Severe Acute Respiratory Syndrome Coronavirus 2 P.2 Lineage Associated with Reinfection Case, Brazil, June-October 2020

Abstract

A 37-year-old healthcare worker from the northeastern region of Brazil experienced 2 clinical episodes of coronavirus disease. Infection with severe acute respiratory syndrome coronavirus 2 was confirmed by reverse transcription PCR in samples collected 116 days apart. Whole-genome sequencing revealed that the 2 infections were caused by the most prevalent lineage in Brazil, B.1.1.33, and the emerging lineage P.2. The first infection occurred in June 2020; Bayesian analysis suggests reinfection at some point during September 14-October 11, 2020, a few days before the second episode of coronavirus disease. Of note, P.2 corresponds to an emergent viral lineage in Brazil that contains the mutation E484K in the spike protein. The P.2 lineage was initially detected in the state of Rio de Janeiro, and since then it has been found throughout the country. Our findings suggest not only a reinfection case but also geographic dissemination of the emerging Brazil clade P.2.

Keywords: Brazil; COVID-19; P.2; SARS-CoV-2; coronavirus disease; reinfection; respiratory infections; secondary infection; severe acute respiratory syndrome coronavirus 2; viruses; zoonoses.

Figure 1

Maximum-likelihood tree of severe acute respiratory syndrome coronavirus 2 whole-genome sequences from Paraíba in study of reinfection case, Brazil, June–October 2020. Branching pattern of whole-genome sequences (29779 nt) from Paraíba (n = 77) are shown classified within lineages B.1.1.28 (red), B1.1.33 (blue), and others B.1.1 (black). Sequences derived from the primary infection and reinfection are highlighted with different colors as indicated. Nodes with high statistical support (approximate-likelihood ratio test >9.0) are marked by the smaller circular shapes.

Figure 2

Emergence of the P.2 clade in study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection case, Brazil. A) Maximum-likelihood phylogenetic tree of B.1.1.28 SARS-CoV-2 whole-genome sequences (29,779-nt) from Brazil (n = 376). Shaded box highlights the P.2 clade (n = 47), and its statistical support (approximate-likelihood ratio test = 1.0) is indicated in the cladogram. Sequences from Paraíba are indicated in orange and sequences from the reinfection case are indicated by green. B) Time-scaled Bayesian maximum clade credibility tree of SARS-CoV-2 whole-genome sequences from the P.2 clade (n = 47). Branches are colored according to the most probable location state of their descendent nodes as indicated. The 5 lineage-defining single-nucleotide polymorphisms are indicated at the maximum clade credibility tree root node. Circular shapes mark nodes with high statistical support (posterior probability>9.0), and a square tip shape indicates the sequence from reinfection case. AL, Alagoas; AM, Amazonas; PB, Paraíba; PR, Parana; RJ, Rio de Janeiro; UTR, untranslated region.