Genomic Surveillance of SARS‐CoV‐2 in Rio de Janeiro (2020–2021): Temporal Distribution of Viral Variants During the Early Pandemic Genomic Surveillance of SARS‐CoV‐2 in Brazil

Genomic surveillance of SARS‐CoV‐2 is essential for monitoring the emergence and spread of variants in complex urban settings such as Rio de Janeiro, one of the epicenters of Coronavirus disease 2019 (COVID‐19) in Brazil. This retrospective observational study aimed to describe the temporal distribution of SARS‐CoV‐2 variants between October 2020 and December 2021, linking genomic findings to acute and post–acute clinical manifestations. A total of 52 SARS‐CoV‐2‐positive samples were analyzed, selected from 19,022 samples tested by RT‐qPCR. Viral detection was performed using a multiplex assay. Variants were screened using commercial kits targeting key genetic mutations (N501Y, E484K, and L452R, among others). Clinical data were obtained through questionnaires administered during the acute phase of infection and post‐COVID‐19 follow‐up. A predominance of the Zeta (P.2) variant was observed between October and December 2020, followed by a predominance of the Gamma (P.1) variant between March and May 2021. The Gamma variant was more frequently associated with persistent symptoms such as fatigue and headache. The results highlight the temporal replacement of viral variants in a major urban center, reflecting the evolutionary dynamics of SARS‐CoV‐2 in Brazil. The integration of genomic surveillance and clinical data proves fundamental to support public health and epidemiological surveillance strategies, especially in light of the ongoing risk of emerging variants.