Analysis of the prevalence, spread, and mutation patterns of SARS-CoV-2 variants: data from COVID-19 testing expansion strategy study in salvador, Northeast Brazil
This study investigated the prevalence and genomic epidemiology of SARS-CoV-2 variants as part of the TQT-COVID-19 Project, which aimed to expand COVID-19 testing, quarantine, and telemonitoring strategies. A total of 177 samples were analyzed between July 2022 and April 2023 from patients of 17 Primary Health Care (PHC) units in Salvador, Bahia, Brazil. Sequencing was done using Oxford Nanopore MinION technology and bioinformatics analysis for variant typing and phylodynamic spread assessment. Most participants were women (68.5%), under 39 years old (48.9%), used public transportation (66.4%), had no comorbidities (66.1%), presented mild COVID-19 symptoms (40.8%), and had received a second booster dose of a COVID-19 vaccine (88.2%). Nevertheless, 11.8% had never received a COVID-19 vaccine. The most prevalent Omicron subvariants were BA.5 (32.6%), BA.4 (21.7%), B (18.8%), and BQ.1 (26.3%), with other variants like XBB also identified. Vaccinated and unvaccinated individuals had different spike gene mutations. While multiple variant introductions occurred over time, SARS-CoV-2 geographic spread was mainly localized, with occasional rapid spread associated with inter-city travel or containment failures. These findings underscore the need to track viral spread and mutations to develop targeted strategies for breaking transmission chains.
Authors
- Luciane Amorim Santos (ORCID: https://orcid.org/0000-0003-0261-3495)
- Leandro Martins de Freitas (ORCID: https://orcid.org/0000-0003-4327-2922)
- Leonardo S. Santos (ORCID: https://orcid.org/0000-0002-1697-4200)
- J. Matos (ORCID: https://orcid.org/0000-0002-5641-9690)
- Alan Ferreira Leite de Lima (ORCID: https://orcid.org/0000-0001-7959-8778)
- Hellen Braga Martins Oliveira (ORCID: https://orcid.org/0000-0002-8516-5810)
- Lucas Miranda Marques (ORCID: https://orcid.org/0000-0002-8276-8149)
- Fernanda Khouri Barreto
- Laio Magno (ORCID: https://orcid.org/0000-0003-3752-0782)
- Guilherme Barreto Campos (ORCID: https://orcid.org/0000-0001-6493-4652)
- Anna Carolina Saúde Dantas
- Thiago S. Torres (ORCID: https://orcid.org/0000-0002-2557-601X)
- Fabiane Veloso Soares (ORCID: https://orcid.org/0000-0002-8036-3244)
- Danielle Souto de Medeiros (ORCID: https://orcid.org/0000-0002-2480-8990)
- Orlando da Costa Ferreira
- Taiana Tainá Silva Pereira
- Ana M. S. Guimarães (ORCID: https://orcid.org/0000-0002-8261-5863)
- Valdilea Gonçalves Veloso (ORCID: https://orcid.org/0000-0002-6622-3165)
- Laise Eduarda Paixão de Moraes (ORCID: https://orcid.org/0000-0001-9095-5860)
- Inês Dourado (ORCID: https://orcid.org/0000-0003-1675-2146)
- Thaís Aranha
Institutions
- Universidade Federal do Rio de Janeiro (BR)
- Universidade Federal da Bahia (BR)
- Instituto Federal da Bahia (BR)
- Universidade do Estado da Bahia (BR)
- Universidade de São Paulo (BR)
- Universidade Brasil (BR)
- Southwest Bahia State University (BR)
- Secretaria da Educação do Estado da Bahia (BR)
- Instituto de Saúde (BR)
- Fundação Oswaldo Cruz (BR)
Publication Details
- Journal
- Scientific Reports
- Published
- 2025-08-29
- DOI
- https://doi.org/10.1038/s41598-025-17691-x
- Primary Topic
- SARS-CoV-2 and COVID-19 Research
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior