Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil

Abstract

The COVID-19 epidemic in Brazil experienced two major lineage replacements until mid-2021. The first was driven by lineage P.2, in late 2020, and the second by lineage Gamma, in early 2021. To understand how these SARS-CoV-2 lineages spread in Brazil, we analyzed 11,724 genomes collected throughout the country between September 2020 and April 2021. Our findings indicate that lineage P.2 probably emerged in July 2020 in the Rio de Janeiro state and Gamma in November 2020 in the Amazonas state. Both states were the main hubs of viral disseminations to other Brazilian locations. We estimate that Gamma was 1.56-3.06 times more transmissible than P.2 in Rio de Janeiro and that the median effective reproductive number (Re) of Gamma varied according to the geographic context (Re = 1.59-3.55). In summary, our findings support that lineage Gamma was more transmissible and spread faster than P.2 in Brazil.

Keywords: Biological sciences; Phylogeny; viral microbiology.

Graphical abstract

Figure 1

Genomic epidemiology of COVID-19 in Brazil from September 2020 to March 2021 (A) Daily number of deaths due to COVID-19 and 7-day rolling average (line). (B) Weekly number of genomes generated in this study. (C) Proportion of SARS-CoV-2 lineages circulating in Brazil in the study period. (D) Proportion of SARS-CoV-2 genomes harboring mutation Spike:484E/K in Brazil in the study period.

Figure 2

Temporal analysis of the P.2 and Gamma sequence datasets (A) Plots of the root-to-tip divergence against dates of sample collection for P.2 and Gamma datasets. Outliers excluded from the further analysis were colored gray. (B) Leaf-dating Bayesian molecular clock of the four sequences excluded due to probably wrong collection date annotation. Reported collection dates are indicated by the dotted lines. Boxplots represent the median and the 95% HPD interval of the estimated collection dates. (C) Time-calibrated maximum clade credibility tree for P.2 and Gamma spatiotemporal representative datasets. The median estimated T_MRCA (with 95% HPD in parentheses) for each clade are shown on the root.

Figure 3

Spatiotemporal spread of SARS-CoV-2 lineage P.2 in Brazil (A) Inter-state circular migration flow plot as estimated from the Markov jumps analysis complementary to the phylogeographic model. Arrows indicate the direction of the migration and thickness is relative to the number of jumps. (B) Contribution of each state in seeding P.2 to other locations through time measured as the proportion of the total Markov per day. (C) Time distribution (95% HPD) of jumps from RJ to other Brazilian states. (D) T_MRCA of each highly supported [Shimodaira–Hasegawa-like approximate Likelihood Ratio Test (SH-aLRT) > 80] state-specific clades with more than three genomes.

Figure 4

Spatiotemporal spread of SARS-CoV-2 VOC Gamma in Brazil (A) Inter-state circular migration flow plot as estimated from the Markov jumps analysis complementary to the phylogeographic model. Arrows indicate the direction of the migration and thickness is relative to the number of jumps. (B) Contribution of each state in seeding Gamma to other locations through time measured as the proportion of the total Markov jumps per day. (C) Time distribution (95% HPD) of jumps from AM to other Brazilian states. The vertical green line shows the time of Gamma first notification and vertical red line shows the starting date of patients with COVID-19 transferring from AM to other states. (D) T_MRCA of each highly supported (SH-aLRT > 80) state-specific clades with more than three genomes.

Figure 5

Phylodynamics analyses of SARS-CoV-2 variants P.2 and Gamma (A) in Rio de Janeiro state. (B) in Amazonas state. (C) in São Paulo state. Effective reproductive number (R_e) [median (solid lines) and 95% HPD (highlighted area)], as estimated by Bayesian phylogenetics methods, is shown in green and brown for Gamma and P.2, respectively. Along with R_e, SARI cases are shown as a black line. PANGO lineages proportions per month are shown in the bottom panel, colored according to the legend.