Norovirus diversity in children with gastroenteritis in South Africa from 2009 to 2013: GII.4 variants and recombinant strains predominate

Mans, Janet; Murray, Tanya Y.; Nadan, Sandrama; Netshikweta, Rembuluwani; Page, Nicola; Taylor, Maureen B.

doi:10.1017/s0950268815002150

Cited by 37 publications

(29 citation statements)

References 38 publications

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“…Norovirus GII was the dominant circulating genogroup detected (n = 17: 77.2 %). This finding is consistent with most studies worldwide, including those from Africa, in which NoV GII was reported to be predominantly responsible for gastroenteritis outbreaks and sporadic cases [3,6,21,22,29,49,53,54]. Nucleotide sequence and phylogenetic analysis of the NoV GII strains revealed that GII.17 NoVs comprise the predominant genotype (36.4 %) detected in this study.…”

Section: Genogrouping/genotyping Of Human Enteric Virusessupporting

confidence: 92%

“…The role of NoVs and SaVs as causative agents of gastroenteritis and their diversity in Africa is not well studied, except in some reports from a few African countries [20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36]. There has been only one published study from Ethiopia regarding the presence and genetic diversity of NoVs [37], and none for SaVs to date.…”

Section: Introductionmentioning

confidence: 99%

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Prevalence and molecular characterization of human noroviruses and sapoviruses in Ethiopia

et al. 2016

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Viral gastroenteritis is a major public health problem worldwide. In Ethiopia, very limited studies have been done on the epidemiology of enteropathogenic viruses. The aim of this study was to detect and characterize noroviruses (NoVs) and sapoviruses (SaVs) from acute gastroenteritis patients of all ages. Fecal samples were collected from diarrheic patients (n = 213) in five different health centers in Addis Ababa during June-September 2013. The samples were screened for caliciviruses by reverse transcription polymerase chain reaction (RT-PCR) using universal and genogroup-specific primer pairs. Phylogenetic analyses were conducted using the sequences of the PCR products. Of the clinical samples, 25.3 % and 4.2 % were positive for NoV and SaV RNA, respectively. Among the norovirus positives, 22 were sequenced further, and diverse norovirus strains were identified: GI (n = 4), GII (n = 17) and GIV (n = 1). Most strains were GII (n = 17/22: 77.2 %), which were further divided into three different genotypes (GII.4, GII.12/GII.g recombinant-like and GII.17), with GII.17 being the dominant (7/17) strain detected. GI noroviruses, in particular GI.4 (n = 1), GI.5 (n = 2) and GI.8 (n = 1), were also detected and characterized. The GIV strain detected is the first from East Africa. The sapoviruses sequenced were also the first reported from Ethiopia. Collectively, this study showed the high burden and diversity of noroviruses and circulation of sapoviruses in diarrheic patients in Ethiopia. Continued surveillance to assess their association with diarrhea is needed to define their epidemiology, disease burden, and impact on public health.

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Section: Genogrouping/genotyping Of Human Enteric Virusessupporting

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Prevalence and molecular characterization of human noroviruses and sapoviruses in Ethiopia

et al. 2016

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“…This novel GII.P16-GII.2 recombinant virus caused at least seven outbreaks in the United States in 2016 as early as August. While GII.P16 polymerases associated with different GII capsids have circulated for decades (17,18,42,(49)(50)(51)(52)(53)(54) and caused occasional outbreaks (16,55,56), the GII.P16 polymerase associated with GII.4 Sydney and GII.2 genotypes appears to have made these viruses evolve toward greater transmissibility.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2017

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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.

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“…Table 1. Continued Continued recombination breakpoints have been identified across the norovirus genome, they are most frequently found in the ORF1-ORF2 junction region [29][30][31][32][33][34][35][36]. Dual typing (ORF1-RdRp=P type, ORF2=genotype) is now used routinely in many laboratories worldwide and at least 14 GI P-types and 27 GII P-types as well as 9 GI capsid genotypes and 22 GII capsid genotypes have been described [2,19,27].…”

Section: Introductionmentioning

confidence: 99%

Updated classification of norovirus genogroups and genotypes

Chhabra

Graaf

Parra

et al. 2019

Journal of General Virology

608

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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Norovirus diversity in children with gastroenteritis in South Africa from 2009 to 2013: GII.4 variants and recombinant strains predominate

Cited by 37 publications

References 38 publications

Prevalence and molecular characterization of human noroviruses and sapoviruses in Ethiopia

Prevalence and molecular characterization of human noroviruses and sapoviruses in Ethiopia

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

Updated classification of norovirus genogroups and genotypes

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