Forecasting HIV-1 genetic cluster growth in Illinois, United States

Manon Ragonnet-Cronin*, Christina Hayford, Richard D'Aquila, Fangchao Ma, Cheryl Ward, Nanette Benbow, Joel O. Wertheim

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

11 Scopus citations

Abstract

Background: HIV intervention activities directed toward both those most likely to transmit and their HIV-negative partners have the potential to substantially disrupt HIV transmission. Using HIV sequence data to construct molecular transmission clusters can reveal individuals whose viruses are connected. The utility of various cluster prioritization schemes measuring cluster growth have been demonstrated using surveillance data in New York City and across the United States, by the Centers for Disease Control and Prevention (CDC). Methods: We examined clustering and cluster growth prioritization schemes using Illinois HIV sequence data that include cases from Chicago, a large urban center with high HIV prevalence, to compare their ability to predict future cluster growth. Results: We found that past cluster growth was a far better predictor of future cluster growth than cluster membership alone but found no substantive difference between the schemes used by CDC and the relative cluster growth scheme previously used in New York City (NYC). Focusing on individuals selected simultaneously by both the CDC and the NYC schemes did not provide additional improvements. Conclusion: Growth-based prioritization schemes can easily be automated in HIV surveillance tools and can be used by health departments to identify and respond to clusters where HIV transmission may be actively occurring.

Original languageEnglish (US)
Pages (from-to)49-55
Number of pages7
JournalJournal of Acquired Immune Deficiency Syndromes
Volume89
Issue number1
DOIs
StatePublished - Jan 1 2022

Funding

Supported by an administrative supplement to an NIH-NIAID P30 AI117943 award, an NIH-NIAID K01 Career Development Award (K01AI110181), and an NIH-NIAID R01 (AI135992). MRC is jointly funded by the United Kingdom Medical Research Council (MRC) and the United Kingdom Department for International Development (DFID) under the MRC/DFID Concordat agreement and this award is part of the EDCTP2 programme supported by the European Union (MR/R015600/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the article. J.O.W. received funding from Gilead Sciences, LLC, as a grant paid to his institution. The remaining authors have no conflicts of interest to disclose.

Keywords

  • Cluster
  • Genetic
  • HIV
  • MSM
  • Network
  • Phylogenetics

ASJC Scopus subject areas

  • Infectious Diseases
  • Pharmacology (medical)

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