Genetic and Epidemiologic Trends of Norovirus Outbreaks in the United States from 2013 to 2016 Demonstrated Emergence of Novel GII.4 Recombinant Viruses

Abstract

Noroviruses are the most frequent cause of epidemic acute gastroenteritis in the United States. Between September 2013 and August 2016, 2,715 genotyped norovirus outbreaks were submitted to CaliciNet. GII.4 Sydney viruses caused 58% of the outbreaks during these years. A GII.4 Sydney virus with a novel GII.P16 polymerase emerged in November 2015, causing 60% of all GII.4 outbreaks in the 2015-2016 season. Several genotypes detected were associated with more than one polymerase type, including GI.3, GII.2, GII.3, GII.4 Sydney, GII.13, and GII.17, four of which harbored GII.P16 polymerases. GII.P16 polymerase sequences associated with GII.2 and GII.4 Sydney viruses were nearly identical, suggesting common ancestry. Other common genotypes, each causing 5 to 17% of outbreaks in a season, included GI.3, GI.5, GII.2, GII.3, GII.6, GII.13, and GII.17 Kawasaki 308. Acquisition of alternative RNA polymerases by recombination is an important mechanism for norovirus evolution and a phenomenon that was shown to occur more frequently than previously recognized in the United States. Continued molecular surveillance of noroviruses, including typing of both polymerase and capsid genes, is important for monitoring emerging strains in our continued efforts to reduce the overall burden of norovirus disease.

Keywords: genetic recombination; genotypic identification; noroviruses.

FIG 1

Distribution, by month, of norovirus genotypes from outbreaks submitted to CaliciNet from 1 September 2013 through 31 August 2016. “Other” includes the following capsid genotypes: GI.1, GI.2, GI.4, GI.6, GI.7, GI.9, GII.1, GII.5, GII.7, GII.8, GII.4 New Orleans, GII.4 Den Haag, GII.10, GII.12, GII.14, GII.15, a tentative novel genotype, GIV, and mixed outbreaks containing more than one GI or GII genotype.

FIG 2

Number of GII.4 Sydney outbreaks from 1 September 2014 through 31 August 2016 submitted to CaliciNet with dual-typing information available. The percentage of all GII.4 outbreaks with polymerase typing information (percent coverage) is presented above the bars for each month. GII.P4 New Orleans; GII.Pe-GII.4 Sydney is a mixed outbreak with some specimens typing as GII.P4 New Orleans-GII.4 Sydney and others typing as GII.Pe-GII.4 Sydney.

FIG 3

Maximum likelihood phylogenetic analysis of GII.P16 polymerase sequences (172 nucleotides) from GII.2, GII.3, GII.4 Sydney, and GII.13 outbreaks in CaliciNet for the period 2013 to 2016. Bootstrap support is indicated (percentage from 500 replicates) with values below 50% hidden. Evolutionary distances were computed using the Kimura two-parameter method with rate variation among sites modeled with a gamma distribution (shape parameter, 0.55). This substitution model was determined to be the best fit, producing the lowest BIC (Bayesian information criterion) and Akaike information criterion (corrected) scores, as determined by the maximum likelihood model testing tool (MEGA, version 7.0.18). Reference strains are represented by their GenBank accession numbers and indicated with filled circles. Sequences obtained in this study are indicated as follows: ▲, GII.4 Sydney; △, GII.2; ◽, GII.3; ■, GII.13.

FIG 4

Ribbon structure (PDB accession number 1SH0) indicating amino acid changes to the polymerase of GII.Pe-GII.4 Sydney resulting in the GII.P16 polymerase of GII.4 Sydney and GII.2 genotypes detected in the United States as early as 2015. Colors indicate the subdomains and motifs where the amino acid changes reside in the three-dimensional structure and correspond to those outlined in the text box.

FIG 5

Specific amino acid changes, compared to reference strains, within VP1 corresponding to sites under positive selection, antibody recognition epitopes, or HBGA binding sites for three GII.4 Sydney viruses in circulation from 2013 to 2016 in the United States. Consensus sequences were derived by an alignment of all GII.4 Sydney specimens for which complete VP1 sequences or P2 region sequences were available. Epitope binding regions A, B, C, D, and E and the NERK motif that blocks access to epitope F are indicated. +, amino acid sites under positive selection; #, sites within HBGA binding site 2. Colors indicate amino acid category, as follows: yellow, hydrophobic; green, uncharged; blue, positively charged; red, negatively charged; purple, special. NO, New Orleans.