The increase in SARS-CoV-2 lineages during 2020-2022 in a state in the Brazilian Northeast is associated with a number of cases

Moises Thiago de Souza Freitas; Ludmila Oliveira Carvalho Sena; Kiyoshi Ferreira Fukutani; Cliomar Alves Dos Santos; Francisco das Chagas Barros Neto; Julienne Sousa Ribeiro; Erica Santos Dos Reis; Valdir de Queiroz Balbino; Sérgio de Sá Paiva Leitão; Marcus Vinicius de Aragão Batista; Michael Wheeler Lipscomb; Tatiana Rodrigues de Moura

doi:10.3389/fpubh.2023.1222152

The increase in SARS-CoV-2 lineages during 2020-2022 in a state in the Brazilian Northeast is associated with a number of cases

Front Public Health. 2023 Dec 14:11:1222152. doi: 10.3389/fpubh.2023.1222152. eCollection 2023.

Authors

Affiliations

¹ Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Brazil.
² Parasitic Biology Graduate Program, Federal University of Sergipe, São Cristóvão, Brazil.
³ Health Foundation Parreiras Horta, Central Laboratory of Public Health (LACEN/SE), Sergipe State Health Secretariat, Aracaju, Brazil.
⁴ Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States.
⁵ Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Brazil.
⁶ Department of Genetics, Federal University of Pernambuco, Recife, Brazil.
⁷ Academic Unit of Serra Talhada, Rural Federal University of Pernambuco, Serra Talhada, Brazil.
⁸ Department of Pharmacology, University of Minnesota, Minneapolis, MN, United States.

Abstract

SARS-CoV-2 has caused a high number of deaths in several countries. In Brazil, there were 37 million confirmed cases of COVID-19 and 700,000 deaths caused by the disease. The population size and heterogeneity of the Brazilian population should be considered in epidemiological surveillance due to the varied tropism of the virus. As such, municipalities and states must be factored in for their unique specificities, such as socioeconomic conditions and population distribution. Here, we investigate the spatiotemporal dispersion of emerging SARS-CoV-2 lineages and their dynamics in each microregion from Sergipe state, northeastern Brazil, in the first 3 years of the pandemic. We analyzed 586 genomes sequenced between March 2020 and November 2022 extracted from the GISAID database. Phylogenetic analyses were carried out for each data set to reconstruct evolutionary history. Finally, the existence of a correlation between the number of lineages and infection cases by SARS-CoV-2 was evaluated. Aracaju, the largest city in northeastern Brazil, had the highest number of samples sequenced. This represented 54.6% (320) of the genomes, and consequently, the largest number of lineages identified. Studies also analyzed the relationship between mean lineage distributions and mean monthly infections, daily cases, daily deaths, and hospitalizations of vaccinated and unvaccinated patients. For this, a correlation matrix was created. Results revealed that the increase in the average number of SARS-CoV-2 variants was related to the average number of SARS-CoV-2 cases in both unvaccinated and vaccinated individuals. Thus, our data indicate that it is necessary to maintain epidemiological surveillance, especially in capital cities, since they have a high rate of circulation of resident and non-resident inhabitants, which contributes to the dynamics of the virus.

Keywords: SARS-CoV-2 genomes; Sergipe; epidemiology; genomic surveillance; phylogenetic analysis.

MeSH terms

Brazil / epidemiology
COVID-19* / epidemiology
Humans
Phylogeny
SARS-CoV-2* / genetics

Supplementary concepts

SARS-CoV-2 variants