Inferring the Clonal Structure of Viral Populations from Time Series Sequencing
Fig 3
(A) A pedagogic evolution recombination network with four mutations and two recombination events across two segments. (B) Typical haplotype tables arising from (A). (Ci) Two clusters of mutations grouped by paired reads on two segments. (Cii) Clones C1000 and C0010 undergo within segment recombination into C1010, with a crossover site between M1 and M3. (Ciii) Clones C1001 and C1110 undergo between segment recombination (reassortment) into C1111. (D) Recombination networks arising from the haplotype tables in (B). (E) The prevalence of the four mutations across five days. (F) Phylogenetic network associated with (A). (G) Point and range prevalence estimates. (Hi) A network consistent with the two networks of (D). (Hii) Incompatible prevalence conditions associated with (Hi).