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. 2016 Aug 15;214(4):556-64.
doi: 10.1093/infdis/jiw208. Epub 2016 May 24.

The Evolution and Transmission of Epidemic GII.17 Noroviruses

Jing Lu  1 , Lin Fang  2 , Huanying Zheng  2 , Jiaqian Lao  2 , Fen Yang  2 , Limei Sun  2 , Jianpeng Xiao  3 , Jinyan Lin  2 , Tie Song  2 , Tao Ni  4 , Jayna Raghwani  5 , Changwen Ke  2 , Nuno R Faria  5 , Thomas A Bowden  4 , Oliver G Pybus  5 , Hui Li  2
Affiliations

The Evolution and Transmission of Epidemic GII.17 Noroviruses

Jing Lu et al. J Infect Dis. .

Abstract

Background: In recent decades, the GII.4 norovirus genotype has predominated in epidemics worldwide and been associated with an increased rate of evolutionary change. In 2014, a novel GII.17 variant emerged and persisted, causing large outbreaks of gastroenteritis in China and sporadic infections globally. The origin, evolution, and transmission history of this new variant are largely unknown.

Methods: We generated 103 full capsid and 8 whole-genome sequences of GII.17 strains collected between August 2013 and November 2015 in Guangdong, China. Phylogenetic analyses were performed by integrating our data with those for all publically available GII.17 sequences.

Results: The novel emergent lineage GII.17_Kawasaki_2014 most likely originated from Africa around 2001 and evolved at a rate of 5.6 × 10(-3) substitutions/site/year. Within this lineage, a new variant containing several important amino acid changes emerged around August 2013 and caused extensive epidemics in 2014-2015. The phylodynamic and epidemic history of the GII.17_Kawasaki lineage shows similarities with the pattern observed for GII.4 norovirus evolution. Virus movements from Hong Kong to neighboring coastal cities were frequently observed.

Conclusions: Our results provide new insights into GII.17 norovirus evolution and transmission and highlight the potential for a rare norovirus genotype to rapidly replace existing strains and cause local epidemics.

Keywords: epidemic; norovirus; phylogenetic; phylogeographic; virus transmission.

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Figures

Figure 1.
Figure 1.
Outbreaks of GII.4 and GII.17 infections in Guangdong China, 2013–2015. A, Time series of the number of GII norovirus (NoV) outbreaks during the study period, from January 2013 to November 2015. GII.4 (blue) and GII.17 (red) were detected as major causes of outbreaks in different epidemic seasons and are presented with bar charts. The dotted line represented the total number of NoV outbreaks. B, Geographic distribution of GII.4 and GII.17 NoV outbreaks in Guangdong from January 2013 to November 2015.
Figure 2.
Figure 2.
Molecular clock phylogeny of GII.17 VP1 gene sequences. The tree shown is a maximum clade credibility phylogeny, Branch colors represent the most probable ancestral locations of each branch, inferred using a phylogeographic model (Supplementary Materials and Methods). Long internal branches with uncertain locations are in gray. Three major lineages of GII.17 noroviruses are denoted on the right. Black circles indicate posterior probabilities of >0.80 at selected nodes. Location posterior probabilities are noted above 3 specific branches.
Figure 3.
Figure 3.
Inferred phylogeny, demographic history, and spatial dissemination of GII.17 norovirus in Guangdong. A, maximum clade credibility phylogeny with branches colored according to the most probable posterior ancestral location (see legend). Black circles indicate posterior probabilities of >0.80 at selected nodes. Long internal branches with uncertain locations are in gray. B, Demographic history of GII.17 norovirus in Guangdong, inferred using the Bayesian Skyline plot approach. C, Well-supported virus translocation events (Bayes factor >3) are represented on a map of Guangdong. Arrow thickness represents the relative number of well-supported movement events for each pair of locations. The inset on the bottom right shows the water flows among the cities in Guangdong among which virus movement was inferred. Ne(τ), effective population size.
Figure 3.
Figure 3.
Inferred phylogeny, demographic history, and spatial dissemination of GII.17 norovirus in Guangdong. A, maximum clade credibility phylogeny with branches colored according to the most probable posterior ancestral location (see legend). Black circles indicate posterior probabilities of >0.80 at selected nodes. Long internal branches with uncertain locations are in gray. B, Demographic history of GII.17 norovirus in Guangdong, inferred using the Bayesian Skyline plot approach. C, Well-supported virus translocation events (Bayes factor >3) are represented on a map of Guangdong. Arrow thickness represents the relative number of well-supported movement events for each pair of locations. The inset on the bottom right shows the water flows among the cities in Guangdong among which virus movement was inferred. Ne(τ), effective population size.
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