Genomic surveillance of emerging viral pathogens: Lessons from the Past Outbreaks.

Viral pathogens have long been a significant threat to human health, including
but not limited to the outbreaks of H5N1(1997), SARS(2003), H1N1(2009), MERS(2012), Ebola(2013), H7N9(2013) and SARS2(2019). Many of them are fast evolving RNA viruses with great variety maintained in animals, underpinning their capability of jumping species barrier and frequent zoonotic emergence. Their fast evolution also expedites the emergence of antigenic variant or drug resistance, creating recurrent threats of expansive spread, failed treatment and ineffective vaccination. On the other hand, the transmission and adaptation of these viral pathogens leave considerable genetic footprints in their genomes. Next generation sequencing and phylodynamics analyses open new opportunity for studying their genomic information to understand the processes of emergence and spread in high resolutions. In this talk I will review the use of genomic surveillance to track the origin, spread and evolution of some important pathogens including influenza virus and coronavirus, and will share the insights into the emergence and evolutionary patterns of these pathogens. Some bioinformatics tools to assist the evolutionary analyses of viral genomes will be introduced as well.