Fig. 2: Forward transmission of the Omicron BA.1.23 subvariant.

a Maximum likelihood (ML) phylogenetic subtree with SARS-CoV-2 (BA.1) sequences from the persistent infection case P1 (red) and the onward transmissions (P2, P3, P4 in cyan, yellow and green respectively), in a global background of sequences available in GISAID. Branches are colored to identify each patient. The number of days after the first SARS-CoV-2 positive specimen of P1 is indicated in brackets. Sibling clusters are collapsed for easier visualization. The x-axis shows the number of nucleotide substitutions relative to the root of the phylogenetic tree. Bootstrap support values above 70% are shown for the un-collapsed branches. The distinct BA.1 subvariant that was transmitted was designated as PANGO lineage BA.1.23. The bottom-right insert shows a time-scaled ML phylogeny and the estimates for the time of the most recent ancestors (TMRCA) and 95% confidence intervals, for the nodes where the transmissions from the index case are positioned. b Frequency of single nucleotide variants (SNV), and amino acid substitutions for SARS-CoV-2 genomic positions with consensus changes from ancestral Wuhan-1 and Omicron BA.1. Positions with mixed nucleotides below consensus levels are also shown for intrahost SNVs (miSNVs) seen in more than one time point. The sequenced specimens are shown sequentially for P1 with prolonged BA.1 infection and transmission cases of BA.1.23 (P2, P3 and P4). The viral genomes from P1 show progressive accumulation of mutations in the N-terminal domain (NTD), receptor binding domain (RBD), and S1/S2 furin cleavage site (FCS); The same constellation of mutations was subsequently detected in three documented transmission cases (P2, P3 and P4). The number of days since the first positive test in P1 is shown on the left, with the number of days after the first positive test for each patient between brackets. Positions with nonsynonymous SNVs are marked by filled circles. Specimen type is indicated on the right by open circles (anterior nares) or filled diamonds (nasopharynx). Positions are numbered according to the reference genome sequence NC_045512.2. Arrows on the left indicate the likely window of transmission from the index patient between days 64–72. Source data is provided in the Source Data file.