Genomic monitoring unveils a high prevalence of severe acute respiratory syndrome coronavirus 2 Omicron variant in vaccine breakthrough cases in Bahia, Brazil

Abstract

OBJECTIVE: Genome sequencing has been proved to be an excellent tool to monitor the molecular epidemiology of the disease caused by severe acute respiratory syndrome coronavirus 2, i.e., coronavirus disease 2019. Some reports of infected, vaccinated individuals have aroused great interest because they are primarily being infected with circulating variants of concern. To investigate the cases of infected, vaccinated individuals in Salvador, Bahia, Brazil, we performed genomic monitoring to estimate the magnitude of the different variants of concern in these cases. METHODS: Nasopharyngeal swabs from infected (symptomatic and asymptomatic), vaccinated or unvaccinated individuals (n=29), and quantitative reverse transcription polymerase chain reaction cycle threshold value (Ct values) of ≤30 were subjected to viral sequencing using nanopore technology. RESULTS: Our analysis revealed that the Omicron variant was found in 99% of cases and the Delta variant was found in only one case. 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 variants of concern not neutralized by the currently available vaccines. CONCLUSION: It is important to acknowledge the limitations of these vaccines and to develop new vaccines to emergent variants of concern, as is the case of influenza vaccine; going through new doses of the same coronavirus vaccines is "more of the same. " KEYWORDS: COVID-19. SARS-CoV-2. Genome. Vaccines.Newly generated SARS-CoV-2 sequences have been deposited in GISAID under the following accession numbers: EPI_ISL_9265729,

Profile and Outcomes of Hospitalized COVID-19 Patients during the Prevalence of the Omicron Variant According to the Brazilian Regions: A Retrospective Cohort Study from 2022

“…The reduction in the effectiveness of vaccines after 4-6 months [3,4] again increased the risk of fully vaccinated people (two doses/single dose), especially elderly people who were the first to be vaccinated, such that a booster dose was recommended in September 2021 in Brazil [5]. The Omicron variant and subvariants, with numerous mutations, are more transmissible, infective, and capable of evading immunity induced by vaccines or previous infection [6,7], and became dominant in several countries, including Brazil [8]. Omicron caused a third wave, whose peak occurred in March 2022.…”