FROM PROMISE TO REALIZATION: SEQUENCING AND SURVEILLANCE FROM HIV-1 TO SARS-CoV-2

ABSTRACT

The advent of cheaper viral sequencing and opportunity to offer customized treatment through identification of resistance mutations in patients with HIV-1, also offered the first large-scale opportunity to use sequencing to generate insights into a global infectious disease pandemic. Using HIV-1 sequences, scientists were able to track mutations globally and within countries and use them to gain groundbreaking understanding of virus transmission and the evolution of resistance. Though invaluable in contributing to our knowledge of virus dynamics, much of what was feasible with HIV-1 was difficult to extend to other viruses due to the challenges and expense of full-genome sequences and the difficulty of obtaining samples from acute infections. More recent advances have made next-generation sequencing (NGS) possible and affordable, and growing realization of the insights sequencing can contribute has increased interest in generating sequences for an increasing variety of viruses. Against this backdrop of an advent of a new age of genomics in viral research, the SARSCoV- 2 pandemic has thrown sequencing and phylogenetics into the limelight, allowing the collection and sequencing of more samples than could even be conceived prior to 2020. It's a opportune time to consider not only where we've come from, but how the promise of 14 million sequences has been realized, and what the future holds for sequence-enabled pathogen research.