Complete genome sequence analysis of the norovirus GII.P16-GII.2 variant in Beijing

Abstract

Objective To amplify the complete genomes of two noroviruses (NoVs) GII.P16-GII.2 variants in Beijing, 2017 and to analyze the genetic characteristics of the strains. Methods The complete genome sequences of the two GII.P16-GII.2 NoVs strains were amplified by one-Step RT-PCR, and the PCR products were sequenced. The sequences were assembled by the DNAStar 7.0 and BioEdit, and the phylogenetic trees were generated using the maximum-likelihood method by Mega 5.05. The SimPlot software was used for similarity analysis. The amino acid mutations within or near histo-blood group antigen (HBGA) binding site were also analyzed. Results Both NoVs strains detected in Beijing formed a new cluster frow other GII.P16-GII.2 2016-2017 strains in the phylogenetic trees of the complete genome sequences and VP1 sequences. However, the two strains, other GII.P16-GII.2 2016-2017 strains and GII.P16-GII.4_Sydney 2015-2016 strains formed a mixed branch in the phylogenetic tree of RDRP. The phylogenetic trees of the VP1 sequences and RDRP also indicated that the GII.P16-GII.2 2016-2017 strains were the closest to the strains in 2011, comparing to those found before 2016. Both strains had one amino acid mutation nearing HBGA binding site comparing to other GII.P16-GII.2 strains. Conclusions The two NoVs strains detected in Beijing in 2017 were confirmed to be GII.P16-GII.2 recombinant strains by complete sequence analysis, and they may originated from GII.P16-GII.2 strains in 2011. Key words: Norovirus; Complete genome; Phylogenetic analysis