Genomic Epidemiology in SARS-CoV-2: new tools and challenges

Synopsis

Since the start of the COVID-19 pandemic, scientists around the world have sequenced over 2 million SARS-CoV-2 genomes in an effort to monitor and understand the evolution and transmission of this virus. Virus sequences can help us understand the emergence of new variants with new phenotypes, track the virus' geographical movements and, at local levels, can help us to understand local transmission. In this talk I will describe a new method to using SARS-CoV-2 genomes to estimate serial intervals: the time between symptoms (or in some cases, sample collection) in infector-infectee pairs. Serial intervals are important because they underlie estimates of the reproductive number, Rt, which in turn is used to help understand the strength of transmission and the impact of different levels of vaccine coverage. I will discuss broader challenges and opportunities for the genomic surveillance of SARS-CoV-2.