Prevalent subtypes and one-year outcomes of an HIV-cohort from an urban Philippine center

Abstract

Circulating HIV subtypes in the Philippines have increasingly diversified, potentially affecting treatment. We monitored outcomes of a treatment-naïve cohort and their virus subtype prevalence. Retrospective/prospective study cohort. HIV-I-REACT clinic patients co-enrolled in the Virology Quality Assurance Program (RUSH-VQA) from 7/2017-6/2019 were included. Relevant demographic and laboratory information were collected. The ViroSeq HIV-1 Genotyping System v.3 and HIV-1 Integrase Genotyping Kit identified protease-reverse transcriptase and integrase drug resistance mutations (DRM). Sequence subtyping followed using the Stanford University Drug Resistance Database and the REGA HIV-1 Subtyping Tool v.3. The jpHMM HIV-1 Tool and REGA HIV-1 Subtyping Tool provided additional subtype analysis of this cohort’s 5’LTR-VIF regions after Sanger sequencing. One-year outcomes included virologic suppression, mortality, and follow-up. 86/88 patients were males. Median age was 30 (range 19–65) years; 61/88 were MSM. 15/85 carried baseline DRM. ViroSeq-generated sequences included subtypes CRF01_AE (66/85), B (14/85), and newer recombinants (4/85). Extensive sequencing (n = 71) of the 5’-LTR-GAG-Pol genes showed CRF01_AE (n = 50), subtype B (n = 7), and other recombinants (n = 13). Bootstrap analysis identified 7 pairs of highly related strains. Discordant DRM appeared in 2/7 pairs, where 1/2 strains displayed DRM. After 1 year, 87 individuals were alive, with 19 lost to care. Viral load (VL) was repeated for only 31/77 (40.2%). Follow-up CD4 testing for 39/77 (50.6%) showed an increase to a median of 327 cells/mm3. Our cohort currently carries subtype CRF01_AE (∼68%–70%), followed by subtype B and CRF01_AE/B recombinants. Outcomes were favorable, regardless of subtype after 1 year on cART.