Integration of Contact Tracing and Phylogenetics in an Investigation of Acute HIV Infection

Sex Transm Dis. 2018 Apr;45(4):222-228. doi: 10.1097/OLQ.0000000000000726.


Background: The integration of traditional contact tracing with HIV sequence analyses offers opportunities to mitigate some of the barriers to effective network construction. We used combined analyses during an outbreak investigation of spatiotemporally clustered acute HIV infections to evaluate if the observed clustering was the product of a single outbreak.

Methods: We investigated acute and recent HIV index cases reported in North Carolina from 2013 to 2014 and their reported contacts. Contact tracing networks were constructed with surveillance data and compared with phylogenetic transmission clusters involving an index case using available HIV-1 pol sequences including 1672 references. Clusters were defined as clades of 2 or more sequences with a less than 1.5% genetic distance and a bootstrap of at least 98% on maximum-likelihood phylogenies.

Results: In total, 68 index cases and 210 contacts (71 HIV infected) were reported. The contact tracing network involved 58 components with low overall density (1.2% statewide); 33% of first-degree contacts could not be located. Among 38 (56%) of 68 index cases and 34 (48%) of 71 contacts with sequences, 13 phylogenetic clusters were identified (size 2-4 members). Four clusters connected network components that were not linked in contact tracing. The largest component (n = 28 cases) included 2 distinct phylogenetic clusters and spanned 2 regions.

Conclusions: We identified the concurrent expansion of multiple small transmission clusters rather than a single outbreak in a largely disconnected contact tracing network. Integration of phylogenetic analyses provided timely information on transmission networks during the investigation. Our findings highlight the potential of combined methods to better identify high-risk networks for intervention.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adult
  • Cluster Analysis
  • Contact Tracing / methods*
  • Disease Outbreaks / prevention & control*
  • Female
  • Genotype
  • HIV Infections / epidemiology*
  • HIV Infections / prevention & control
  • HIV-1 / genetics*
  • Humans
  • Male
  • Middle Aged
  • North Carolina / epidemiology
  • Phylogeny*
  • Sequence Analysis, DNA
  • Sexual Partners
  • Young Adult