Protocols for sampling viral sequences to study epidemic dynamics

J. Conrad Stack, J. David Welch, Matthew Joseph Ferrari, Beth U. Shapiro, Bryan T. Grenfell

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

With more emphasis being put on global infectious disease monitoring, viral genetic data are being collected at an astounding rate, both within and without the context of a long-term disease surveillance plan. Concurrent with this increase have come improvements to the sophisticated and generalized statistical techniques used for extracting population-level information from genetic sequence data. However, little research has been done on how the collection of these viral sequence data can or does affect the efficacy of the phylogenetic algorithms used to analyse and interpret them. In this study, we use epidemic simulations to consider how the collection of viral sequence data clarifies or distorts the picture, provided by the phylogenetic algorithms, of the underlying population dynamics of the simulated viral infection over many epidemic cycles. We find that sampling protocols purposefully designed to capture sequences at specific points in the epidemic cycle, such as is done for seasonal influenza surveillance, lead to a significantly better view of the underlying population dynamics than do less-focused collection protocols. Our results suggest that the temporal distribution of samples can have a significant effect on what can be inferred from genetic data, and thus highlight the importance of considering this distribution when designing or evaluating protocols and analysing the data collected thereunder.

Original languageEnglish (US)
Pages (from-to)1119-1127
Number of pages9
JournalJournal of the Royal Society Interface
Volume7
Issue number48
DOIs
StatePublished - Jul 6 2010

Fingerprint

Population dynamics
Population Dynamics
Sampling
Virus Diseases
Human Influenza
Communicable Diseases
Monitoring
Research
Population

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Biophysics
  • Bioengineering
  • Biomaterials
  • Biochemistry
  • Biomedical Engineering

Cite this

Stack, J. Conrad ; Welch, J. David ; Ferrari, Matthew Joseph ; Shapiro, Beth U. ; Grenfell, Bryan T. / Protocols for sampling viral sequences to study epidemic dynamics. In: Journal of the Royal Society Interface. 2010 ; Vol. 7, No. 48. pp. 1119-1127.
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Protocols for sampling viral sequences to study epidemic dynamics. / Stack, J. Conrad; Welch, J. David; Ferrari, Matthew Joseph; Shapiro, Beth U.; Grenfell, Bryan T.

In: Journal of the Royal Society Interface, Vol. 7, No. 48, 06.07.2010, p. 1119-1127.

Research output: Contribution to journalArticle

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