Persistence of HIV transmission clusters among people who inject drugs

Rebecca Rose, Sissy Cross, Susanna L. Lamers, Jacquie Astemborski, Greg D. Kirk, Shruti H. Mehta, Matthew Sievers, Craig Martens, Daniel Bruno, Andrew D. Redd, Oliver Laeyendecker

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


Objective: We investigated the duration of HIV transmission clusters.Design:Fifty-four individuals newly infected at enrollment in the ALIVE cohort were included, all of whom had sequences at an intake visit (T1) and from a second (T2) and/or a third (T3) follow-up visit, median 2.9 and 5.4 years later, respectively.Methods:Sequences were generated using the 454 DNA sequencing platform for portions of HIV pol and env (HXB2 positions 2717-3230; 7941-8264). Genetic distances were calculated using tn93 and sequences were clustered over a range of thresholds (1 - 5%) using HIV-TRACE. Analyses were performed separately for individuals with pol sequences for T1 + T2 (n = 40, 'Set 1') and T1 + T3 (n = 25; 'Set 2'), and env sequences for T1 + T2 (n = 47, 'Set 1'), and T1 + T3 (n = 30; 'Set 2').Results:For pol, with one exception, a single cluster contained more than 75% of samples at all thresholds, and cluster composition was at least 90% concordant between time points/thresholds. For env, two major clusters (A and B) were observed at T1 and T2/T3, although cluster composition concordance between time points/thresholds was low (<60%) at lower thresholds for both sets 1 and 2. In addition, several individuals were included in clusters at T2/T3, although not at T1.Conclusion:Caution should be used in applying a single threshold in population studies where seroconversion dates are unknown. However, the retention of some clusters even after 5 + years is evidence for the robustness of the clustering approach in general.

Original languageEnglish (US)
Pages (from-to)2037-2044
Number of pages8
Issue number14
StatePublished - Nov 15 2020


  • epidemic
  • genetic linkage
  • intravenous drug use
  • next-generation sequencing

ASJC Scopus subject areas

  • Infectious Diseases
  • Immunology and Allergy
  • Immunology


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