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Updated: Oct 11, 2025

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
Published on: December 27, 2010
Do partner services linked to molecular clusters yield people with viremia or new HIV?
John A Schneider1,2, Christina Hayford3, Anna Hotton1
1University of Chicago Medicine.
Insights
Molecular cluster membership did not significantly increase the identification of HIV transmission potential among partners in Chicago. Partner services yielded similar results whether index clients were in a cluster or not.
Area of Science:
- Epidemiology
- Public Health
- Molecular Biology
Background:
- Identifying HIV transmission potential is crucial for public health interventions.
- Molecular epidemiology aids in understanding HIV transmission networks.
- Previous research suggests cluster analysis can guide public health efforts.
Purpose of the Study:
- To investigate the association between molecular cluster membership and public health identification of HIV transmission potential.
- To determine if identifying HIV transmission potential differs between index clients in molecular clusters and those not in clusters.
Main Methods:
- A historical cohort study analyzed HIV surveillance and partner services data from 2012-2016 in Chicago.
- HIV molecular clusters were constructed using HIV-TRACE with a genetic distance threshold of 0.5%.
- Multivariable Poisson regression examined factors associated with identifying partners with HIV transmission potential.
Main Results:
- Of 5208 index clients, 191 partners were linked to index cases in a cluster; 16% were new diagnoses or viremic.
- No statistically significant difference was found in identifying partners with HIV transmission potential between index clients in rapidly growing clusters and those not in clusters.
- Partner services from index clients in clusters showed similar new HIV case finding as those not in clusters.
Conclusions:
- Molecular cluster membership did not enhance the identification of HIV transmission potential through partner services in this Chicago cohort.
- The findings may be influenced by temporal factors, unobserved cluster members, or challenges in partner services implementation.
- Further research is needed to understand the utility of molecular clusters in public health HIV case finding.
Objectives:
We examined whether molecular cluster membership was associated with public health identification of HIV transmission potential among named partners in Chicago.
Design:
Historical cohort study.
Methods:
We matched and analyzed HIV surveillance and partner services data from HIV diagnoses (2012-2016) prior to implementation of cluster detection and response interventions. We constructed molecular clusters using HIV-TRACE at a pairwise genetic distance threshold of 0.5% and identified clusters exhibiting recent and rapid growth according to the Centers for Disease Control and Prevention definition (three new cases diagnosed in past year). Factors associated with identification of partners with HIV transmission potential were examined using multivariable Poisson regression.
Results:
There were 5208 newly diagnosed index clients over this time period. Average age of index clients in clusters was 28; 47% were Black, 29% Latinx/Hispanic, 6% female and 89% MSM. Of the 537 named partners, 191 (35.6%) were linked to index cases in a cluster and of those 16% were either new diagnoses or viremic. There was no statistically significant difference in the probability of identifying partners with HIV transmission potential among index clients in a rapidly growing cluster versus those not in a cluster [adjusted relative risk 1.82, (0.81-4.06)].
Conclusion:
Partner services that were initiated from index clients in a molecular cluster yielded similar new HIV case finding or identification of those with viremia as did interviews with index clients not in clusters. It remains unclear whether these findings are due to temporal disconnects between diagnoses and cluster identification, unobserved cluster members, or challenges with partner services implementation.
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