CoV Genome Tracker: tracing genomic footprints of Covid-19 pandemic

Saymon Akther; Edgaras Bezrucenkovas; Brian Sulkow; Christopher Panlasigui; Li Li; Weigang Qiu; Lia Di

Genomic epidemiology comparatively analyzes pathogen genome sequences to uncover 33 the evolutionary origin, trace the global spread, and reveal molecular mechanisms of infectious 34 disease outbreaks including the latest coronavirus pandemic caused by the viral species SARS- At the micro-evolutionary time scale, a key distinction of CoV Genome Tracker from the 45 Nextstrain Covid-19 browser (https://nextstrain.org/ncov) (6) is our adoption of a haplotype net-46 work -instead of a phylogenetic tree -as the analytic framework as well as the visual guide (Fig 47 1) . A haplotype network offers several advantages over a phylogenic tree. First, at the time scale 48 of days and months, loss and fixation of alleles are rare and the ancestral and descendant gen-49 otypes are both present in the population. As such, tree-based phylogenies can be misleading 50 because tree-based phylogenetic algorithms compel all sampled genomes into leaf nodes re-51 gardless of ancestral or descendant genotypes, meanwhile introducing hypothetical ancestors 52 as internal nodes. Second, phylogenetic reconstruction typically assumes a mutation-driven pro-53 cess with complete lineage sorting. Violation of these assumptions results in misleading evolu-54 tionary relations, for example, when recombination is present or when genes remain polymorphic 55 (8,9). Third, a haplotype network requires less abstract comprehension of evolutionary pro-56 cesses than a phylogenetic tree does. For example, edges of a haplotype network depict genetic 57 changes from a parent to a descendant genome, while branches of a phylogenetic tree represent 58 genetic changes from a hypothetical ancestor to another hypothetical or sampled genome. 59