Near-Complete Genome Sequences of Several New Norovirus Genogroup II Genotypes

Chhabra, Preeti; Aswath, Kshama; Collins, Nikail; Ahmed, Tahmeed; Olórtegui, Maribel Paredes; Kosek, Margaret; Cebelinski, Elizabeth; Cooper, Philip J.; Bucardo, Filemón; López, María Reneé; Castro, Christina J.; Marine, Rachel L.; Ng, Terry Fei Fan; Vinjé, Jan

doi:10.1128/genomea.00007-18

Cited by 20 publications

(9 citation statements)

References 10 publications

(12 reference statements)

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“…In recent years, several new GII and GIV genotypes from different geographic locations around the world have been reported [41,43,45,46,48]. With the addition of five novel genotypes GII.…”

Section: Discussionmentioning

confidence: 99%

“…Inclusion of norovirus diagnostic testing by real-time quantitative reverse transcription PCR into clinical and public health routine in recent years [27,[37][38][39] has confirmed the importance of GI and GII noroviruses globally [13,31,33,35,37,[40][41][42][43][44]. The increasing use of pathogen genome sequencing to unravel modes of transmission, sources of outbreaks, or to study the burden of infections has led to identification of several new candidate norovirus genogroups and genotypes since the last norovirus classification update in 2013 [9,12,33,40,41,43,[45][46][47][48][49]. In this paper, we update the classification scheme for noroviruses by proposing new genogroups and genotypes based on the complete capsid amino acid sequences using the previously agreed criteria [19].…”

Section: Introductionmentioning

confidence: 99%

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Updated classification of norovirus genogroups and genotypes

Chhabra

Graaf

Parra

et al. 2019

Journal of General Virology

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621

611

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Noroviruses are genetically diverse RNA viruses associated with acute gastroenteritis in mammalian hosts. Phylogenetically, they can be segregated into different genogroups as well as P (polymerase)-groups and further into genotypes and P-types based on amino acid diversity of the complete VP1 gene and nucleotide diversity of the RNA-dependent RNA polymerase (RdRp) region of ORF1, respectively. In recent years, several new noroviruses have been reported that warrant an update of the existing classification scheme. Using previously described 2× standard deviation (sd) criteria to group sequences into separate clusters, we expanded the number of genogroups to 10 (GI-GX) and the number of genotypes to 49 (9 GI, 27 GII, 3 GIII, 2 GIV, 2 GV, 2 GVI and 1 genotype each for GVII, GVIII, GIX [formerly GII.15] and GX). Viruses for which currently only one sequence is available in public databases were classified into tentative new genogroups (GNA1 and GNA2) and genotypes (GII.NA1, GII.NA2 and GIV. NA1) with their definitive assignment awaiting additional related sequences. Based on nucleotide diversity in the RdRp region, noroviruses can be divided into 60 P-types (14 GI, 37 GII, 2 GIII, 1 GIV, 2 GV, 2 GVI, 1 GVII and 1 GX), 2 tentative P-groups and 14 tentative P-types. Future classification and nomenclature updates will be based on complete genome sequences and will be coordinated and disseminated by the international norovirus classification-working group.

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“…In recent years, several new GII and GIV genotypes from different geographic locations around the world have been reported [41,43,45,46,48]. With the addition of five novel genotypes GII.…”

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Updated classification of norovirus genogroups and genotypes

Chhabra

Graaf

Parra

et al. 2019

Journal of General Virology

Self Cite

621

611

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show abstract

“…These genogroups exhibit high diversity, with up to 60% difference in the amino acid sequences of the major capsid gene [18]. The genogroups can be further divided into genotypes based on sequence diversity of the capsid gene, with at least nine for GI and 25 for GII having been described [19,21]. The most frequently occurring genotype, GII.4, is often further divided into specific variants, with new emerging variants often accounting for the recurrent seasonal pandemics [19,22,23,24].…”

Section: Norovirus—a Family With Many Membersmentioning

confidence: 99%

Genetic Susceptibility to Human Norovirus Infection: An Update

Nordgren

Svensson

2019

Viruses

135

148

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Noroviruses are the most common etiological agent of acute gastroenteritis worldwide. Despite their high infectivity, a subpopulation of individuals is resistant to infection and disease. This susceptibility is norovirus genotype-dependent and is largely mediated by the presence or absence of human histo-blood group antigens (HBGAs) on gut epithelial surfaces. The synthesis of these HBGAs is mediated by fucosyl- and glycosyltransferases under the genetic control of the FUT2 (secretor), FUT3 (Lewis) and ABO(H) genes. The so-called non-secretors, having an inactivated FUT2 enzyme, do not express blood group antigens and are resistant to several norovirus genotypes, including the predominant GII.4. Significant genotypic and phenotypic diversity of HBGA expression exists between different human populations. Here, we review previous in vivo studies on genetic susceptibility to norovirus infection. These are discussed in relation to population susceptibility, vaccines, norovirus epidemiology and the impact on public health.

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“…Previous reports have suggested that the GII.P2 and GII.P16 RdRp regions exhibit a large genetic divergence as does the VP1 gene encoded in ORF2 (Nagasawa et al, 2018a). The RdRp genotypes of GII viruses are currently classified into nearly 30 genotypes on the basis of their RdRp region sequences (Vinjé, 2015; Chhabra et al, 2018). Furthermore, recombination of the norovirus genome frequently occurs at ORF1 and at two junctions, resulting in the formation of new chimeric viruses (Bull et al, 2005; Bull et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase Region in Norovirus Genogroup II

Ozaki

Matsushima²,

Nagasawa

et al. 2018

Front. Microbiol.

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Noroviruses are the leading cause of viral gastroenteritis in humans across the world. RNA-dependent RNA polymerase (RdRp) plays a critical role in the replication of the viral genome. Although there have been some reports on a limited number of genotypes with respect to the norovirus evolution of the RdRp region, no comprehensive molecular evolution examination of the norovirus GII genotype has yet been undertaken. Therefore, we conducted an evolutionary analysis of the 25 genotypes of the norovirus GII RdRp region (full-length), collected globally using different bioinformatics technologies. The time-scaled phylogenetic tree, generated using the Bayesian Markov Chain Monte Carlo (MCMC) method, indicated that the common ancestor of GII diverged from GIV around 1443 CE [95% highest posterior density (HPD), 1336–1542]. The GII RdRp region emerged around 1731 CE (95% HPD, 1703–1757), forming three lineages. The evolutionary rate of the RdRp region of the norovirus GII strains was estimated at over 10−3 substitutions/site/year. The evolutionary rates were significantly distinct in each genotype. The composition of the phylogenetic distances differed among the strains for each genotype. Furthermore, we mapped the negative selection sites on the RdRp protein and many of these were predicted in the GII.P4 RdRp proteins. The phylodynamics of GII.P4, GII.P12, GII.P16, and GII.Pe showed that their effective population sizes increased during the period from 2003 to 2014. Our results cumulatively suggest that the RdRp region of the norovirus GII rapidly and uniquely evolved with a high divergence similar to that of the norovirus VP1 gene.

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Near-Complete Genome Sequences of Several New Norovirus Genogroup II Genotypes

Cited by 20 publications

References 10 publications

Updated classification of norovirus genogroups and genotypes

Updated classification of norovirus genogroups and genotypes

Genetic Susceptibility to Human Norovirus Infection: An Update

Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase Region in Norovirus Genogroup II

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