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Phylogenetics in HIV transmission: taking within-host diversity into account

Phylogenetics in HIV transmission: taking within-host diversity into account Purpose of review Within-host diversity complicates transmission models because it recognizes that between-host virus phylogenies are not identical to the transmission history among the infected hosts. This review presents the biological and theoretical foundations for recent development in this field, and shows that modern phylodynamic methods are capable of inferring realistic transmission histories from HIV sequence data. Recent findings Transmission of single or multiple genetic variants from a donor's HIV population results in donor-recipient phylogenies with combinations of monophyletic, paraphyletic, and polyphyletic patterns. Large-scale simulations and analyses of many real HIV datasets have established that transmission direction, directness, or common source often can be inferred based on HIV sequence data. Phylodynamic reconstruction of HIV transmissions that include within-host HIV diversity have recently been established and made available in several software packages. Summary Phylodynamic methods that include realistic features of HIV genetic diversification have come of age, significantly improving inference of key epidemiological parameters. This opens the door to more accurate surveillance and better-informed prevention campaigns. Theoretical Biology & Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA Correspondence to Thomas Leitner, Theoretical Biology & Biophysics Group T-6, Mail Stop K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. Tel: +1 505 667 3898; e-mail: tkl@lanl.gov Written work prepared by employees of the Federal Government as part of their official duties is, under the U.S. Copyright Act, a “work of the United States Government” for which copyright protection under Title 17 of the United States Code is not available. As such, copyright does not extend to the contributions of employees of the Federal Government. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Current Opinion in HIV and Aids Wolters Kluwer Health

Phylogenetics in HIV transmission: taking within-host diversity into account

Leitner, Thomas
Current Opinion in HIV and Aids , Volume 14 (3) – May 1, 2019
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Publisher
Wolters Kluwer Health
ISSN
1746-630X
eISSN
1746-6318
DOI
10.1097/COH.0000000000000536
Publisher site
See Article on Publisher Site

Abstract

Purpose of review Within-host diversity complicates transmission models because it recognizes that between-host virus phylogenies are not identical to the transmission history among the infected hosts. This review presents the biological and theoretical foundations for recent development in this field, and shows that modern phylodynamic methods are capable of inferring realistic transmission histories from HIV sequence data. Recent findings Transmission of single or multiple genetic variants from a donor's HIV population results in donor-recipient phylogenies with combinations of monophyletic, paraphyletic, and polyphyletic patterns. Large-scale simulations and analyses of many real HIV datasets have established that transmission direction, directness, or common source often can be inferred based on HIV sequence data. Phylodynamic reconstruction of HIV transmissions that include within-host HIV diversity have recently been established and made available in several software packages. Summary Phylodynamic methods that include realistic features of HIV genetic diversification have come of age, significantly improving inference of key epidemiological parameters. This opens the door to more accurate surveillance and better-informed prevention campaigns. Theoretical Biology & Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA Correspondence to Thomas Leitner, Theoretical Biology & Biophysics Group T-6, Mail Stop K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. Tel: +1 505 667 3898; e-mail: tkl@lanl.gov Written work prepared by employees of the Federal Government as part of their official duties is, under the U.S. Copyright Act, a “work of the United States Government” for which copyright protection under Title 17 of the United States Code is not available. As such, copyright does not extend to the contributions of employees of the Federal Government.

Journal

Current Opinion in HIV and Aids – Wolters Kluwer Health

Published: May 1, 2019

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