Spatiotemporal Dynamics of SARS-CoV-2 Variants During the First Year of the Pandemic Highlight the Earlier Emergence of the Zeta Variant of Interest in Brazil

During the COVID-19 pandemic, SARS-CoV-2 caused an alarming number of cases and deaths worldwide. Brazil was severely affected from late 2020 onward, especially after the emergence of variants of concern (VOCs) and variants of interest (VOIs). Although much is known about the dynamics and evolution of SARS-CoV-2 VOIs and VOCs in the country, information is still lacking on how the cocirculation of several SARS-CoV-2 lineages, along with the lack of vaccination and low adherence to social isolation measures, shaped the first year of the COVID-19 pandemic in Brazil. We used a combination of genomic and epidemiological data to understand the transmission dynamics of SARS-CoV-2 variants from March to November 2020 within a medium-sized city in São Paulo state. By generating 627 SARS-CoV-2 whole genomes, we were able to identify 10 different SARS-CoV-2 lineages that were cocirculating in the municipality. Although many introduction events have been identified, B.1.1.28 and B.1.1.33 variants were the most frequent during the sampling period. We also detected the presence of the Zeta and N.9 variants earlier than had previously been reported in Brazil. These findings reinforce the need for active genomic surveillance to detect new viral introductions that may impact health systems during public health emergencies.