Spread and changes of SARS-CoV-2 during three COVID-19 waves in Southern Brazil, including rapid growth of the P.1 variant

Ninety SARS-CoV-2 genomes from Rio Grande do Sul, Brazil, reveal significant genomic diversity across three epidemic peaks.

• The first reported cases included lineages B.1 (33.3%), B.1.1.28 (26.7%), B.1.1 (13.3%), B.1.1.33 (10.0%), and A (6.7%), indicating both international and local transmission.
• During the first peak (July-August 2020), B.1.1.33 (50.0%) and B.1.1.28 (35.0%) were the most prevalent lineages.
• The second peak (November-December 2020) saw the emergence of the P.2 lineage (55.6%).
• In the third peak (February-April 2021), P.1 and related sequences accounted for 78.4% of the cases.
• Eighteen novel mutation combinations were identified among P.1 genomes, along with 22 different spike mutations and/or deletions in P.1 and its related sequences.
• These findings underscore the high genetic diversity and ongoing evolution of SARS-CoV-2 in Southern Brazil.

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