Genotype diversity and molecular evolution of noroviruses: A 30-year (1982-2011) comprehensive study with children from Northern Brazil

Siqueira, Jones Anderson Monteiro; Bandeira, Renato da Silva; Oliveira, Darleise de Souza; SANTOS, Larissa Santana1 VALENTE DOS; Gabbay, Yvone Benchimol

doi:10.1371/journal.pone.0178909

Cited by 21 publications

(17 citation statements)

References 70 publications

(80 reference statements)

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“…(iii) GII.1 capsid genotype found in this study has been recently reported in Cameroon [48], Brazil [49,50], Australia [51], India [52], and elsewhere [53][54][55]. is genotype is frequently reported from both clinical cases and environmental samples.…”

Section: Discussionsupporting

confidence: 74%

Molecular Characterization of Norovirus Strains Isolated from Older Children and Adults in Impoverished Communities of Vhembe District, South Africa

Mulondo

Khumela

Kabue

et al. 2020

Advances in Virology

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Background. Human norovirus (NoV) is an etiological agent associated with acute gastroenteritis (AGE) in both children and adults worldwide. However, very few studies have been reported on the prevalence and genetic diversity of NoV strains in children older than 5 years of age and adults with little or inadequate water and sanitation conditions. Objectives. The aim of this study was assessing the prevalence of the human norovirus in older children and adults suffering with diarrhoea from rural communities in the Vhembe district, Limpopo province. Methods. Between August 2017 and October 2018, stool samples were collected from outpatients suffering from AGE and screened for NoV strains using the RIDA©GENE norovirus I and II real-time one-step RT-PCR. RNA extracts of NoV-positive samples were subjected to RT-PCR amplification and nucleotide sequencing to genotype the positive NoV strains. Results. Out of 80 collected stool samples, 13 (16%) were tested positive for norovirus. Genogroup GII was identified in 6/13 (46%) samples and genogroup GI in 7/13 (54%) samples. The sequence analyses showed multiple genotypes including GII.Pg, GII.1, GII.2, GII.4, and GI.3. Phylogenetic analysis revealed the relatedness of NoV genotypes identified with other strains reported globally. Conclusion. Continued systematic surveillance to evaluate norovirus association with diarrhoea is needed to assist with epidemiological surveillance and disease burden in people of all the age groups.

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Section: Discussionsupporting

confidence: 74%

Molecular Characterization of Norovirus Strains Isolated from Older Children and Adults in Impoverished Communities of Vhembe District, South Africa

Mulondo

Khumela

Kabue

et al. 2020

Advances in Virology

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“…The relaxed-clock estimations calculated similar rates of evolution in Manaus (Sydney: 7.7 × 10 − 3 ; New Orleans: 6.3 × 10 − 3 ) to other studies, which reported 6.99 × 10 − 3 and 7.3 × 10 − 3 subst./site/year for full VP1 and subdomain P2 gene sequences, respectively [ 48 , 49 ]. In a study conducted in Belem, a state adjacent to Manaus, over 30 years, Siqueira et al [ 50 ] found an evolutionary rate of 9.05 × 10 − 3 subs./site/year for other GII.4 variants. The time-scale evolutional was constructed based on the subdomain P2, which is the most hypervariable region in VP1, which are under selection pressure of the immunological system.…”

Section: Discussionmentioning

confidence: 99%

“…This methodology has already been used in other studies, carried out in the Amazon region, establishing higher positive rates [ 44 , 52 , 53 ]. Uncommon recombinants strains (GII.P21/GII.2, GII.13/GII.17, GII.P21/GII.3) and emergent variants (GII.4_Sydney) were also detected by EIA [ 50 , 54 ].…”

Section: Discussionmentioning

confidence: 99%

Molecular epidemiology and temporal evolution of norovirus associated with acute gastroenteritis in Amazonas state, Brazil

et al. 2018

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BackgroundGlobally, Norovirus (NoV) is considered the most common cause of diarrheal episodes across all age groups. Despite its wide genetic diversity, the GII.4 strain is the most predominant and has been associated with epidemics worldwide. In this study, we characterized sporadic cases of diarrhea from NoV-positive children, during a five-year period (2010–2014).MethodsA total of 250 NoV-positive samples identified by an enzyme immunoassay (EIA) were subjected to RT-PCR and partial nucleotide sequencing for polymerase and capsid genes. Phylogenetic analysis was performed to identify NoV genotypes using the binary classification. In addition, sequences from the P2 subdomain (capsid) gene of GII-4 variants were characterized by evolutionary analyses, using the MCMC method implemented in the BEAST package. A 3D structure was built using protein modeling.ResultsPhylogenetic analysis demonstrated a predominance of genotype GII.4 (52.4% - 99/189), variants New Orleans_2009 and Sydney_2012 followed by GII.P7/GII.6 with 6.3% (12/189). Amino acid analyses of the GII.4 strains showed several important amino acid changes. A higher evolutionary rate was found, 7.7 × 10− 3 in the Sydney variant and 6.3 × 10− 3 in the New Orleans. Based in evolutionary analysis the time to the most recent common ancestor (TMRCA) has been calculated as estimates of the population divergence time. Thus, TMRCA for New Orleans and Sydney variant were 2008.7 and 2010.7, respectively. Also, we observed a lineage of transition between New Orleans and Sydney.ConclusionThis study describes the different strains of norovirus isolated from Amazonas state in Brazil during a five-year period. Considering that NoV are capable of changing their antigenic epitopes rapidly, a continuous surveillance is important to monitor the occurrence and changes of the NoV in the community through epidemiological studies. These results contribute to the understanding of NoV molecular epidemiology and its evolutionary dynamics in Amazonas state, Brazil.Electronic supplementary materialThe online version of this article (10.1186/s12879-018-3068-y) contains supplementary material, which is available to authorized users.

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“…Conformational epitope analyses using in silico approaches also enable us to identify and map binding sites of host antibodies on three-dimensional structures of proteins (Potocnakova et al, 2016 ). For HuNoV, a large number of studies on viral evolution have been performed using bioinformatics (Giammanco et al, 2014 ; Kimura et al, 2015 ; Kobayashi et al, 2015 , 2016 ; Lu et al, 2016 ; Parra et al, 2017 ; Siqueira et al, 2017 ; Tohma et al, 2017 ). Previous reports described the evolutionary rates of some HuNoV genotypes using the Bayesian MCMC method and linear regression analyses, which suggested differences in such rates among the genotypes (Parra et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Molecular Evolution of the VP1 Gene in Human Norovirus GII.4 Variants in 1974–2015

et al. 2017

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Human norovirus (HuNoV) is a leading cause of viral gastroenteritis worldwide, of which GII.4 is the most predominant genotype. Unlike other genotypes, GII.4 has created various variants that escaped from previously acquired immunity of the host and caused repeated epidemics. However, the molecular evolutionary differences among all GII.4 variants, including recently discovered strains, have not been elucidated. Thus, we conducted a series of bioinformatic analyses using numerous, globally collected, full-length GII.4 major capsid (VP1) gene sequences (466 strains) to compare the evolutionary patterns among GII.4 variants. The time-scaled phylogenetic tree constructed using the Bayesian Markov chain Monte Carlo (MCMC) method showed that the common ancestor of the GII.4 VP1 gene diverged from GII.20 in 1840. The GII.4 genotype emerged in 1932, and then formed seven clusters including 14 known variants after 1980. The evolutionary rate of GII.4 strains was estimated to be 7.68 × 10−3 substitutions/site/year. The evolutionary rates probably differed among variants as well as domains [protruding 1 (P1), shell, and P2 domains]. The Osaka 2007 variant strains probably contained more nucleotide substitutions than any other variant. Few conformational epitopes were located in the shell and P1 domains, although most were contained in the P2 domain, which, as previously established, is associated with attachment to host factors and antigenicity. We found that positive selection sites for the whole GII.4 genotype existed in the shell and P1 domains, while Den Haag 2006b, New Orleans 2009, and Sydney 2012 variants were under positive selection in the P2 domain. Amino acid substitutions overlapped with putative epitopes or were located around the epitopes in the P2 domain. The effective population sizes of the present strains increased stepwise for Den Haag 2006b, New Orleans 2009, and Sydney 2012 variants. These results suggest that HuNoV GII.4 rapidly evolved in a few decades, created various variants, and altered its evolutionary rate and antigenicity.

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Genotype diversity and molecular evolution of noroviruses: A 30-year (1982-2011) comprehensive study with children from Northern Brazil

Cited by 21 publications

References 70 publications

Molecular Characterization of Norovirus Strains Isolated from Older Children and Adults in Impoverished Communities of Vhembe District, South Africa

Molecular Characterization of Norovirus Strains Isolated from Older Children and Adults in Impoverished Communities of Vhembe District, South Africa

Molecular epidemiology and temporal evolution of norovirus associated with acute gastroenteritis in Amazonas state, Brazil

Molecular Evolution of the VP1 Gene in Human Norovirus GII.4 Variants in 1974–2015

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