Fig. 2: Maximum likelihood tree of SARS-CoV-2 based on complete genome sequences from São José do Rio Preto and all Brazilian regions. | Communications Medicine

Fig. 2: Maximum likelihood tree of SARS-CoV-2 based on complete genome sequences from São José do Rio Preto and all Brazilian regions.

From: Impact of SARS-CoV-2 Gamma lineage introduction and COVID-19 vaccination on the epidemiological landscape of a Brazilian city

Fig. 2: Maximum likelihood tree of SARS-CoV-2 based on complete genome sequences from São José do Rio Preto and all Brazilian regions.

Phylogenetic tree reconstructed using GTR + F + R2 as nucleotide substitution model. The reliability of branching patterns was tested using Ultrafast Bootstrap (UFBoot) combined with SH-like Approximate Likelihood-ratio test (SH-aLRT). The analysis involved 272 complete genome sequences from SJdRP and 509 from five Brazilian regions. The analysis was conducted in IQ-TREE v. 2.0.3, and the final tree was visualized and edited in FigTree v.1.4.4. Branches are colored according to SARS-CoV-2 lineages classified by Pangolin v.3.1.14. Tip nodes are colored according to the origin of the sequences (except the reference sequence from Wuhan), which are from the study area of São José do Rio Preto (SJdRP) and all the Brazilian regions (North, Northeast, Midwest, South, and Southeast). Branch lengths are represented by a scale bar (labelled 0.2) at the bottom of the phylogenetic tree.

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