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Ko D, McLaughlin S, Deng W, Mullins JI, Dragavon J, Harb S, Coombs RW, Frenkel LM. Development and Validation of a Genotypic Assay to Quantify CXCR4- and CCR5-Tropic Human Immunodeficiency Virus Type-1 (HIV-1) Populations and a Comparison to Trofile ®. Viruses 2024; 16:510. [PMID: 38675853 PMCID: PMC11053691 DOI: 10.3390/v16040510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
HIV-1 typically infects cells via the CD4 receptor and CCR5 or CXCR4 co-receptors. Maraviroc is a CCR5-specific viral entry inhibitor; knowledge of viral co-receptor specificity is important prior to usage. We developed and validated an economical V3-env Illumina-based assay to detect and quantify the frequency of viruses utilizing each co-receptor. Plasma from 54 HIV+ participants (subtype B) was tested. The viral template cDNA was generated from plasma RNA with unique molecular identifiers (UMIs). The sequences were aligned and collapsed by the UMIs with a custom bioinformatics pipeline. Co-receptor usage, determined by codon analysis and online phenotype predictors PSSM and Geno2pheno, were compared to existing Trofile® data. The cost of V3-UMI was tallied. The sequences interpreted by Geno2pheno using the most conservative cut-off, a 2% false-positive-rate (FPR), predicted CXCR4 usage with the greatest sensitivity (76%) and specificity (100%); PSSM and codon analysis had similar sensitivity and lower specificity. Discordant Trofile® and genotypic results were more common when participants had specimens from different dates analyzed by either assay. V3-UMI reagents cost USD$62/specimen. A batch of ≤20 specimens required 5 h of technical time across 1.5 days. V3-UMI predicts HIV tropism at a sensitivity and specificity similar to those of Trofile®, is relatively inexpensive, and could be performed by most central laboratories. The adoption of V3-UMI could expand HIV drug therapeutic options in lower-resource settings that currently do not have access to phenotypic HIV tropism testing.
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Affiliation(s)
- Daisy Ko
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98109, USA; (D.K.)
| | - Sherry McLaughlin
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98109, USA; (D.K.)
| | - Wenjie Deng
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA; (W.D.); (J.I.M.)
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA; (W.D.); (J.I.M.)
- Department of Medicine, University of Washington, Seattle, WA 98104, USA
- Department of Global Health, University of Washington, Seattle, WA 98105, USA
| | - Joan Dragavon
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; (J.D.); (S.H.); (R.W.C.)
| | - Socorro Harb
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; (J.D.); (S.H.); (R.W.C.)
| | - Robert W. Coombs
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; (J.D.); (S.H.); (R.W.C.)
| | - Lisa M. Frenkel
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98109, USA; (D.K.)
- Department of Medicine, University of Washington, Seattle, WA 98104, USA
- Department of Global Health, University of Washington, Seattle, WA 98105, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; (J.D.); (S.H.); (R.W.C.)
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
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