Abstract
The COVID-19 pandemic has created an unprecedented need for epidemiological monitoring using diverse strategies. We conducted a project combining prevalence, seroprevalence, and genomic surveillance approaches to describe the initial pandemic stages in Betim City, Brazil. We collected 3239 subjects in a population-based age-, sex- and neighborhood-stratified, household, prospective; cross-sectional study divided into three surveys 21 days apart sampling the same geographical area. In the first survey, overall prevalence (participants positive in serological or molecular tests) reached 0.46% (90% CI 0.12–0.80%), followed by 2.69% (90% CI 1.88–3.49%) in the second survey and 6.67% (90% CI 5.42–7.92%) in the third. The underreporting reached 11, 19.6, and 20.4 times in each survey. We observed increased odds to test positive in females compared to males (OR 1.88 95% CI 1.25–2.82), while the single best predictor for positivity was ageusia/anosmia (OR 8.12, 95% CI 4.72–13.98). Thirty-five SARS-CoV-2 genomes were sequenced, of which 18 were classified as lineage B.1.1.28, while 17 were B.1.1.33. Multiple independent viral introductions were observed. Integration of multiple epidemiological strategies was able to adequately describe COVID-19 dispersion in the city. Presented results have helped local government authorities to guide pandemic management.
Highlights
MATERIALS AND METHODSSince its emergence in December 2019, the new human coronavirus has had a tremendous impact on humanity due to the pandemic nature of its infection, called COVID-19 (Zhou et al, 2020)
In Brazil, the first case of COVID-19 was reported on February 26, 2020, in the city of São Paulo (Araujo et al, 2020)
A town located in the Minas Gerais State in Brazil with an estimated population of 439,340 in 2019, had its first reported SARS-CoV-2 case on March 23, 2020, in two patients returning from Europe
Summary
Since its emergence in December 2019, the new human coronavirus has had a tremendous impact on humanity due to the pandemic nature of its infection, called COVID-19 (Zhou et al, 2020). A town located in the Minas Gerais State in Brazil with an estimated population of 439,340 in 2019, had its first reported SARS-CoV-2 case on March 23, 2020, in two patients returning from Europe. We have validated antibody tests using serum samples from subjects who were SARS-CoV-2 positive confirmed with RT-PCR. We set the model with six discrete categories: Betim City, Minas Gerais State, Rio de Janeiro State, São Paulo State, other Brazilian States, and foreign sequences. These locations were represented by 18, 2, 22, 71, 79, and 66 sequences in dataset B.1.1.28 while B.1.1.33 dataset composition was 17, 20, 53, 52, 73, and 69 sequences from each region, respectively. All logs and trees are available in https://github.com/LBI-lab/SARS-CoV-2_ phylogenies.git
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