Background
Genomic sequencing plays an essential role in the ongoing monitoring of SARS-CoV-2 genome evolution, as phylogenetic analyses can identify genomic signatures of circulating strains, thus helping to track transmission or spreading events. By understanding the spread of SARS-CoV-2, public health strategies can be deployed (at various levels) to reduce new infections and mitigate the impact of the pandemic. The study aimed to investigate the prevalence and genomic spread of SARS-CoV-2 variants in a study focused on expanding COVID-19 testing, quarantine, and telemonitoring strategies (TQT-COVID-19 Project).
Methods
A total of 177 samples collected between July 2022 and April 2023 from users of 17 Primary Health Care (PHC) units in Salvador, Bahia, were analyzed. The samples were sequenced using Oxford Nanopore MinION technology and analyzed through bioinformatics for variant typing and genomic spread assessment.
Results
The majority of participants were women (68.9%), under the age of 39 (50.6%), used public transportation (66.5%), and had no comorbidities (66.5%). Most presented mild COVID-19 symptoms (41.5%) and had received the second booster dose of the vaccine (40.6%). The most prevalent Omicron subvariants were BA.5 (32.57%), BA.4 (21.71%), B (18.86%), and BQ.1 (26.2%). However, other variants, such as XBB, were also identified. The virus spread predominantly in a controlled and localized manner, with low dissemination. However, sporadic events of rapid spread were identified, possibly linked to inter-municipal travel, superspreader events, or containment failures. Upon mutation analysis, vaccinated individuals presented a consistent accumulation of mutations in the spike protein, whereas unvaccinated individuals showed a different set of mutations.
Conclusions
This study observed the circulation of multiple lineages and several introduction events of new variants over time. Identifying and understanding these events may help develop more targeted intervention strategies to break the chain of transmission.