Detection and molecular characterization of the novel recombinant norovirus GII.P16-GII.4 Sydney in southeastern Brazil in 2016

Submitted by Janaína Nascimento ([email protected]) on 2019-08-08T14:54:21Z No. of bitstreams: 1 ve_Barreira_Débora_etal_INI_2017.pdf: 4321989 bytes, checksum: e9dcb6968a4161fd2eff30b73b4de183 (MD5)Approved for entry into archive by Janaína Nascimento ([email protected]) on 2019-08-08T15:08:47Z (GMT) No. of bitstreams: 1 ve_Barreira_Débora_etal_INI_2017.pdf: 4321989 bytes, checksum: e9dcb6968a4161fd2eff30b73b4de183 (MD5)Made available in DSpace on 2019-08-08T15:08:47Z (GMT). No. of bitstreams: 1 ve_Barreira_Débora_etal_INI_2017.pdf: 4321989 bytes, checksum: e9dcb6968a4161fd2eff30b73b4de183 (MD5) Previous issue date: 2017Federal University of Espírito Santo. Health Science Center. Pathology Department. Laboratory of Virology and Infectious Gastroenteritis. Vitória, ES, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Virologia Comparada e Ambiental. Rio de Janeiro, RJ, Brasil.Federal University of Espírito Santo. Health Science Center. Pathology Department. Laboratory of Virology and Infectious Gastroenteritis. Vitória, ES, Brazil.Federal University of Espírito Santo. Health Science Center. Pathology Department. Laboratory of Virology and Infectious Gastroenteritis. Vitória, ES, Brazil.Federal University of Espírito Santo. Health Science Center. Pathology Department. Laboratory of Virology and Infectious Gastroenteritis. Vitória, ES, Brazil.Central Laboratory of Public Health. Vitória, ES, Brazil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Virologia Comparada e Ambiental. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Virologia Comparada e Ambiental. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Doenças Febris Agudas. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Escola Nacional de Saúde Pública Sérgio Arouca. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Virologia Comparada e Ambiental. Rio de Janeiro, RJ, Brasil.Federal University of Espírito Santo. Health Science Center. Pathology Department. Laboratory of Virology and Infectious Gastroenteritis. Vitória, ES, Brazil.Noroviruses are the leading cause of acute gastroenteritis (AGE) in all age groups worldwide. Despite the high genetic diversity of noroviruses, most AGE outbreaks are caused by a single norovirus genotype: GII.4. Since 1995, several different variants of norovirus GII.4 have been associated with pandemics, with each variant circulating for 3 to 8 years. The Sydney_2012 variant was first reported in Australia and then in other countries. A new variant, GII.P16-GII.4, was recently described in Japan and South Korea and then in the USA, France, Germany and England. In our study, 190 faecal specimens were collected from children admitted to a paediatric hospital and a public health facility during a surveillance study of sporadic cases of AGE conducted between January 2015 and July 2016. The norovirus was detected by RT-qPCR in 51 samples (26.8%), and in 37 of them (72.5%), the ORF1-2 junction was successfully sequenced. The new recombinant GII.P16-GII.4 Sydney was revealed for the first time in Brazil in 2016 and predominated among other strains (9 GII.Pe-GII.4, 3 GII.P17-GII.17, 1 GII.Pg-GII.1, 1 GII.P16-GII.3 and 1 GII.PNA-GII.4). The epidemiological significance of this new recombinant is still unknown, but continuous surveillance studies may evaluate its impact on the population, its potential to replace the first recombinant GII.Pe-GII.4 Sydney 2012 variant, and the emergence of new recombinant forms of GII.P16

Norovirus diversity in diarrheic children from an African-descendant settlement in Belém, Northern Brazil.

Norovirus (NoV), sapovirus (SaV) and human astrovirus (HAstV) are viral pathogens that are associated with outbreaks and sporadic cases of gastroenteritis. However, little is known about the occurrence of these pathogens in relatively isolated communities, such as the remnants of African-descendant villages ("Quilombola"). The objective of this study was the frequency determination of these viruses in children under 10 years, with and without gastroenteritis, from a "Quilombola" Community, Northern Brazil. A total of 159 stool samples were obtained from April/2008 to July/2010 and tested by an enzyme immunoassay (EIA) and reverse transcription-polymerase chain reaction (RT-PCR) to detect NoV, SaV and HAstV, and further molecular characterization was performed. These viruses were detected only in the diarrheic group. NoV was the most frequent viral agent detected (19.7%-16/81), followed by SaV (2.5%-2/81) and HAstV (1.2%-1/81). Of the 16 NoV-positive samples, 14 were sequenced with primers targeting the B region of the polymerase (ORF1) and the D region of the capsid (ORF2). The results showed a broad genetic diversity of NoV, with 12 strains being classified as GII-4 (5-41.7%), GII-6 (3-25%), GII-7 (2-16.7%), GII-17 (1-8.3%) and GI-2 (1-8.3%), as based on the polymerase region; 12 samples were classified, based on the capsid region, as GII-4 (6-50%, being 3-2006b variant and 3-2010 variant), GII-6 (3-25%), GII-17 (2-16.7%) and GII-20 (1-8.3%). One NoV-strain showed dual genotype specificity, based on the polymerase and capsid region (GII-7/GII-20). This study provides, for the first time, epidemiological and molecular information on the circulation of NoV, SaV and HAstV in African-descendant communities in Northern Brazil and identifies NoV genotypes that were different from those detected previously in studies conducted in the urban area of Belém. It remains to be determined why a broader NoV diversity was observed in such a semi-isolated community

Distribution of norovirus genotypes detected in samples collected between January 2015 and July 2016 (n = 37) of the southeastern Brazilian coast state, Espírito Santo.

<p>Distribution of norovirus genotypes detected in samples collected between January 2015 and July 2016 (n = 37) of the southeastern Brazilian coast state, Espírito Santo.</p

Phylogenetic analysis of GII norovirus based on the partial nucleotide sequences of the polymerase and capsid regions, using the MON431 (nt 4820–4839) and G2SKR (nt 5367–5389) primers.

<p>(a) Phylogenetic tree of 231 bp within the polymerase region (3’-ORF1). (b) Phylogenetic tree of 277 bp within the capsid region (5’-ORF2). References strains of norovirus genotypes are named according to GenBank with their respectively accession numbers. Brazilian strains are marked with black filled diamonds. Recombinant strains of GII.P16-GII.4 are marked with green filled diamonds, and recombinant strains of GII.P16 grouping with non-GII.4 capsid genotypes are highlighted with unfilled green diamonds. The bootstrap values (2,000 replicates) are indicated in the phylogenetic tree, and values less than 70% are not represented. The bar at the bottom of the figure is proportional to the genetic distance.</p

Dendograms constructed using the partial region of the norovirus RNA polymerase sequence (ORF1-B) (A) and capsid region (ORF2-D) (B) amplified from 14 strains from diarrheic children of Abacatal “Quilombola” Community, metropolitan region of Belém, Pará State, Brazil.

<p>April/2008 to July/2010. Prototype strains are presented together with strains from other locations. The number above each branch corresponds to the bootstrap value (2,000 replicates). The scale bar is proportional to the genetic distance. Study samples were marked (♦): PA-local/Qui-code in the study+F_x-Number of the stool/country/month+year of collection.</p

Monthly distribution of the positive cases of norovirus, sapovirus and astrovirus (including their genotypes) detected in stool specimens from diarrheic children of the Abacatal “Quilombola” Community, Pará State, Brazil.

<p>April/2008 to July/2010.</p

Map showing the location of the Abacatal “Quilombola” Community, in the metropolitan region of Belém city, Pará State, Amazon region, Brazil.

<p>Map showing the location of the Abacatal “Quilombola” Community, in the metropolitan region of Belém city, Pará State, Amazon region, Brazil.</p

Complete genetic characterization of a Brazilian dengue virus type 3 strain isolated from a fatal outcome

We have determined the complete nucleotide and the deduced amino acid sequences of Brazilian dengue virus type 3 (DENV-3) from a dengue case with fatal outcome, which occurred during an epidemic in the state of Rio de Janeiro, Brazil, in 2002. This constitutes the first complete genetic characterization of a Brazilian DENV-3 strain since its introduction into the country in 2001. DENV-3 was responsible for the most severe dengue epidemic in the state, based on the highest number of reported cases and on the severity of clinical manifestations and deaths reported