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

Abstract

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.

Norovirus RNA in serum associated with increased fecal viral load in children: Detection, quantification and molecular analysis

“…As observed in other studies including stool samples collected in a similar period to ours, the partial genotyping of the positive samples demonstrated a high detection rate of NoV GII.4 [ 32 , 33 ]. The second more common circulating genotype was found to be GII.6, which has been recorded at low frequencies in other countries [ 34 , 35 ], but it seems to be frequent in Manaus-Amazonas as described by Hernandez et al, 2018 [ 36 ].…”

“…Another one is the use of EIA for NoV fecal screening instead of quantitative PCR (qPCR) that was used only for quantification of the NoV-positive samples. However, previous researches conducted with samples collected in the Amazon region demonstrated a good performance of EIA technique, obtaining higher positivity rates as well as the detection of uncommon recombinant strains and emergent variants [ 36 , 40 – 45 ].…”

Evolutionary and Molecular Analysis of Complete Genome Sequences of Norovirus From Brazil: Emerging Recombinant Strain GII.P16/GII.4

“…This study on the emergence of the GII.P16/GII.4 strain started from previous data from studies conducted with samples from the cities Belém and Manaus in northern Brazil (Hernandez et al, 2018;Reymão et al, 2018).…”

“…GII.4 was the genotype most frequently detected, with the emergence of the GII.P31/GII.4-Sydney 2012, GII.17_2014 and GII.P16/GII.4 strains. Reports about GII.P31/GII.4 and GII.17_2014, as well as the temporal distribution and emergence period of these strains, have already been described (Silva et al, 2013;Hernandez et al, 2018;Reymão et al, 2018;Costa et al, 2019).…”

Human Enteric Circulating Viruses and Co-infections Among Hospitalized Children with Severe Acute Gastroenteritis in Chihuahua, Mexico, During 2010 - 2011

“…For example, after implementation of the rotavirus vaccine in 2006, caliciviruses were mostly begun to detect in association with gastroenteritis symptoms, followed by adenovirus, which was listed as the second or third diarrhea-causing viral agent, whereas astrovirus was predominantly observed among children up to two years of age showing severe gastrointestinal problems (2,7,8). These new findings reveal the lack of detailed information regarding the prevalence of enteroviruses associated with severe acute gastroenteritis.…”