Fig. 1
Panel of information related to the recombination event. a Schematic overview of the recombination events. Three representative isolates of prototype Omicron variant (PANGO lineage B.1.1.529), OL920485, OL901845, and OL902308, were hybridized into a genomic fraction from the minor parent MW737421 at the same position (21593-23118 nt). This recombination event can be detected via five statistical test methods, RDP (P = 1.410 × 10−10), GENECONV (P = 1.028 × 10−8), MaxChi (P = 8.468 × 10−5), Chimaera (P = 8.286 × 10−5), and 3Seq (P = 1.381 × 10−7). b, c Split UPGMA trees of the fractions derived from major and minor parents. The genetic distances between the prototype Omicron variant and the major and minor parents within the phylogenetic trees of non-recombined (b) and recombined (c) fractions are consistent with recombination signatures. In the non-recombination fraction, Omicron variants appear to be closer to the major parents, while in the recombination fraction, the opposite is true. d the plot diagram checked by the RDP method, shows its P-value. e The temporal order and isolation frequency of the PANGO lineages involves the recombination event and the VOCs, VOIs, VUMs, and FMVs. The dates that BA.1, B.35, the prototype Omicron variant, and other PANGO lineages were recorded into the database for the first time are displayed. The dot areas are calculated according to the natural logarithm of the isolate numbers within each PANGO lineage. B.35 is used as a reference to show the proportion of others. The data were derived from the EpiCoVTM database of the Global Initiative on Sharing All Influenza Data (GISAID, accessed 23 January 2022). In a, b, c, and d, curves or sequences in red, green, and blue are potential recombinants, the major and minor parents, respectively.
