SARS-CoV-2 Lineage P.4 Detection in Southeast Brazil: A Retrospective Genomic and Clinical Overview

Abstract

São Paulo state has been the epicenter of the Coronavirus Disease 2019 (COVID-19) in Brazil, ranking first by state with over six million reported cases. In February 2021, the P.4 lineage was reported in 21 cities across the state by public health authorities due to the L452R mutation. Here, by analyzing 17,304 genome sequences of SARS-CoV-2 sampled between February and August of 2021 in 476 distinct cities in São Paulo, we assess the transmission dynamics of the P.4 lineage and other SARS-CoV-2 variants that were, at the time of the study, co-circulating in the state. Additionally, clinical parameters from the city of Araras, São Paulo (N = 251) were considered to estimate the potential risk and mortality rate associated with the P.4 lineage since its higher prevalence was observed in that city. Our data suggest a low frequency (0.55%) of the P.4 lineage across the state, with the gamma variant being the dominant form in all regions (90%) at that time. Furthermore, no evidence of increased transmissibility and disease severity related to the P.4 lineage was observed. The displacement through the time of different lineages in São Paulo highlights how challenging genomic surveillance appears to track the emergence of new SARS-CoV-2 lineages, which could better guide the implementation of control measures.

Molecular epidemiology of SARS‐CoV‐2 variants in circulation in the state of Maranhão, Brazil

“…1.1.529), due to rapid dissemination in their countries of origin, the high number of mutations in the Spike protein and the growing body of evidence of their ability to evade antibodies, they were classified as VOCs. [3][4][5] Brazil had the first case of COVID-19 reported in February 26, 2020 in the state of São Paulo in a patient who had traveled to Italy. 6 By the beginning of 2023, over 36 million cases have been registered, with almost 700 000 deaths in the country.…”

“…Depending on their impact on public health, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variants can be classified as Variants of Concern (VOC), Variants Under Monitoring (VUM) and Variants of Interest (VOI) 1,2 . Thus, variants such as Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Omicron (B.1.1.529), due to rapid dissemination in their countries of origin, the high number of mutations in the Spike protein and the growing body of evidence of their ability to evade antibodies, they were classified as VOCs 3–5 …”