Population Genomics of GII.4 Noroviruses Reveal Complex Diversification and New Antigenic Sites Involved in the Emergence of Pandemic Strains

Abstract

GII.4 noroviruses are a major cause of acute gastroenteritis. Their dominance has been partially explained by the continuous emergence of antigenically distinct variants. To gain insights into the mechanisms of viral emergence and population dynamics of GII.4 noroviruses, we performed large-scale genomics, structural, and mutational analyses of the viral capsid protein (VP1). GII.4 noroviruses exhibited a periodic replacement of predominant variants with accumulation of amino acid substitutions. Genomic analyses revealed (i) a large proportion (87%) of conserved residues; (ii) variable residues that map on the previously determined antigenic sites; and (iii) variable residues that map outside the antigenic sites. Residues in the third pattern category formed motifs on the surface of VP1, which suggested extensions of previously predicted and new uncharacterized antigenic sites. The role of two motifs (C and G) in the antigenic makeup of the GII.4 capsid protein was confirmed with monoclonal antibodies and carbohydrate blocking assays. Amino acid profiles from antigenic sites (A, C, D, E, and G) correlated with the circulation patterns of GII.4 variants, with three of them (A, C, and G) containing residues (352, 357, 368, and 378) linked with the diversifying selective pressure on the emergence of new GII.4 variants. Notably, the emergence of each variant was followed by stochastic diversification with minimal changes that did not progress toward the next variant. This report provides a methodological framework for antigenic characterization of viruses and expands our understanding of the dynamics of GII.4 noroviruses and could facilitate the design of cross-reactive vaccines. IMPORTANCE Noroviruses are an important cause of viral gastroenteritis around the world. An obstacle delaying the development of norovirus vaccines is inadequate understanding of the role of norovirus diversity in immunity. Using a population genomics approach, we identified new residues on the viral capsid protein (VP1) from GII.4 noroviruses, the predominant genotype, that appear to be involved in the emergence and antigenic topology of GII.4 variants. Careful monitoring of the substitutions in those residues involved in the diversification and emergence of new viruses could help in the early detection of future novel variants with pandemic potential. Therefore, this novel information on the antigenic diversification could facilitate GII.4 norovirus vaccine design.

Diversity of Noroviruses throughout Outbreaks in Germany 2018

“…In previous studies, it was shown that the current circulating GII.P16 variants exhibit amino acid changes in the polymerase. Five mutations were found in different studies: D173E; S293T; V332I; K357Q; and, T360A [ 8 , 11 , 18 ]. In this study, fourteen RdRp-sequences (234bp) were analyzed in the ORF1 region, amino acid changes S293T and V332I were found in all sequences ( Figure 5 ).…”

“…It has been shown for GII.4 viruses that amino acid changes in epitopes of the VP1 region resulted in global epidemics for decades. Antigenic drift variants of GII.4 persist for years until they are replaced by a new variant in a chronological sequential emergence [ 8 ], similar to influenza A viruses (reviewed by G.I. Parra [ 28 ]).…”

“…Analysis of specific antigenic sites within the capsid protein that interact with human antibodies has given important insights into our understanding how genotype GII.4 strains escape from herd immunity and drive pandemic outbreaks. Different antigenic sites (A–G) in the P domain were identified for GII.4 variants, three of them (A, C, and G) were supposed to be drivers of selection and emergence of new GII.4 variants [ 8 ].…”

“…The P domain of VP1 is further subdivided into the P1 and P2 domain. The P2 region is the most variable and exposed region of the VP1 protein containing antigenic epitopes [ 4 , 5 , 6 , 7 , 8 ].…”

Evolutionary and Molecular Analysis of Complete Genome Sequences of Norovirus From Brazil: Emerging Recombinant Strain GII.P16/GII.4

“…Norovirus presents multiple genotypes, but GII.4 strains are the predominant worldwide. GII.4 noroviruses have been shown the emergence of variants that present changes in antigenic sites, which facilitate escape from herd immunity elicited by previous variants (Debbink et al, 2012;Tohma et al, 2019).…”