The identification of recent HIV-1 infections among people with new diagnoses is important to both tailoring and assessing the impact of HIV-1 prevention strategies.
We developed a Multiplexed Primer ID-Next Gen Sequencing (MPID-NGS) approach to identify recent infections by measuring the intra-host viral diversity over multiple regions of the HIV-1 genome, in addition to detecting drug resistance mutations (DRMs) and phylogenetically linked clusters. We summarize the field implementation of this all-in-one platform among persons with newly diagnosed HIV-1 by the North Carolina State Laboratory of Public Health in 2018.
Overall, recent infection was identified in 94 (35%) of 268 new diagnoses. People younger than 30 years old and people who inject drugs were more likely to be diagnosed as recent infection. The RT region K103N was the most commonly detected DRM (approximately 15%). We found a total of 28 clusters, and persons with recent infection were more likely to be cluster members compared to those with chronic infections (p = 0.026).
We demonstrate the rapid identification of recent infection and pre-treatment DRMs coupled with cluster analysis that will allow prioritization of linkage to care, treatment and prevention interventions to those at highest risk of onward transmission.

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