Phenotypic and Genotypic Co-receptor Tropism Testing in HIV-1 Epidemic Region of Tanzania Where Multiple Non-B Subtypes Co-circulate

George P Judicate; Godfrey Barabona; Doreen Kamori; Macdonald Mahiti; Toong Seng Tan; Seiya Ozono; Amina Shaban Mgunya; Takeo Kuwata; Shuzo Matsushita; Bruno Sunguya; Eligius Lyamuya; Kenzo Tokunaga; Takamasa Ueno

doi:10.3389/fmicb.2021.703041

Phenotypic and Genotypic Co-receptor Tropism Testing in HIV-1 Epidemic Region of Tanzania Where Multiple Non-B Subtypes Co-circulate

Front Microbiol. 2021 Jul 7:12:703041. doi: 10.3389/fmicb.2021.703041. eCollection 2021.

Authors

George P Judicate¹, Godfrey Barabona¹, Doreen Kamori², Macdonald Mahiti², Toong Seng Tan¹, Seiya Ozono³, Amina Shaban Mgunya⁴, Takeo Kuwata¹, Shuzo Matsushita¹, Bruno Sunguya^{1

2}, Eligius Lyamuya^{1

2}, Kenzo Tokunaga^{1

3}, Takamasa Ueno^{1

2}

Affiliations

¹ Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.
² Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.
³ Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan.
⁴ Muhimbili National Hospital, Dar es Salaam, Tanzania.

Abstract

HIV human immunodeficiency virus type I (HIV-1) entry inhibitor potency is dependent on viral co-receptor tropisms and thereby tropism determination is clinically important. However, phenotypic tropisms of HIV-1 non-B subtypes have been poorly investigated and the genotypic prediction algorithms remain insufficiently validated. To clarify this issue, we recruited 52 treatment-naïve, HIV-1-infected patients in Tanzania, where multiple HIV-1 non-B subtypes co-circulate. Sequence analysis of 93 infectious envelope clones isolated from their plasma viral RNA revealed the co-circulation of subtypes A1, C, D, and inter-subtype recombinant forms (isRFs). Phenotypic tropism assays revealed that lentivirus reporters pseudotyped with 75 (80.6%) and 5 (5.4%) envelope clones could establish infection toward U87.CD4 cells expressing CCR5 (R5) and CXCR4 (X4), respectively; whereas the remaining 13 (14%) clones could infect both cells. Genotypic analyses by widely used algorithms including V3 net charge, Geno2pheno, WebPSSM, and PhenoSeq showed that almost all phenotypic X4-tropic clones and only 15 of 75 phenotypic R5-tropic clones were concordantly predicted. However, the remaining 60 phenotypic R5-tropic clones were discordantly predicted by at least one algorithm. In particular, 2 phenotypic R5-tropic clones were discordantly predicted by all algorithms tested. Taken together, the results demonstrate the limitation of currently available genotypic algorithms for predicting co-receptor inference among co-circulating multiple non-B subtypes and emerging isRFs. Also, the phenotypic tropism dataset presented here could be valuable for retraining of the widely used genotypic prediction algorithms to enhance their performance.

Keywords: HIV-1; co-receptor tropism; entry; envelope; inter-subtype recombinant form; non-B subtypes.