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.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Stadler T,Kouyos R,von Wyl V,Yerly S,Böni J,Bürgisser P,Klimkait T,Joos B,Rieder P,Xie D,Günthard HF,Drummond AJ,Bonhoeffer S,Swiss HIV Cohort Study.doi
10.1093/molbev/msr217subject
Has Abstractpub_date
2012-01-01 00:00:00pages
347-57issue
1eissn
0737-4038issn
1537-1719pii
msr217journal_volume
29pub_type
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