#HIV-1 #Phylodynamics to Detect and Characterize Active #Transmission #Clusters in North Carolina (J Infect Dis., abstract)

[Source: Journal of Infectious Diseases, full page: (LINK). Abstract, edited.]

HIV-1 Phylodynamics to Detect and Characterize Active Transmission Clusters in North Carolina

Ann M Dennis, MD, Stéphane Hué, PhD, Rachael Billock, MSPH, Sara Levintow, MSPH, Joseph Sebastian, PhD, William C Miller, MD, PhD, Joseph J Eron, MD

The Journal of Infectious Diseases, jiz176, https://doi.org/10.1093/infdis/jiz176

Published: 27 April 2019




HIV-1 phylodynamics can be used to monitor epidemic trends and help target prevention through identification and characterization of transmission clusters.


We analyzed HIV-1 pol sequences sampled in North Carolina from 1997-2014. Putative clusters were identified using maximum-likelihood trees and dated using Bayesian Markov Chain Monte Carlo inference. Active clusters were defined as clusters including internal nodes 2009-2014. Effective reproductive numbers (Re) were estimated using birth-death models for large clusters that expanded ≥2-fold from 2009-2014.


Of 14,921 persons, 7,508 (50%) sequences were identified in 2,264 clusters. Only 288 (13%) clusters were active from 2009-2014; 37 were large (10-36 members). Compared to smaller clusters, large clusters were increasingly populated by men and younger persons; however, nearly 60% included ≥1 women. Clusters with ≥3 members demonstrated assortative mixing by gender, age, and sample region. Of 15 large clusters with ≥2-fold expansion, nearly all had Re ~1 by 2014.


Phylodynamics revealed transmission cluster expansion in this densely sampled region and allowed estimates of Re to monitor active clusters, showing the propensity for steady, onward propagation. Associations with clustering and cluster characteristics vary by cluster size. Harnessing sequence-derived epidemiologic parameters within routine surveillance could allow refined monitoring of local sub-epidemics.

HIV-1, Molecular Epidemiology, Transmission, Phylogeny,Southeastern United States

Issue Section: Major Article

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Keywords: HIV; USA.


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Giuseppe Michieli

I am an Italian blogger, active since 2005 with main focus on emerging infectious diseases such as avian influenza, SARS, antibiotics resistance, and many other global Health issues. Other fields of interest are: climate change, global warming, geological and biological sciences. My activity consists mainly in collection and analysis of news, public services updates, confronting sources and making decision about what are the 'signals' of an impending crisis (an outbreak, for example). When a signal is detected, I follow traces during the entire course of an event. I started in 2005 my blog ''A TIME'S MEMORY'', now with more than 40,000 posts and 3 millions of web interactions. Subsequently I added an Italian Language blog, then discontinued because of very low traffic and interest. I contributed for seven years to a public forum (FluTrackers.com) in the midst of the Ebola epidemic in West Africa in 2014, I left the site to continue alone my data tracking job.