Extended Data Fig. 3: Phylogenetic analysis of the assembled SARS-CoV-2 genomes.
From: Viral and host factors related to the clinical outcome of COVID-19
a, A total of 94 SARS-CoV-2 genome sequences and 221 published sequences (as in Fig. 1a) were used for construction of a time-resolved rectangular phylogeny tree. Clade I and clade II are marked, and variations that distinguish branches of the phylogeny tree are indicated. Each tip circle represents a single sample. The position of each sample along the x-axis corresponds to the sample collection date. Case locations are marked by colours (see key). GISAID accession identifiers are displayed alongside each tip circle. Cases with or without a history of contact with HSWM are highlighted. b, Box plot (centre, median; box, interquartile range (IQR); whiskers, 1.5× IQR) of pairwise similarity scores within clade I (n = 22,791), clade II (n = 5,050) and between clades I and II (interclade I–II, n = 21,614). Two-sided unpaired t-test. c, Alignment of sequences around nucleotides 8,782 and 28,144 using Bat-SARS-CoV-RaTG13 sequence and SARS-CoV-2 sequences recovered from patients with or without known history of exposure to HSWM.
