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Genome characterization and temporal evolution analysis of a non-epidemic norovirus variant GII.8

Author:
Xue, Liang, Cai, Weicheng, Gao, Junshan, Zhang, Le, Wu, Haoming, Pang, Rui, Li, Ying, Wang, Juan, Zhang, Jumei, Wu, Shi, Ye, Qinghua, Lei, Tao, Wu, Qingping
Source:
Infection, genetics, and evolution 2019 v.70 pp. 15-23
ISSN:
1567-1348
Subject:
Norovirus, amino acids, capsid, enzymes, epitopes, gastroenteritis, genome, genotype, mutation, oligodeoxyribonucleotides, open reading frames, proteins, China
Abstract:
Noroviruses are the primary cause of non-bacterial acute gastroenteritis worldwide, and GII.8 belongs to a non-epidemic genotype with a limited understanding currently. In this study, we assembled the first GII.8 norovirus genome from China and clarified the temporal evolutionary process of this non-epidemic variant. Using the “4+1+1” application strategy with newly designed primer sets, the genome of one GII.8 strain GZ2017-L601 from China was firstly sequenced that comprised 7476 nucleotides. The homology of the new genome and the previous only GII.8 genome reached 93.8% identity at the nucleotide level, but only 10, 6, 7 amino acid mutations occurred in three ORFs. When compared the new strain with other GII reference strains, p22 and P2 were calculated as the variable encoding regions, and NTPase, VPg, 3CL, RdRp and S were shown as the conserved ones. We then reconstructed the evolutionary process of the GII.8 genotype using other available sequences in GenBank. Based on the partial N/C region, all GII.8 strains could be subdivided chronologically into four clusters, which spans 1967–1994, 1997–2005, 2003–2009, and 2007–2017, respectively. Moreover, differences of capsid P proteins between GII.8 strains and the epidemic GII.4 strain VA387 were also compared. There existed 147/310 distinct amino acid sites in the alignment, including two insertion and three deletion mutations. Distribution of antigen epitopes of two GII.8 variants was comparable, but the numbers of antigenic sites of GII.8 strains were less than that of VA387. In summary, the first GII.8 genome from China was assembled and extensively characterized, and a time-order evolutionary process of this genotype was identified with a static pattern of antigenic variations.
Agid:
6344372