Genomic surveillance of SARS-CoV-2 in the state of Parana, Southern Brazil, reveals the cocirculation of the VOC P.1, P.1-like-II lineage and a P.1 cluster harboring the S:E661D mutation (preprint)

ABSTRACT

We report a genomic surveillance of SARS-CoV-2 lineages circulating in Parana, Southern Brazil, from March 2020 to April 2021. Our analysis, based on 333 genomes, revealed that the first variants detected in the state of Parana in March 2020 were the B.1.1.33 and B.1.1.28 variants. The variants B.1.1.28 and B.1.1.33 were predominant throughout 2020 until the introduction of the variant P.2 in August 2020 and a variant of concern (VOC), P.1, in January 2021. Phylogenetic analyses of the SARS-CoV-2 genomes that were previously classified as the VOC P.1 lineage by PANGO showed that some genomes from February to April 2021 branched in a monophyletic clade and that these samples grouped together with genomes recently described with the lineage P.1-like-II. An extended phylogenetic analysis, including SARS-CoV-2 genomes from all over Brazil, showed that the P.1-like-II lineage appears at a high frequency in the southern region of the country. The P.1-like-II lineage genomes share some, but not all, defining mutations of the VOC P.1. For instance, it has the previously described ORF1aD2980H and NP383 L unique mutations and the newly detected ORF1aP1213 L and ORF1bK2340N mutations. Additionally, a new mutation (E661D) in the spike (S) protein has been identified in nearly 10\% of the genomes classified as the VOC P.1 from Parana in March and April 2021. We also report the identification of the SW152C mutation in one genome from Parana, classified as the N.10 variant. Finally, we analyzed the correlation between the lineage and the P.1 variant frequency, age group (patients younger or older than 60 years old) and the clinical data of 86 cases from the state of Parana. This analysis does not support an association between the P.1 variant prevalence and COVID-19 severity or age strata. Our results provided a reliable picture of the evolution of the SARS-CoV-2 pandemic in the state of Parana characterized by the dominance of the P.1 strain, as well as a high frequencies of the P.1-like-II lineage and the SE661D mutations. Epidemiological and genomic surveillance efforts should be continued to unveil the biological relevance of the novel mutations detected in the VOC P.1 in Parana.