New infections by SARS-CoV-2 variants of concern after natural infections and post-vaccination in Rio de Janeiro, Brazil

Abstract

After a one-year rollout of the pandemic caused by SARS-CoV-2, the continuous dissemination of the virus has generated a number of variants with increased transmissibility and infectivity, called variants of concern (VOC), which now predominate worldwide. Concerns about the susceptibility of humans that have already been infected before or those already vaccinated to infection by VOC rise among scientists and clinicians. Herein, we assessed the prevalence of different VOC among recent infections at the Brazilian National Cancer Institute (Rio de Janeiro, Brazil). By using a Sanger-based sequencing approach targeting the viral S gene to identify VOC, we have analyzed 72 recent infections. The overall prevalence of VOC was 97%. Among the subjects analyzed, six had been vaccinated with the ChAdOx1-S/nCoV-19 ( n = 4; one with two doses and three with one dose) or the CoronaVac ( n = 2; both with 2 doses) vaccine, while five subjects represented reinfection cases, being two of them also part of the vaccinated group (each one with one vaccine type). All vaccinated and re-infected subjects carried VOC irrespective of the vaccine type taken, the number of doses taken, IgG titers or being previously infected during the first wave of the Brazilian pandemic. Importantly, all six vaccinees only had mild symptoms. We present here several examples of how natural infections or vaccination may not be fully capable of conferring sterilizing immunity against VOC

Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants

“…Other mutations included in the zeta lineage are D614G, V1176F, P314L, L3468V, L3930F, A119S, R203K, G204R, and M234I [64].…”

SARS-CoV-2 variant detection with ADSSpike

“…In contrast to WGS, amplicon deep sequencing focuses on a specific gene or genomic region, providing a greater sequencing depth and coverage while reducing costs and data burden. Sanger-based approaches have been previously employed ( Bezerra et al, 2021 , Goes et al, 2021 ). These are either focused on a small window in the S gene, and hence missing relevant SNPs flanking said region, or target SNPs prevalent to specific VOC/VOIs.…”

Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela

“…6 ). However, E484K mutation is very frequent in Brazilian sequences, either in the Gamma VOC or in the P.2 or B.1.1.33 lineages ( Ferrareze et al, 2021 ; Goes et al, 2021 ). Thus, the presence of E484K mutation in reinfection cases may be only the reflection of the high frequency of circulation of this mutation in the country.…”