Weekly updated phylogenetic inference of San Diego SARS-CoV-2 sequences

UCSD has set up an award-winning COVID-19 response program, “Return to Learn”, that has dramatically reduced COVID-19 rates on campus relative to peer institutions. A key component of this program has been to sequence the SARS-CoV-2 genome from wastewater collected across campus on a daily basis from over 100 automated samplers and from essentially all clinical cases, as well as additional samples from research projects in the community, public and private schools, and the California Department of Public Health. A crucial component to understanding the new sequences and to use them for public health investigations is performing phylogenetic analysis, building an evolutionary tree that relates the genomes and allows a determination of which are closely related (e.g. because they are part of the same outbreak). However, the pace of sequencing has already outstripped our ability to perform the phylogenetic analysis, which now takes 1-2 weeks to do from scratch. The phylogenetic analysis needs to be done in less than a day, and ideally within hours, to be useful for case investigation and for response testing, especially when a novel variant arises and starts to spread. We have now developed a method and tested it extensively on Expanse for enabling such analyses. The aim of this project is to enable the twice-a-week reconstruction of this phylogeny and related analyses needed to ensure accuracy.