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Phylogenetic Inference of HIV Transmission Clusters

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      Abstract

      Better understanding the structure and dynamics of HIV transmission networks is essential for designing the most efficient interventions to prevent new HIV transmissions, and ultimately for gaining control of the HIV epidemic. The inference of phylogenetic relationships and the interpretation of results rely on the definition of the HIV transmission cluster. The definition of the HIV cluster is complex and dependent on multiple factors, including the design of sampling, accuracy of sequencing, precision of sequence alignment, evolutionary models, the phylogenetic method of inference, and specified thresholds for cluster support. While the majority of studies focus on clusters, non-clustered cases could also be highly informative. A new dimension in the analysis of the global and local HIV epidemics is the concept of phylogenetically distinct HIV sub-epidemics. The identification of active HIV sub-epidemics reveals spreading viral lineages and may help in the design of targeted interventions. HIV clustering can also be affected by sampling density. Obtaining a proper sampling density may increase statistical power and reduce sampling bias, so sampling density should be taken into account in study design and in interpretation of phylogenetic results. Finally, recent advances in long-range genotyping may enable more accurate inference of HIV transmission networks. If performed in real time, it could both inform public-health strategies and be clinically relevant (e.g., drug-resistance testing).

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      Most cited references 98

      • Record: found
      • Abstract: not found
      • Article: not found

      Confidence Limits on Phylogenies: An Approach Using the Bootstrap

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        • Record: found
        • Abstract: not found
        • Article: not found

        Bootstrap Methods: Another Look at the Jackknife

         B Efron (1979)
          Bookmark
          • Record: found
          • Abstract: not found
          • Article: not found

          An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis

           D. Hillis,  J. Bull (1993)
            Bookmark

            Author and article information

            Affiliations
            From Department of Immunology & Infectious Diseases, Harvard School of Public Health, United States.
            From Department of Immunology & Infectious Diseases, Harvard School of Public Health, United States.
            From Department of Immunology & Infectious Diseases, Harvard School of Public Health, United States.
            Author notes
            Correspondence to: Vlad Novitsky, Email: vnovi@hsph.harvard.edu.
            Contributors
            From Department of Immunology & Infectious Diseases, Harvard School of Public Health, United States.
            From Department of Immunology & Infectious Diseases, Harvard School of Public Health, United States.
            From Department of Immunology & Infectious Diseases, Harvard School of Public Health, United States.
            Journal
            Infectious Diseases and Translational Medicine
            Infect. Dis. Transl. Med.
            Infect. Dis. Transl. Med.
            International Biological and Medical Journals Publishing House Co., Limited (Room E16, 3/f, Yongda Commercial Building, No.97, Bonham Stand (Sheung Wan), HongKong )
            2411-2917
            31 October 2017
            31 October 2017
            : 3
            : 2
            : 51-59 (pp. )
            10.11979/idtm.201702007

            This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

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            Figures: 1, Tables: 0, References: 101, Pages: 9
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