Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Dec 19;13(1):3.
doi: 10.3390/pathogens13010003.

Norovirus Epidemiology and Genotype Circulation during the COVID-19 Pandemic in Brazil, 2019-2022

Sylvia Kahwage Sarmento  1 , Juliana da Silva Ribeiro de Andrade  1 , Fábio Correia Malta  1 , Alexandre Madi Fialho  1 , Mateus de Souza Mello  1 , Fernanda Marcicano Burlandy  1 , Tulio Machado Fumian  1
Affiliations

Norovirus Epidemiology and Genotype Circulation during the COVID-19 Pandemic in Brazil, 2019-2022

Sylvia Kahwage Sarmento et al. Pathogens. .

Abstract

Norovirus stands out as a leading cause of acute gastroenteritis (AGE) worldwide, affecting all age groups. In the present study, we investigated fecal samples from medically attended AGE patients received from nine Brazilian states, from 2019 to 2022, including the COVID-19 pandemic period. Norovirus GI and GII were detected and quantified using RT-qPCR, and norovirus-positive samples underwent genotyping through sequencing the ORF1/2 junction region. During the four-year period, norovirus prevalence was 37.2%, varying from 20.1% in 2020 to 55.4% in 2021. GII genotypes dominated, being detected in 92.9% of samples. GII-infected patients had significantly higher viral concentrations compared to GI-infected patients (median of 3.8 × 107 GC/g and 6.7 × 105 GC/g, respectively); and patients aged >12-24 months showed a higher median viral load (8 × 107 GC/g) compared to other age groups. Norovirus sequencing revealed 20 genotypes by phylogenetic analysis of RdRp and VP1 partial regions. GII.4 Sydney[P16] was the dominant genotype (57.3%), especially in 2019 and 2021, followed by GII.2[P16] (14.8%) and GII.6[P7] (6.3%). The intergenogroup recombinant genotype, GIX.1[GII.P15], was detected in five samples. Our study is the first to explore norovirus epidemiology and genotype distribution in Brazil during COVID-19, and contributes to understanding the epidemiological dynamics of norovirus and highlighting the importance of continuing to follow norovirus surveillance programs in Brazil.

Keywords: Brazil; RT-qPCR; genotyping; molecular epidemiology; norovirus; viral load.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Monthly distribution of tested acute gastroenteritis samples (AGE), norovirus-positive samples and norovirus detection rates in Brazil during 2019–2022. The dotted line was the period where non-pharmaceutical interventions (wearing masks, surface disinfection, social distancing, hand hygiene, and school closure) were adopted during COVID-19 pandemic. The two pink columns show the strict lockdown period in Brazil.
Figure 2
Figure 2
Norovirus viral load expressed as log10 genome copies per gram of stool (GC/g) among genogroups I (GI) and GII (a), and different age groups (b) detected in Brazil, from 2019 to 2022. Box-and-whisker plots show the first and third quartiles (equivalent to the 5th and 95th percentiles), the median (the horizontal line in the box), and range of norovirus viral load concentrations. **** p  ≤  0.0001, *** p  ≤  0.001, ** p  ≤  0.01.
Figure 3
Figure 3
Distribution of norovirus genotypes identified with high and low frequencies from genotyped samples in Brazil between 2019 and 2022. (a) Bimonthly distribution of norovirus P-types and capsid genotypes identified during the study period. (b) Numbers to the right of the bars indicate the number of sequences detected for each dual type.
Figure 4
Figure 4
Phylogenetic analyses based on ORF1 (a) and ORF2 (b) nucleotide (nt) sequences of GI norovirus Brazilian strains. Reference strains were downloaded from GenBank and labelled with their genotypes followed by country, year, and accession number. Strains obtained (marked with a diamond) are shown as per country followed by the LVCA, internal register number, year, and genotype of collection (i.e., BRA/LVCA33973/2022/GI.P4). The neighbor-joining phylogenetic tree was constructed with MEGA X software v. 10.1.7 and bootstrap tests (2000 replicates), based on the Kimura two-parameter model. Bootstrap values above 60% are given at branch nodes.
Figure 5
Figure 5
(a). Phylogenetic analyses based on ORF1 nucleotide (nt) sequences of GII norovirus Brazilian strains. Reference strains were downloaded from GenBank and labelled with their genotypes followed by country, year, and accession number. Strains obtained (marked with a diamond) are shown as per country followed by the LVCA, internal register number, year, and genotype of collection (i.e., BRA/LVCA30732/2020/GII.P7). The neighbor-joining phylogenetic tree was constructed with MEGA X software v.10.1.7 and bootstrap tests (2000 replicates), based on the Kimura two-parameter model. Bootstrap values above 60% are given at branch nodes. (b). Phylogenetic analyses based on ORF2 nucleotide (nt) sequences of GII norovirus Brazilian strains. Reference strains were downloaded from GenBank and labelled with their genotypes followed by country, year, and accession number. Strains obtained (marked with a diamond) are shown as per country followed by the LVCA, internal register number, year, and genotype of collection (i.e., BRA/LVCA34323/2022/GII.9). The neighbor-joining phylogenetic tree was constructed with MEGA X software v.10.1.7 and bootstrap tests (2000 replicates), based on the Kimura two-parameter model. Bootstrap values above 60% are given at branch nodes.
Figure 5
Figure 5
(a). Phylogenetic analyses based on ORF1 nucleotide (nt) sequences of GII norovirus Brazilian strains. Reference strains were downloaded from GenBank and labelled with their genotypes followed by country, year, and accession number. Strains obtained (marked with a diamond) are shown as per country followed by the LVCA, internal register number, year, and genotype of collection (i.e., BRA/LVCA30732/2020/GII.P7). The neighbor-joining phylogenetic tree was constructed with MEGA X software v.10.1.7 and bootstrap tests (2000 replicates), based on the Kimura two-parameter model. Bootstrap values above 60% are given at branch nodes. (b). Phylogenetic analyses based on ORF2 nucleotide (nt) sequences of GII norovirus Brazilian strains. Reference strains were downloaded from GenBank and labelled with their genotypes followed by country, year, and accession number. Strains obtained (marked with a diamond) are shown as per country followed by the LVCA, internal register number, year, and genotype of collection (i.e., BRA/LVCA34323/2022/GII.9). The neighbor-joining phylogenetic tree was constructed with MEGA X software v.10.1.7 and bootstrap tests (2000 replicates), based on the Kimura two-parameter model. Bootstrap values above 60% are given at branch nodes.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Pires S.M., Fischer-Walker C.L., Lanata C.F., Devleesschauwer B., Hall A.J., Kirk M.D., Duarte A.S.R., Black R.E., Angulo F.J. Aetiology-Specific Estimates of the Global and Regional Incidence and Mortality of Diarrhoeal Diseases Commonly Transmitted through Food. PLoS ONE. 2015;10:e0142927. doi: 10.1371/journal.pone.0142927. - DOI - PMC - PubMed
    1. Lanata C.F., Fischer-Walker C.L., Olascoaga A.C., Torres C.X., Aryee M.J., Black R.E., for the Child Health Epidemiology Reference Group of the World Health Organization and UNICEF Global Causes of Diarrheal Disease Mortality in Children <5 Years of Age: A Systematic Review. PLoS ONE. 2013;8:e72788. doi: 10.1371/journal.pone.0072788. - DOI - PMC - PubMed
    1. Ahmed S.M., Hall A.J., Robinson A.E., Verhoef L., Premkumar P., Parashar U.D., Koopmans M., Lopman B.A. Global Prevalence of Norovirus in Cases of Gastroenteritis: A Systematic Review and Meta-Analysis. Lancet Infect. Dis. 2014;14:725–730. doi: 10.1016/S1473-3099(14)70767-4. - DOI - PMC - PubMed
    1. Lopman B. Global Burden of Norovirus and Prospects for Vaccine Development. CDC Foundation; Atlanta, GA, USA: 2015. 46p
    1. Payne D.C., Vinjé J., Szilagyi P.G., Edwards K.M., Staat M.A., Weinberg G.A., Hall C.B., Chappell J., Bernstein D.I., Curns A.T., et al. Norovirus and Medically Attended Gastroenteritis in U.S. Children. N. Engl. J. Med. 2013;368:1121–1130. doi: 10.1056/NEJMsa1206589. - DOI - PMC - PubMed