Invited workshop: Virus adaptation on multi-host fitness landscapes

When: July 17, 2008

Where: 510 Mueller Lab, Penn State's University Park campus (map)

Contact: Kim Pepin

Confirmed participants

Santiago Elena (Universidad Politecnica de Valencia)
Eddie Holmes (Penn State)
Jamie Lloyd-Smith (Penn State)
Yuseob Kim (Arizona State University)
Kim Pepin (Penn State)
Art Poon (UC San Diego)
Mary Poss (Penn State)
Andrew Read (Penn State)
Beth Shapiro (Penn State)
Daniel Weinreich (Brown University)
Claus Wilke (University of Texas)

Agenda

8:15-8:45 Breakfast (to be provided in Mueller 510)

Introduction

8:45-8:50 Kim Pepin:

Outline of questions and goals

8:50-9:10 Jamie Lloyd-Smith

The epidemiological context: typical framework of epidemiological models and their assumptions
Strategies for incorporating pathogen adaptation and host switching

Brief insight talks from participants: 15-20 minute talk, 10-15 minute discussion

9:15-9:30 Dan Weinreich

The fitness landscape analogy: what is it? (to get us all on the same page…)
What have we learned from empirical measures of fitness landscapes?

9:45-10:00 Santiago Elena

What are the components of virus fitness? Can they be summarized by a single measure?
What has experimental evolution taught us about virus adaptation, population genetics, and mechanisms of host switching?

10:15-10:30 Yuseob Kim

How are current theories of adaptation limited for understanding virus evolution?
How can we integrate population genetic models of allele frequency change in an epidemiological framework where population demographics are dynamic?

10:45-11:00 Coffee Break

11:00-11:15 Claus Wilke

What are the effects of mutation rate and population size on adaptation?
Why shouldn't we assume independence of mutational effects?
Can we develop a testable theory of virus emergence? (Opinion of critical components)

11:30-11:45 Beth Shapiro

Why might traditional phylogenetic methods fail at estimating evolutionary parameters of virus adaptation?
What improvements have been made? What still needs to be tackled?
How can we estimate epistasis from sequence data?

12:00-12:15 Art Poon

How can sequence data be used to understand sources of selection and virus adaptation to novel hosts?
What are the limitations of these methods?

12:30-2:00 Lunch

Afternoon work session

2:00-2:30 Full group—identify specific problems to work on in the next few hours; this work is meant to be the foundation for integrated epidemiological models

What evolutionary and epidemiological factors should a realistic (yet parsimonious) theory of virus adaptation include?
What are the most challenging theoretical issues that can be addressed today?

2:30-5:00 Groups work on solving specific theoretical challenges, and building the groundwork for a research paper

Focus for theorists:

How can we integrate population genetic theory for virus adaptation into epidemiological models?
Can we extend the models to describe adaptation in changing environments? (context: virus adaptation to novel hosts)

Focus for empiricists:

How can we apply our theory of adaptation to sequence data to test mechanisms of virus emergence?
What parameters must the model have in order for it to be applicable?
How should we ideally sample sequence data and measure virus fitness to verify our theory?
What are the most pressing/interesting biological questions that can be answered with our model? (i.e., the questions to underlie our first paper)

Summary of workshop output and discussion of immediate next steps

5:00-5:30 Full group

6:00 Dinner