Viral pathogen sequencing for diagnosis and disease tracking

Lycett, S. (Invited speaker)

Activity: Academic talk or presentation typesInvited talk


Sequencing pathogens from infected animals has become much more affordable and widespread in recent years, especially during outbreaks and in endemic disease settings with targeted surveillance programmes. Consequently, there are growing collections of animal pathogen sequences from around the globe. Pathogen sequences accumulate mutations over time, some mutations are markers for pathogenicity, host adaptation and drug resistance, but viral sequences especially have fast enough substitution rates to enable transmission patterns between places or local cross species transmission to be inferred.

Here the use of time resolved phylogenies and phylodynamic methodologies for understanding the occurrence and spread of viral pathogens in animal populations will be described. The amount of sequence variation between samples is highly informative and using avian influenza, porcine reproductive and respiratory syndrome and bovine viral diarrhoea examples, I will show how whole genomes or short regions are being used for analysing epidemic and endemic situations, including the potential role of sequencing in disease eradication programmes.
Period14 Nov 2018
Event titleInfectious Disease Diagnosis Symposium: null
Event typeSymposium
LocationMidlothian, United Kingdom
Degree of RecognitionLocal


  • phylodynamics
  • phylogeography
  • virus
  • pathogen
  • epidemiology