Genomic monitoring unveils a high prevalence of SARS-CoV-2 Omicron variant in vaccine breakthrough cases

Abstract

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.

Analysis of incidence, mortality and lethality by COVID-19 in the States of Pará and Rio Grande do Sul, Brazil: epidemiological aspects of evolution 2020-2022

“…This variant, first identified in South Africa and Botswana in November, was classified as a variant of concern by the World Health Organization 33 . The designation was due to its numerous mutations 34 , making it more transmissible than the original strain of the virus. The rise in cases and deaths during this period underscores the challenges posed by the Omicron variant and its potential impact on the trajectory of the COVID-19 pandemic.…”