Divergent Evolution of Norovirus GII/4 by Genome Recombination from May 2006 to February 2009 in Japan

Abstract

Norovirus GII/4 is a leading cause of acute viral gastroenteritis in humans. We examined here how the GII/4 virus evolves to generate and sustain new epidemics in humans, using 199 near-full-length GII/4 genome sequences and 11 genome segment clones from human stool specimens collected at 19 sites in Japan between May 2006 and February 2009. Phylogenetic studies demonstrated outbreaks of 7 monophyletic GII/4 subtypes, among which a single subtype, termed 2006b, had continually predominated. Phylogenetic-tree, bootscanningplot, and informative-site analyses revealed that 4 of the 7 GII/4 subtypes were mosaics of recently prevalent GII/4 subtypes and 1 was made up of the GII/4 and GII/12 genotypes. Notably, single putative recombination breakpoints with the highest statistical significance were constantly located around the border of open reading frame 1 (ORF1) and ORF2 (P < 0.000001), suggesting outgrowth of specific recombinant viruses in the outbreaks. The GII/4 subtypes had many unique amino acids at the time of their outbreaks, especially in the N-term, 3A-like, and capsid proteins. Unique amino acids in the capsids were preferentially positioned on the outer surface loops of the protruding P2 domain and more abundant in the dominant subtypes. These findings suggest that intersubtype genome recombination at the ORF1/2 boundary region is a common mechanism that realizes independent and concurrent changes on the virion surface and in viral replication proteins for the persistence of norovirus GII/4 in human populations.

Recombination within the Pandemic Norovirus GII.4 Lineage

“…Full-length GII.4 genome sequences were obtained from GenBank and then combined with 25 new sequences generated as part of this study. In the combined data set (262 sequences), there was an overrepresentation of highly homogeneous 2006b sequences from two large Japanese data sets of full-length GII.4 genomes identified between 2006 and 2009 (37,59). Other GII.4 clades, such as Farmington Hills 2002, were also found to contain highly homogeneous sequences.…”

“…Furthermore, six distinct GII.4 variants have been associated with global epidemics of acute gastroenteritis from 1996 to the present and include US 1995/96 in 1996 (25,26), Farmington Hills in 2002 (27,28) ; however, these viruses were associated with epidemics localized to a particular region rather than a global pandemic (7,8,(33)(34)(35)(36)(37)(38).…”

“…NoV intergenotype recombinants are frequently identified in molecular epidemiological studies (30,48,53,54); however, recent work suggests that intragenotype recombination may have also played a role in the emergence of some GII.4 variants (37,55). Full-length genome sequencing is not common practice in NoV molecular epidemiological studies, and the lack of full-length GII.4 sequence data has hindered the search for bona fide intragenotype recombination within the NoV GII.4 lineage.…”

Genetic diversity of noroviruses in Brazil

“…This is probably due to the absence of protective immunity in the susceptible community, causing new outbreaks of acute gastroenteritis; this allows the GII.4 genotype to remain a prevalent strain. The GII.4 variant substitution phenomenon was observed in all continents throughout the investigation period (Siebenga et al 2009, Motomura et al 2010, Zheng et al 2010.…”

Qualitative and Quantitative Analysis of the Binding of GII.4 Norovirus Variants onto Human Blood Group Antigens

“…The 162 GII.4 NoV sequences from the study of Motomura et al were kindly provided by Hironori Sato (29). We thank Kim Y.…”