The incidence and geographical spread of SARS-CoV-2 in Rio de Janeiro, Brazil based on RT-PCR test results

Abstract INTRODUCTION Rio de Janeiro has hardly experienced coronavirus disease. METHODS Here, 87,442 reverse transcription polymerase chain reaction (RT-PCR) test results for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were reported among Rio de Janeiro residents (March to September 2020). RESULTS Overall, RT-PCR positivity of 44.6% decreased over time towards 20%. Positivity was greater among males (OR=1.22; 95%CI:1.19-1.26); Black (OR=1.10; 95%CI:1.02-1.19), Brown (OR=1.16; 95%CI:1.10-1.22), and indigenous people (OR=2.11; 95%CI:0.88-5.03) compared to Whites and increased with age; with epidemic spread from the capital to inland regions. CONCLUSIONS SARS-CoV-2 keeps spreading in Rio de Janeiro, and reopening of activities may fuel the epidemic.

A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B 1 1 33 Circulating in Brazil

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in Brazil was dominated by two lineages designated as B.1.1.28 and B.1.1.33. The two SARS-CoV-2 variants harboring mutations at the receptor-binding domain of the Spike (S) protein, designated as lineages P.1 and P.2, evolved from lineage B.1.1.28 and are rapidly spreading in Brazil. Lineage P.1 is considered a Variant of Concern (VOC) because of the presence of multiple mutations in the S protein (including K417T, E484K, N501Y), while lineage P.2 only harbors mutation S:E484K and is considered a Variant of Interest (VOI). On the other hand, epidemiologically relevant B.1.1.33 deriving lineages have not been described so far. Here we report the identification of a new SARS-CoV-2 VOI within lineage B.1.1.33 that also harbors mutation S:E484K and was detected in Brazil between November 2020 and February 2021. This VOI displayed four non-synonymous lineage-defining mutations (NSP3:A1711V, NSP6:F36L, S:E484K, and NS7b:E33A) and was designated as lineage N.9. The VOI N.9 probably emerged in August 2020 and has spread across different Brazilian states from the Southeast, South, North, and Northeast regions.