Emergence of norovirus strains: A tale of two genes

Abstract

Noroviruses are a very diverse group of viruses that infect different mammalian species. In humans, norovirus is a major cause of acute gastroenteritis. Multiple norovirus infections can occur in a lifetime as the result of limited duration of acquired immunity and cross-protection among different strains. A combination of advances in sequencing methods and improvements on surveillance has provided new insights into norovirus diversification and emergence. The generation of diverse norovirus strains has been associated with (1) point mutations on two different genes: ORF1, encoding the non-structural proteins, and ORF2, encoding the major capsid protein (VP1); and (2) recombination events that create chimeric viruses. While both mechanisms are exploited by all norovirus strains, individual genotypes utilize each mechanism differently to emerge and persist in the human population. GII.4 noroviruses (the most prevalent genotype in humans) present an accumulation of amino acid mutations on VP1 resulting in the chronological emergence of new variants. In contrast, non-GII.4 noroviruses present co-circulation of different variants over long periods with limited changes on their VP1. Notably, genetic diversity of non-GII.4 noroviruses is mostly related to the high number of recombinant strains detected in humans. While it is difficult to determine the precise mechanism of emergence of epidemic noroviruses, observations point to multiple factors that include host-virus interactions and changes on two regions of the genome (ORF1 and ORF2). Larger datasets of viral genomes are needed to facilitate comparison of epidemic strains and those circulating at low levels in the population. This will provide a better understanding of the mechanism of norovirus emergence and persistence.

Keywords: caliciviruses; evolution; gastroenteritis; norovirus; recombination.

Figure 1.

Norovirus structure and genome organization. (A) The ORFs and their encoded proteins are shown. ORF1 encodes six NS proteins involved in viral replication, ORF2 and ORF3 encode for the major (VP1) and minor (VP2) capsid proteins, respectively. The 5′-end of the genome is capped with the VPg (virion protein genome-linked) protein, while the 3′-end consists of an untranslated region and a poly-A tail. Genome regions utilized for norovirus characterization and typing include the RdRp and the major capsid protein (VP1). (B) Structural model of norovirus VP1 showing the protruding and shell domains. A model of the capsid (T:3) is shown at the right-side of the VP1. The molecular model of the VP1 was visualized using an X-ray solved structure (Protein Data Bank record: 1IHM) and rendered in Chimera (Pettersen et al. 2004).

Figure 2.

Classification of noroviruses based on the phylogeny of the major capsid protein (VP1). Genogroups are based on phylogenetic clustering and amino acid differences. Genogroups can be further divided into genotypes. Each genogroup is indicated with different colors and associated with infection of specific species (indicated by shadow figures). Viruses from genotypes GII.11, GII.18, and GII.19 infect porcine species, and viruses from GIV.1 and GIV.NA1 infect humans. Abbreviation for species: Bo, bovine; Ca, canine; Fe, feline; Hu, human; Mu, murine; Ov, ovine; Sw, swine. The phylogenetic tree was constructed using representative strains from each genotype and/or genogroup and the neighbor-joining method as implemented in MEGA (Kumar, Stecher, and Tamura 2016).

Figure 3.

Evolution of GII.4 noroviruses. (A) Maximum clade credibility (MCC) tree showing the circulation of different variants over time. Variants are identified by different colors and names. (B) Same phylogenetic tree indicating the RdRp (P) types associated with each variant. Variants that caused large epidemics and spread worldwide are indicated with gray shadows. The MCC tree was constructed using the BEAST package (Drummond et al. 2012) and visualized in FigTree v1.4.3. For tree reconstruction, thirty strains were randomly selected per variant, except for the Sydney_2012 variant in which forty strains were used (Tohma et al. 2019).

Figure 4.

Evolution of GII.2 noroviruses. (A) MCC tree showing the circulation of different GII.2 noroviruses over time (Tohma et al. 2017). Branches with strains associated with the RdRp types GII.P2 and GII.P16 are indicated with dark red and orange, respectively. GII.2P[16] strains that caused large epidemics and spread worldwide are indicated with a gray shadow. The MCC tree was constructed using the BEAST package (Drummond et al. 2012) and visualized in FigTree v1.4.3. (B) A structural model of the norovirus RdRp is shown indicating the substitutions (blue) presented by the GII.2[P16] strains that predominated during 2016–17 in different countries (Kwok et al. 2017; Lu et al. 2017; Tohma et al. 2017). Substitutions on residue 291 (red) were shown to alter the mutation rate of GII.4 polymerases (Bull et al. 2010). The molecular model of the RdRp was visualized using an X-ray solved structure of norovirus RdRp (Protein Data Bank record: 4QPX) and was rendered in Chimera (Pettersen et al. 2004).