Niven Lecture: Genomic Epidemiology in SARS-CoV-2: new models and challenges

About the Niven Lectures: Ivan Niven was a famous number theorist and expositor; his textbooks won numerous awards, have been translated into many languages and are widely used to this day.  Niven was born in Vancouver in 1915, earned his Bachelor's and Master's degrees at UBC in 1934 and 1936 and his Ph.D. at the University of Chicago in 1938.  He was a faculty member at the University of Oregon from 1947 until his retirement in 1982.  The annual Niven Lecture Series, held at UBC since 2005, is funded in part through a generous bequest from Ivan and Betty Niven to the UBC Mathematics Department.

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 can help us to understand local transmission. However, there are mathematical and statistical challenges in making the most of this potentially rich source of information about viruses and how they spread.  In this talk I will introduce the field of genomic epidemiology in general, and then describe recent research in our group.  We have developed a method to use 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 describe the results of this method applied to data from Victoria, Australia. I will conclude by noting some broader challenges and opportunities for the genomic surveillance of SARS-CoV-2.