Temporal evolutionary analysis of re-emerging recombinant GII.P16_GII.2 norovirus with acute gastroenteritis in patients from Hubei Province of China, 2017

Abstract

Norovirus (NoV) is a major pathogenic agent of human acute viral gastroenteritis that occurs worldwide. In March 2017, a series of acute NoV-associated gastroenteritis outbreaks occurred in Hubei Province in central China. Here, we sought to better understand the main genotypes and potential evolutionary advantages of circulating NoV strains underlying these outbreaks. During the outbreak, 111 fecal swabs and stool samples were collected from outpatients with acute NoV-associated gastroenteritis in Hubei Province. RNA was extracted from the samples and used as a template for real-time RT-PCR. Sequencing of a portion of the capsid gene and the ORF1/ORF2 overlap was used to assess DNA sequence homology, phylogeny, and recombination using pairwise alignments, MEGA, and Simplot, respectively. Bayesian evolutionary inference analysis was performed using the BEAST software platform to assess the genetic relationships, evolution rate, and evolutionary history of norovirus. GII NoV was determined to be the major pathogen of the acute gastroenteritis outbreaks in Hubei Province, with a 57.7% positive rate. Homology and phylogenic analysis of a portion of the capsid region for GII NoV isolates collected during outbreaks in Hubei showed that the isolates had a very high sequence identity and belonged to GII.2 genotype. Phylogenetic analysis of recombination using the ORF1/ORF2 overlap region revealed a recombinant strain, GII.P16_GII.2, in samples isolated from Hubei Province. The partial polymerase region and capsid gene of the recombinant strain had very high identity (98.7-98.8%) with the NoV strains isolated in Germany in 2016. The evolutionary rate of VP1 gene of GII.2 was distinctly higher than that of the partial polymerase region of GII.16. A phylogenetic tree generated using MCMC showed that the recombinant NoV GII.16_GII.2 was significantly divergent from other GII.16_GII.2 strains observed in China and Japan. Continued circulation of this GII.16_GII.2 recombinant could overtake the predominant GII.4 NoV strain with geographic expansion. Further analysis of the evolutionary dynamics of norovirus is necessary to develop more effective prevention and control strategies.

Keywords: Evolutionary dynamic; Norovirus; Phylogenetic analysis; Recombination.