Monitoramento genômico de variantes de interesse e preocupação do SARS-CoV-2 no estado da Bahia, Brasil

Abstract

The emergency in late 2019 of coronavirus SARS-CoV-2, lead to the COVID-19 pandemic. Brazil stands in the 7th position in number of cases and 3rd in number of deaths in 2024. In Bahia state, Northeast Brazil, more than 1.8 million cases were registered with almost 32 thousand deaths. The Laboratório Central de Saúde Pública Profº Gonçalo Moniz – LACEN/Ba centralized the diagnosis and genomic surveillance efforts at the state level to detect the emergence of new variants of concern (VOCs) and interest (VOIs) of SARS-CoV-2 in Bahia. In this study, we monitored the introduction of VOCs and VOIs in Bahia from positive samples to SARS-CoV-2 at LACEN/Ba. Towards do this, we carried out genetic sequencing in samples from municipalities and into two different events of patients identified by epidemiological surveillance with a history of travel in regions with circulation of VOCs and VOIs. Positive samples in molecular screening to sars-cov-2 were submitted to ion semiconductor sequencing (Ion Torrent). Basecalling of raw files and barcode demultiplexing were performed using manufacturer software, and the consensus sequences were generated by de novo assembling. All sequences were aligned and used for phylogenetic inferences performed using the maximum likelihood approach. Also, the mutation pattern of the sequences was analysed. In the first case, we identified the first likely imported case of the SARS-CoV-2 B.1.525 variant, VOI Eta, isolated in a traveller returning from Nigeria to Bahia state. Analysis of the phylogenetic tree indicated our sample clustered within a clade containing other sequences previously assigned as the B.1.525 and no newly acquired mutations were identified. In the second case, phylogenetic analysis in new whole genome sequences of 11 COVID-19 cases with travel history from Amazonas revealed the introduction of P.1 lineage, VOC Gamma, in Bahia. Phylogenetic analysis also showed that isolates formed two different well-supported monophyletic clusters, one including samples from the capital city of Salvador, isolated from individuals from the same family and the other including samples isolated from patients from two municipalities of the North-Central region of the state. The identification of VOC Gamma and VOI Eta contributed to the landscape of variants in Bahia, the Northeast and Brazil by providing information on mutations that impact transmissibility, disease severity, and vaccine efficacy, prompting continuous monitoring and adaptation of public health responses worldwide.