simple epidemiological dynamics explain phylogenetic clustering of hiv from patients with recent infection简单的流行病动力学解释系统集群与近期感染艾滋病毒的病人.pdfVIP

Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection 1 1 2 2 3 Erik M. Volz *, James S. Koopman , Melissa J. Ward , Andrew Leigh Brown , Simon D. W. Frost 1 Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, United States of America, 2 Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom, 3 Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom Abstract Phylogenies of highly genetically variable viruses such as HIV-1 are potentially informative of epidemiological dynamics. Several studies have demonstrated the presence of clusters of highly related HIV-1 sequences, particularly among recently HIV-infected individuals, which have been used to argue for a high transmission rate during acute infection. Using a large set of HIV-1 subtype B pol sequences collected from men who have sex with men, we demonstrate that virus from recent infections tend to be phylogenetically clustered at a greater rate than virus from patients with chronic infection (‘excess clustering’) and also tend to cluster with other recent HIV infections rather than chronic, established infections (‘excess co- clustering’), consistent with previous reports. To determine the role that a higher infectivity during acute infection may play in excess clustering and co-clustering, we developed a simple model of HIV infection that incorporates an early period of intensified transmission, and explicitly considers the dynamics of phylogenetic clusters alongside the dynamics of acute and chronic infected cases. We explored the potential for clustering statistics to be used for inference of