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Phylodynamics Helps to Evaluate the Impact of an HIV Prevention Intervention

Department of Zoology, University of Oxford, OX1 3SY Oxford, UK
New College, University of Oxford, OX1 3BN Oxford, UK
Alliance for Public Health, Kyiv 03150, Ukraine
Division of Community Health Sciences, University of Illinois at Chicago School of Public Health, Chicago, IL 60612, USA
State Institution “The L.V. Gromashevsky Institute of Epidemiology and Infectious Diseases of NAMS of Ukraine”, Kyiv 03038, Ukraine
Medical School, University of Cyprus, Nicosia 1678, Cyprus
Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 157 72 Athens, Greece
Department of Medicine, University of Chicago, Chicago, IL 60637, USA
Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
Department of Population Health, New York University, New York, NY 10003, USA
Author to whom correspondence should be addressed.
Viruses 2020, 12(4), 469;
Received: 30 January 2020 / Revised: 2 April 2020 / Accepted: 15 April 2020 / Published: 20 April 2020
(This article belongs to the Special Issue HIV Molecular Epidemiology for Prevention)
Assessment of the long-term population-level effects of HIV interventions is an ongoing public health challenge. Following the implementation of a Transmission Reduction Intervention Project (TRIP) in Odessa, Ukraine, in 2013–2016, we obtained HIV pol gene sequences and used phylogenetics to identify HIV transmission clusters. We further applied the birth-death skyline model to the sequences from Odessa (n = 275) and Kyiv (n = 92) in order to estimate changes in the epidemic’s effective reproductive number (Re) and rate of becoming uninfectious (δ). We identified 12 transmission clusters in Odessa; phylogenetic clustering was correlated with younger age and higher average viral load at the time of sampling. Estimated Re were similar in Odessa and Kyiv before the initiation of TRIP; Re started to decline in 2013 and is now below Re = 1 in Odessa (Re = 0.4, 95%HPD 0.06–0.75), but not in Kyiv (Re = 2.3, 95%HPD 0.2–5.4). Similarly, estimates of δ increased in Odessa after the initiation of TRIP. Given that both cities shared the same HIV prevention programs in 2013–2019, apart from TRIP, the observed changes in transmission parameters are likely attributable to the TRIP intervention. We propose that molecular epidemiology analysis can be used as a post-intervention effectiveness assessment tool. View Full-Text
Keywords: HIV; phylodynamics; birth-death model; prevention; intervention HIV; phylodynamics; birth-death model; prevention; intervention
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MDPI and ACS Style

Vasylyeva, T.I.; Zarebski, A.; Smyrnov, P.; Williams, L.D.; Korobchuk, A.; Liulchuk, M.; Zadorozhna, V.; Nikolopoulos, G.; Paraskevis, D.; Schneider, J.; Skaathun, B.; Hatzakis, A.; Pybus, O.G.; Friedman, S.R. Phylodynamics Helps to Evaluate the Impact of an HIV Prevention Intervention. Viruses 2020, 12, 469.

AMA Style

Vasylyeva TI, Zarebski A, Smyrnov P, Williams LD, Korobchuk A, Liulchuk M, Zadorozhna V, Nikolopoulos G, Paraskevis D, Schneider J, Skaathun B, Hatzakis A, Pybus OG, Friedman SR. Phylodynamics Helps to Evaluate the Impact of an HIV Prevention Intervention. Viruses. 2020; 12(4):469.

Chicago/Turabian Style

Vasylyeva, Tetyana I., Alexander Zarebski, Pavlo Smyrnov, Leslie D. Williams, Ania Korobchuk, Mariia Liulchuk, Viktoriia Zadorozhna, Georgios Nikolopoulos, Dimitrios Paraskevis, John Schneider, Britt Skaathun, Angelos Hatzakis, Oliver G. Pybus, and Samuel R. Friedman 2020. "Phylodynamics Helps to Evaluate the Impact of an HIV Prevention Intervention" Viruses 12, no. 4: 469.

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