From the selected samples, 249 (134 from recent versus 115 from chronic infections) env coding regions, including V 1-C5 of gp120 and the gp41 ectodomain of HIV- 1, were successfully amplified and sequenced by next generation sequencing (NGS) using the Illumina MiSeq platform. A total of 597 diagnostic samples obtained in 20 from recently and chronically HIV- 1 infected individuals were selected. To identify recent HIV- 1 infections, we evaluated and compared the performance of 4 sequence-based diversity measures including percent diversity, percent complexity, Shannon entropy and number of haplotypes targeting 13 genetic segments within the env gene of HIV- 1. Identifying recent HIV- 1 infections is crucial for monitoring HIV- 1 incidence and optimizing public health prevention efforts. Kafando, Alexis Fournier, Eric Serhir, Bouchra Martineau, Christine Doualla-Bell, Florence Sangaré, Mohamed Ndongo Sylla, Mohamed Chamberland, Annie El-Far, Mohamed Charest, Hugues HIV- 1 envelope sequence-based diversity measures for identifying recent infections
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