Protocols for sampling viral sequences to study epidemic dynamics

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.

Enhanced use of phylogenetic data to inform public health approaches to HIV among men who have sex with men

“…In order to gain insight into HIV transmission networks from viral phylogenies, a representative sample of adequate size of the HIV-positive population is necessary (47). This can be especially challenging in settings with high social stigma against HIV and/or same-sex sexual behavior, because individuals may be reluctant to disclose MSM status in research or care settings due to fears of discrimination, marginalization, and potential legal prosecution (48).…”

Integrating Phylodynamics and Epidemiology to Estimate Transmission Diversity in Viral Epidemics

“…Correct sampling is crucial to the inference of epidemic history from genetic data [62]. All available 1a, 1b, 3a and 4a subtype samples from distinct HCV-infected patients, tested within a 12-year period (1994–2006), were sorted according to their sampling dates, and at least one sample was randomly selected and sequenced for every 6-month interval.…”

Viral Phylodynamics

“…Phylodynamic approaches have mapped the geographic movement of the human influenza virus [3] and quantified the epidemic spread of rabies virus in North American raccoons [12], [13]. However, nonrepresentative sampling may bias inferences of both R 0 [14] and migration patterns [3]. Phylodynamic approaches have also been used to better understand viral transmission dynamics and spread within infected hosts.…”