Temporal spread and evolution of SARS-CoV-2 in the second pandemic wave in Brazil

Abstract

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning in South America, mainly in Brazil that presented more than 21 million coronavirus disease 2019 cases and 590 000 deaths. The recent emergence of novel lineages carrying several mutations in the spike protein has raised additional public health concerns worldwide. The present study describes the temporal spreading and evolution of SARS-CoV2 in the beginning of the second pandemic wave in Brazil, highlighting the fast dissemination of the two major concerning variants (P.1 and P.2). A total of 2507 SARS-CoV-2 whole-genome sequences (WGSs) with available information from the country (Brazil) and sampling date (July 2020-February 2021), were obtained and the frequencies of the lineages were evaluated in the period of the growing second pandemic wave. The results demonstrated the increasing prevalence of P.1 and P.2 lineages in the period evaluated. P.2 lineage was first detected in the middle of 2020, but a high increase occurred only in the last trimester of this same year and the spreading to all Brazilian regions. P.1 lineage emerged even later, first in the North region in December 2020 and really fast dissemination to all other Brazilian regions in January and February 2021. All SARS-CoV-2 WGSs of P.1 and P.2 were further separately evaluated with a Bayesian approach. The rates of nucleotide and amino acid substitutions were statistically higher in P.1 than P.2 (p < 0.01). The phylodynamic analysis demonstrated that P.2 gradually spread in all the country from September 2020 to January 2021, while P.1 disseminated even faster from December 2020 to February 2021. Skyline plots of both lineages demonstrated a slight rise in the spreading for P.2 and exponential growth for P.1. In conclusion, these data demonstrated that the P.1 (recently renamed as Gamma) and P.2 lineages have predominated in the second pandemic wave due to the very high spreading across all geographic regions in Brazil at the end of 2020 and beginning of 2021.

Keywords: SARS coronavirus; dissemination; pandemic.

Figure 1

(A) Distribution of P.1 (Gamma), P.2, and other lineages in Brazilian regions. (B) Distribution of P.1, P.2, and other lineages between July 2020 and February 2021 in Brazil. Data obtained from GISAID (https://www.gisaid.org). GISAID, Global Initiative on Sharing All Influenza Data

Figure 2

Severe acute respiratory syndrome coronavirus 2 P.1 (Gamma), P.2, and other lineages in Brazilian regions between July 2020 and February 2021

Figure 3

Mean bar chart of nucleotides and amino acids mutations of P.1 (Gamma) and P.2 lineages

Figure 4

(A) Time‐scaled maximum clade credibility tree from the evolutionary reconstruction by Bayesian analysis of SARS‐CoV‐2 P.1 (Gamma) lineage whole‐genome sequences from Brazil available in GISAID (from December 2020 to February 2021). The time of the most recent common ancestor (tMRCA) is demonstrated in the nodes with significant posterior probabilities (≥0.95). (B) Bayesian skyline plot (BSP) of SARS‐CoV‐2 P.1 (Gamma) lineage whole‐genome sequences obtained from GISAID. The effective number of infections is reported on the Y‐axis. The timeline is reported on the X‐axis. The colored area corresponds to the 95% credibility intervals of the highest probability density (95% HPD). The vertical line indicates the 95% lower HPD (dotted) of the tree root. GISAID, Global Initiative on Sharing All Influenza Data; SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2

Figure 5

(A) Time‐scaled maximum clade credibility tree from the evolutionary reconstruction by Bayesian analysis of SARS‐CoV‐2 P.2 lineage whole‐genome sequences from Brazil available in GISAID (from July 2020 to February 2021). The time of the most recent common ancestor (tMRCA) is demonstrated in the nodes with significant posterior probabilities (≥0.95). (B) Bayesian skyline plot (BSP) of SARS‐CoV‐2 P.2 lineage whole‐genome sequences obtained from GISAID. The effective number of infections is reported on the Y‐axis. The timeline is reported on the X‐axis. The colored area corresponds to the 95% credibility intervals of the highest probability density (95% HPD). The vertical line indicates the 95% lower HPD (dotted) of the tree root. GISAID, Global Initiative on Sharing All Influenza Data; SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2