects: Amino Acid Sequence - genetics; Bayes Theorem; Caliciviridae Infections - virology; Capsid protein; Capsid Proteins - genetics; China; Diarrhea - virology; Evolution, Molecular; Gastroenteritis - virology; Genetic Variation - genetics; Genome; Genome, Viral - genetics; Genotype; GII.8; Humans; Molecular evolution; Open Reading Frames - genetics; Phylogenetic analysis; Phylogeny; Sapovirus; Sapovirus - genetics; Sequence Analysis, DNA - methods; China; Phylogenetic analysis; Molecular evolution; GII.8; Capsid protein; Genome; Sapovirus
• ISSN: 1567-1348; 1567-7257
• DOI: 10.1016/j.meegid.2019.05.017

Human sapovirus is regarded as an important viral agent for acute diarrhea worldwide. GII.8, a recently reported genotype, has been detected in a few countries and regions. In this study, we obtained the first genome sequence of a sapovirus GII.8 strain isolated in mainland China, and comprehensively analyzed the genetic diversity and evolutionary process of this genotype. The viral genome of the new GII.8 Guangzhou strain GZ2014-L231 comprised 7433 nucleotides, including two ORFs. Pairwise alignments of the new genome with representative sequences of different genotypes showed inconsistent homology between different protein-encoding regions, of which NS1 and VP2 were found as the variable proteins, and NS3, NS5, and NS6/7 were found as the conserved ones. Compared with other reported GII.8 genomes, the Guangzhou strain introduced 34 new nucleotide changes and one new amino acid change. Phylogenetic analysis based on full-length VP1 sequences demonstrated that 11 GII.8 strains could be divided into 4 clusters A-D, with 88 SNP and 10 SAP spots occurred during their evolutionary process. The Guangzhou strain has higher homology with seven GII.8 strain detected after 2014, especially the US and Peruvian strains of 2015/2016, which have the identical VP1 amino acid sequences. Using a Bayesian coalescent method based on VP1 sequences, GII.8 was predicted to emerge in 2001 with the evolution rate of 1.45 × 10−3 nucleotide substitutions/site/year (strict clock). In summary, the data in this study not only provided reference data from mainland China for sapovirus researches in future, but also firstly described the evolutionary process of the GII.8 genotype.
•The first genome sequence of GII.8 SaV from mainland China was obtained and analyzed.•The new Guangzhou genome employed 34 new SNP and one new SAP.•NS1 and VP2 were found as the variable proteins in the SaV genome.•GII.8 SaV could be further divided into four clusters based on the capsid VP1.•TMRCA and evolution rate for the capsid VP1 gene of GII.8 SaV was estimated.