Genomic epidemiology of SARS-CoV-2 in large university hospital cohort: the UnCoVER-Brazil project

Abstract

This work aimed to study the role of different SARS-CoV-2 lineages in the epidemiology of multiple waves of the COVID-19 pandemic in Ribeirão Preto (São Paulo state), with comparison within Brazil and globally. Viral genomic sequencing was combined with clinical and sociodemographic information of 2,379 subjects at a large Brazilian hospital. On the whole 2,395 complete SARS-CoV-2 genomes were obtained from April 2020 to January 2022. We report variants of concern (VOC) and interest (VOI) dynamics and the role of Brazilian lineages. We identified three World Health Organization VOCs (Gamma, Delta, Omicron) and one VOI (Zeta), which caused distinct waves in this cohort. We also identified 47 distinct Pango lineages. Consistent with the high prevalence of Gamma in Brazil, Pango lineage P.1 dominated infections in this cohort for half of 2021. Each wave of infection largely consisted of a single variant group, with each new group quickly and completely rising to dominance. Despite increasing vaccination in Brazil starting in 2021, this pattern was observed throughout the study and is consistent with the hypothesis that herd immunity tends to be SARS-CoV-2 variant-specific and does not broadly protect against COVID-19.

Keywords: COVID-19; SARS-CoV-2; epidemiology; genome; variants.

Figure 1.

Distribution of SARS-CoV-2 sequenced genomes per epidemiological week, plotted by weekend date (Saturday) of RT-PCR test collection [5]. Bars coloured by SARS-CoV-2 Pango lineage and grouped by VOC, where possible [6]: B & B descendant lineages in shades of purple, Zeta (P.2) in light orange, N lineages in shades of red, non-VOC P lineage in black, Alpha (B.1.1.7) in dark orange, Gamma (P.1) and descendant lineages in shades of blue, Delta (AY lineages) in shades of yellow to brown, and Omicron (BA lineages) in shades of green.