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

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.

Factors Associated with Neutralizing Antibody Responses following 2-Dose and 3rd Booster Monovalent COVID-19 Vaccination in Japanese People Living with HIV

“…To assess the NAb titers of antisera, we employed a lentiviral reporter assay system pseudotyped by SARS-CoV-2 spike protein, as previously reported [ 19 ]. A version of spike protein which had been modified by truncating 19 amino acids from the C terminal end (CΔ19 spike) was used.…”

“…In brief, spike-encoding plasmids (kindly provided by T. Kuwata [ 18 ]) were modified by truncating the last 19 amino acids from the C-terminal end of the cytoplasmic tail to create plasmids designated as SARS-CoV-2 or VOC-Spike CΔ19. The lentiviral backbone, pSG3 ΔENVΔNef -Luc2-IN/HiBit (kindly provided by K. Tokunaga), was previously modified by inserting a HiBiT peptide tag sequence and a luciferase reporter gene [ 19 ]. The 2 modified plasmids were then used to co-transfect overnight-seeded 293T cells at a concentration of 1000 ng and 25 ng for pSG3 ΔENVΔNef -Luc2-IN/HiBit and SARS-CoV-2/VOC-Spike CΔ19, respectively.…”

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“…Moreover, this requires more phenotypic validation results to support this idea. Judicate's study demonstrated the limitation of currently available genotypic algorithms for predicting coreceptor inference among non-B subtypes (44). Therefore, the phenotypic tropism dataset of non-B subtypes is valuable for SGA to detect the HIV-1 variant populations with different coreceptor usages.…”

Evolution of Multiple Domains of the HIV-1 Envelope Glycoprotein during Coreceptor Switch with CCR5 Antagonist Therapy

“…Genotypic algorithms, including Geno2Pheno, WebPSSM, PhenoSeq, SCOTH, CoRSeqV3-C, and THETA, were developed to predict coreceptor use of clade B and non-B HIV-1 subtypes ( 39 , 58 ). However, these approaches may either underestimate or overestimate X4 tropism, depending upon the particular assay and the context in which it was used ( 59 – 61 ).…”