Passing through: the role of transmission bottlenecks in influenza virus host adaptation

SPEAKER: Thomas Friedrich, PhD

Associate Professor, Dept. of Pathobiological Sciences
University of Wisconsin-Madison School of Veterinary Medicine
Head of Virology Services Unit, Wisconsin National Primate Research Center

ABSTRACT

Novel influenza viruses emerge unpredictably from avian reservoirs, causing occasional human pandemics. A handful of recent studies in ferrets have shown that surprisingly few molecular changes may be required for airborne transmission of avian influenza viruses between mammalian hosts. We used deep sequencing to trace the evolutionary pathways of 2 such avian viruses as they replicated and were transmitted in ferrets. Airborne transmission involved genetic bottlenecks that were most often driven by strong selection on the gene encoding the viral attachment protein, hemagglutinin (HA). Bottleneck stringency varied among transmission events, and no single viral genotype was consistently transmitted in each event we observed. The strength and nature of transmission bottlenecks could play an important role in determining the ability of a given avian virus to successfully emerge in humans. All work with infected ferrets was performed prior to the current pause on “gain-of-function” research. 

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Scalable and biologically realistic methods for inferring selective pressures from molecular sequence data

Speaker: Sergei L. Kosakovsky Pond, PhD

Associate Professor of Medicine
Department of Medicine
University of California, San Diego

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Streaming: Watch the seminar live by clicking here when the seminar begins. You can also use this link to watch the seminar after the event.

How predictable is RNA virus evolution?

Speaker: Richard Neher, PhD

Research Group Leader
Max Planck Institute for Developmental Biology

ABSTRACT

To quantitatively monitor diversity and dynamics of entire virus populations, we performed whole genome deep sequencing of HIV-1 populations in 9 untreated patients with 6-12 longitudinal samples spanning 5-8 years of infection. Using this data set, we show that a universal landscape of fitness costs controls minor intrapatient variation and the rate of reversion towards the global HIV-1 consensus. These reproducible patterns of diversity and reversion at single sites are possible only because frequent recombination limits coupling between different parts of the genome. In contrast, segments of influenza viruses don’t recombine. Nevertheless, the shape of phylogenetic trees predicts which of the currently circulating virus variants are most likely to dominate future seasons. Predictive models have the potential to improve strain selection for seasonal influenza vaccines. 

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Streaming: Watch the seminar live by clicking here when the seminar begins. You can also use this link to watch the seminar after the event.

The story of an outbreak: Tracking infectious disease transmission with DNA sequencing

Speaker: Jennifer Gardy, PhD

Canada Research Chair in Public Health Genomics
Senior Scientist, BC Centre for Disease Control
Assistant Professor, School of Population and Public Health, UBC
Associate Member, Microbiology & Immunology, UBC

Abstract

With the advent of next-generation DNA sequencing methods, sequencing the complete genome of every pathogen isolate from an outbreak has become possible. With this new, high-resolution molecular epidemiology data, we are able to reconstruct outbreaks of disease with a degree of accuracy that has previously been unattainable, revealing important aspects of transmission dynamics and providing insight into pathogen evolution and population structure. This emerging field of genomic epidemiology still faces challenges, however, including dealing with biological issues such as within-host genetic diversity, technical hurdles related to sample preparation and sequencing, and questions around clinical implementation, validation, and reporting. In this talk, I’ll discuss a multi-year genomic investigation of a tuberculosis outbreak amongst BC’s homeless population, including both the insights gained into the outbreak and the larger questions about genomic epidemiology that the work raised, which we are now addressing in follow-up projects. 

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Streaming: View seminar live by clicking here when the seminar begins. You can also use this link to watch the seminar after the event.