Early detection of SARS-CoV-2 P.1 variant in Southern Brazil and reinfection of the same patient by P.2

Abstract

Multiple variants of the Severe Acute Respiratory Syndrome coronavirus 2 virus (SARS-CoV-2) have been constantly reported across the world. The B.1.1.28 lineage has been evolving in Brazil since February 2020 and originated the P.1 variant of concern (VOC), recently named as the Gamma variant by the newly WHO nomenclature proposal, and P.2 as a variant of interest (VOI). Here we describe an early case of P.1 primary infection in Southern Brazil in late November 2020, soon after the emergence of the variant in Manaus, Northern Brazil. The same male patient was reinfected by another B.1.1.28 variant, namely P.2, in March, 2021. The genomic analysis confirmed genetically significant differences between the two viruses recovered in both infections, the P.1 lineage in the first episode and P.2 in the reinfection. Due the very early detection of P.1, we have also investigated the circulation of P.1 in the same region by differential RT-qPCR, showing that this was an isolated case of P.1 at the time of detection, and this variant has disseminated and became prominent from late January to the end of March, 2021. SARS-CoV-2 recent reports of reinfection have raised critical questions on whether and how well a first infection protects against reinfection.

Figure 1. Emergence of SARS-CoV-2 P.1 lineage and general situation of COVID-19: (A) Retrospective analysis based on differential RT-qPCR: The gray bars represent the negative results predominating during the first epidemiological weeks. Afterwards, positive samples (represented by pink bars) replaced the parental lineages; (B) COVID-19 new cases; (C) COVID-19 hospitalizations and (D) COVID-19 deaths.

Figure 2. Phylogenetic tree of SARS-CoV-2 complete genomes. The Maximum Likelihood phylogenetic analysis under the General Time Reversible allowing for a proportion of invariable sites, with empirical rates and substitution rates empirically inferred in the IQ-TREE (v2.1.2 web server applying 200 replicates and 1,000 bootstraps).