HiCOMB 2022 Invited Speaker: Pandemic-scale Phylogenetics

Phylogenetics has been central to the genomic surveillance, epidemiology and contact tracing efforts during the COVD-19 pandemic. But the massive scale of genomic sequencing has rendered the pre-pandemic tools quite inadequate for comprehensive phylogenetic analyses. In this talk, I will discuss a high-performance computing (HPC) phylogenetic package that we developed to address the needs imposed by this pandemic. Orders of magnitude gains were achieved by this package through several domain-specific optimization and parallelization techniques. The package comprises four programs: UShER, matOptimize, RIPPLES and matUtils. Using high-performance computing, UShER and matOptimize maintain and refine daily a massive mutation-annotated phylogenetic tree consisting of all (>9M currently) SARSCoV-2 sequences available on online repositories. With UShER and RIPPLES, individual labs - even with modest compute resources - incorporate newly-sequenced SARS-CoV-2 genomes on this phylogeny and discover evidence for recombination in real-time. With matUtils, they rapidly query and visualize massive SARS-CoV-2 phylogenies. This has empowered scientists worldwide to study the SARS-CoV-2 evolutionary and transmission dynamics at an unprecedented scale, resolution and speed. This has laid the groundwork for future genomic surveillance of MOST infectious pathogens.