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Updated: Oct 10, 2025
Pairwise Growth Competition Assay for Determining the Replication Fitness of Human Immunodeficiency Viruses
Published on: May 4, 2015
Forecasting HIV-1 Genetic Cluster Growth in Illinois,United States
Manon Ragonnet-Cronin1,2, Christina Hayford3, Richard D'Aquila3
1Department of Medicine, University of California San Diego, San Diego, CA.
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.
