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Estimating the Basic Reproductive Number from Viral Sequence Data


Stadler, T; Kouyos, R; von Wyl, V; Yerly, S; Böni, J; Bürgisser, P; Klimkait, T; Joos, B; Rieder, P; Xie, D; Günthard, H F; Drummond, A J; Bonhoeffer, S (2012). Estimating the Basic Reproductive Number from Viral Sequence Data. Molecular Biology and Evolution, 29(1):347-357.

Abstract

Epidemiological processes leave a fingerprint in the pattern of genetic structure of virus populations. Here, we provide a new method to infer epidemiological parameters directly from viral sequence data. The method is based on phylogenetic analysis using a birth-death model (BDM) rather than the commonly used coalescent as the model for the epidemiological transmission of the pathogen. Using the BDM has the advantage that transmission and death rates are estimated independently and therefore enables for the first time the estimation of the basic reproductive number of the pathogen using only sequence data, without further assumptions like the average duration of infection. We apply the method to genetic data of the HIV-1 epidemic in Switzerland.

Abstract

Epidemiological processes leave a fingerprint in the pattern of genetic structure of virus populations. Here, we provide a new method to infer epidemiological parameters directly from viral sequence data. The method is based on phylogenetic analysis using a birth-death model (BDM) rather than the commonly used coalescent as the model for the epidemiological transmission of the pathogen. Using the BDM has the advantage that transmission and death rates are estimated independently and therefore enables for the first time the estimation of the basic reproductive number of the pathogen using only sequence data, without further assumptions like the average duration of infection. We apply the method to genetic data of the HIV-1 epidemic in Switzerland.

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62 citations in Web of Science®
43 citations in Scopus®
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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > University Hospital Zurich > Clinic for Infectious Diseases
Dewey Decimal Classification:610 Medicine & health
Language:English
Date:2012
Deposited On:20 Mar 2012 09:20
Last Modified:05 Apr 2016 15:24
Publisher:Oxford University Press
ISSN:0737-4038
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1093/molbev/msr217
PubMed ID:21890480

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