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Genome sequencing proved to be an excellent tool to monitor the molecular epidemiology of the disease caused by SARS-CoV-2, i.e., coronavirus disease (COVID-19). Some reports of infected, vaccinated individuals have aroused great interest because they are primarily being infected with circulating variants of concern (VOCs). To investigate the cases of infected, vaccinated individuals in Salvador, Bahia, Brazil, we performed genomic monitoring to estimate the magnitude of the different VOCs in these cases. Nasopharyngeal swabs from infected (symptomatic and asymptomatic), fully vaccinated individuals (n=29) who were of varying age and had RT-qPCR Ct values of ≤30 were subjected to viral sequencing using Nanopore technology. Our analysis revealed that the Omicron variant was found in 99% of cases and that only one case was due to the Delta variant. Infected, fully vaccinated patients have a favorable clinical prognosis; however, within the community, they become viral carriers with the aggravating factor of viral dissemination of VOCs not neutralized by the vaccines.

Metagenomic next-generation sequencing coupled with capture probe enrichment was used to recover 11 whole and partial Zika virus (ZIKV) genomes from patients in Bahia, Brazil from April 2015 to January 2016, where the majority of suspected Brazilian ZIKV cases have been reported. Phylogenetic reconstructions and molecular clock analyses using the newly generated data uncovered the existence of a Bahia-specific ZIKV lineage sharing a common ancestor in mid-2014, indicating sustained circulation of this strain in Bahia since that date.