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. 2021 Mar 22:12:655567.
doi: 10.3389/fmicb.2021.655567. eCollection 2021.

Molecular Evolution of Human Norovirus GII.2 Clusters

Xingguang Li  1 , Haizhou Liu  2 , Brittany Rife Magalis  3 , Sergei L Kosakovsky Pond  3 , Erik M Volz  4
Affiliations

Molecular Evolution of Human Norovirus GII.2 Clusters

Xingguang Li et al. Front Microbiol. .

Abstract

Background: The human norovirus GII.2 outbreak during the 2016-2017 winter season was of unprecedented scale and geographic distribution.

Methods: We analyzed 519 complete VP1 gene sequences of the human norovirus GII.2 genotype sampled during the 2016-2017 winter season, as well as prior (dating back to 1976) from 7 countries. Phylodynamic analyses of these sequences were performed using maximum likelihood and Bayesian statistical frameworks in order to estimate viral evolutionary and population dynamics associated with the outbreak.

Results: Our results revealed an increase in the genetic diversity of human norovirus GII.2 during the recent Asian outbreak and diversification was characterized by at least eight distinct clusters. Bayesian estimation of viral population dynamics revealed a highly fluctuating effective population size, increasing in frequency during the past 15 years.

Conclusion: Despite an increasing viral diversity, we found no evidence of an elevated evolutionary rate or significant selection pressure in human norovirus GII.2, indicating viral evolutionary adaptation was not responsible for the volatility of or spread of the virus during this time.

Keywords: genetic diversity; human norovirus; phylogenetic analyses; positive selection; virus evolution.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Maximum-likelihood phylogeny of HuNoV GII.2 strains. The two circles of color show geographic location (inner) and phylogenetic cluster (outer).
FIGURE 2
FIGURE 2
Geographic distribution of HuNoV GII.2 clusters identified in the present study. Each GII.2 cluster identified in this study is color-coded, as shown on the left. The figure was created using Adobe Illustrator CS5 version 15.0.0 software, based on the maps obtained from Craft MAP website (craftmap.box-i.net/).
FIGURE 3
FIGURE 3
Regression of the root-to-tip genetic distance against year of sampling for the HuNoV GII.2 sequences. Colors indicate different geographic locations.
FIGURE 4
FIGURE 4
Bayesian skygrid demographic reconstruction of HuNoV GII.2. The vertical axis shows the effective number of infections (Ne) multiplied by mean viral generation time (τ). The solid line and shaded region represent the median and 95% credibility interval, respectively, of the inferred Neτ through time.
FIGURE 5
FIGURE 5
Maximum-clade-credibility tree estimated from complete VP1 gene sequences of HuNoV GII.2. Light blue horizontal bars represent 95% credibility intervals for estimates of node times. Posterior probabilities are shown at the node. Each cluster is shown with different colors.
See this image and copyright information in PMC

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