Genomic and epidemiological characterization of SARS-CoV-2 in Northeastern Brazil: a comprehensive analysis (2020-2024).

SARS-CoV-2, which emerged in Wuhan, China, in December 2019, caused one of the largest viral respiratory pandemics in history. As of February 1, 2025, Brazil had reported approximately 39 million cases and over 714,000 deaths. The Northeast region of Brazil, comprising the states of Alagoas, Paraíba, Pernambuco, and Rio Grande do Norte, is characterized by its socioeconomic and geographic diversity. Understanding the spread of SARS-CoV-2 in this region and identifying patterns of transmission, evolution, and pathogenicity are crucial for identifying vulnerable areas and planning effective interventions. In this study, to trace the spread of SARS-CoV-2 in the Brazilian Northeast, we analyzed 8,442 SARS-CoV-2 genome sequences from the states of Alagoas, Paraíba, Pernambuco, and Rio Grande do Norte, which were obtained from the Global Initiative on Sharing All Influenza Data (GISAID) database. Epidemiological data (cases, deaths, and vaccination records) from 2020 to 2024 were obtained from the Coronavirus Panel of the Ministry of Health and integrated with information from the IBGE (Instituto Brasileiro de Geografia e Estatística). The epidemiological analysis revealed three major and two minor waves of infection and mortality between 2020 and 2023, with a notable increase in cases in early 2024. Metropolitan regions, including Recife (PE), João Pessoa (PB), Maceió (AL), and Natal (RN), showed higher incidence and mortality rates. Vaccination data indicated high adherence to the initial doses but a significant drop in booster shots. Genomic characterization showed that 70.37% of the sequenced genomes were concentrated in metropolitan areas. A total of 43,594 single-nucleotide polymorphisms (SNPs) and 15,366 insertions/deletions (indels) were identified, with mutations concentrated in the ORF1a, ORF1b, S, and N genes. The lineage dynamics demonstrated the successive emergence and dominance of the variants Gamma, Delta, and Omicron, including its sublineages BA.1, BA.2, BA.5, XBB.1.16, and XBB.1.5. Phylogenetic analysis demonstrated the circulation of 27 distinct lineages in the region, with Delta (AY.99.2) and Gamma (P.1) being the most predominant. These results demonstrate the value of integrating epidemiological and genomic data for continuous surveillance and for adapting public-health strategies. Challenges such as low adherence to booster doses and the concentration of sequencing in urban centers must be addressed to improve pandemic control. Expanding genomic sequencing to inland regions would provide more detailed information about the circulation of SARS-CoV-2.