Molecular and evolutionary characterization of norovirus GII.17 in the northern region of Brazil

Abstract

Background: Currently, norovirus (NoV) is associated with one-fifth of all acute gastroenteritis (AGE) cases worldwide. The NoV GII.17_2014 variant has been associated with gastroenteritis outbreaks in several Asian countries, replacing the previously dominant Sydney 2012 variant. There is limited data about circulation of this new strain in Brazil. This study aimed to describe the phylogenetic and evolutionary characteristics of the GII.17_ 2014 strains in the Northern region of Brazil. Methods: NoV was detected by enzyme immunoassay (EIA) in 645 stool samples of AGE cases that were reported in Pará and Amazonas states during 2015-2016. All positive samples were tested for NoV GI and GII by reverse transcription polymerase chain reaction (RT-PCR) and the amplicons were subjected to genome sequencing. The GII.17-positive samples were retested by PCR using different sets of designed primers, which target a highly conserved capsid gene region. Next, the amplicons were sequenced and phylogenetically analyzed using Bayesian inferences. Results: Of the 645 samples tested, 208 (32.2%) tested were positive for NoV by EIA, among which 95 (45.7%) were genotyped. Among the genotyped samples, 12 (12.6%) were characterized as GII.17_2014 with the first case detected in November 2015 (1/30, 3.3%) and the others in 2016 (11/65, 16.9%). All strains found in our study were clustered in clade D (epidemic strain). The uncorrelated log-normal model estimations calculated the rate of evolution for GII-17 strains as 1.95 × 10 − 3 (1.28 × 10 − 3 -2.63 × 10 − 3 ). In total, 36 nucleotide changes were observed after analyzing the VP1 sequence, among which 28 occurred in the P2 region. Conclusions: These data demonstrate the evolutionary dynamics in NoV GII.17_2014 strains, which indicated high mutation rates with nucleotide substitutions and indels that are related to the elevated levels of antigenic diversity. This partly explains the increase in viral prevalence.

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

“…GII.P16/GII.4_Sydney recombinant. In the same period, it was observed the co-circulation of all circulating pandemic strains related worldwide in samples from Northern region of Brazil, including the GII.P16/GII.4 (Costa et al, 2019). In addition, Barreira et al (2017) detected GII.P16/GII.4 circulating in the Southeastern Brazilian coast state among children up 11 years old.…”

“…The GII.P16/GII.4 strain emerged in the Amazon region in 2015 and was detected in 16.9% (16/95) of the cases during 2015-2016, being the second most prevalent virus since GII.P31/GII.4, which corresponded to 50.5% (48/95) of the NoV-positive cases (Costa et al, 2019). In this study, nucleotide analysis by BLASTn indicated that the strains circulating in Brazil had high identity with sequences of GII.P16/GII.4 from the United States (Barclay et al, 2019) and United Kingdom (Ruis et al, 2017).…”

“…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).…”

Norovirus Genotypic Variability in Brazil

“…However, in the Amazon states, between 2011 and 2014, the circulation of a recombinant strain GII.P7 / GII.6 was documented, which may indicate that this strain is already established in the population [2]. A recent study on samples collected during 2015 and 2016 from children under 5 years of age in Pará and Amazonas states demonstrated an increase in the circulation of the emerging GII.17_2014 strain in the Amazon region, and their phylogenetic approach suggests a single introduction of this genotype to the Amazon region [7]. Another strain that has also been detected in Amazonas is Gll.4, including variants GII.4 New Orleans_2009, and Sydney_2012 [2].…”

“…NoVs are strongly associated with acute non-bacterial gastroenteritis; they are highly infectious and can affect all ages. The main routes of transmission of these viruses vary between fecal-oral, contact with infected people, ingestion of contaminated food and/or water, and aerosol produced by vomiting [2,7]. Infection with these viruses is usually acute and limited: vomiting, diarrhea, and nausea are the main symptoms.…”