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Wade KE, Chen L, Deng C, Zhou G, Hu P. Investigating alignment-free machine learning methods for HIV-1 subtype classification. BIOINFORMATICS ADVANCES 2024; 4:vbae108. [PMID: 39228995 PMCID: PMC11371153 DOI: 10.1093/bioadv/vbae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 07/26/2024] [Indexed: 09/05/2024]
Abstract
Motivation Many viruses are organized into taxonomies of subtypes based on their genetic similarities. For human immunodeficiency virus 1 (HIV-1), subtype classification plays a crucial role in infection management. Sequence alignment-based methods for subtype classification are impractical for large datasets because they are costly and time-consuming. Alignment-free methods involve creating numerical representations for genetic sequences and applying statistical or machine learning methods. Despite their high overall accuracy, existing models perform poorly on less common subtypes. Furthermore, there is limited work investigating the impact of sequence vectorization methods, in particular natural language-inspired embedding methods, on HIV-1 subtype classification. Results We present a comprehensive analysis of sequence vectorization methods across machine learning methods. We report a k-mer-based XGBoost model with a balanced accuracy of 0.84, indicating that it has good overall performance for both common and uncommon HIV-1 subtypes. We also report a Word2Vec-based support vector machine that achieves promising results on precision and balanced accuracy. Our study sheds light on the effect of sequence vectorization methods on HIV-1 subtype classification and suggests that natural language-inspired encoding methods show promise. Our results could help to develop improved HIV-1 subtype classification methods, leading to improved individual patient outcomes, and the development of subtype-specific treatments. Availability and implementation Source code is available at https://www.github.com/kwade4/HIV_Subtypes.
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Affiliation(s)
- Kaitlyn E Wade
- Department of Computer Science, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Lianghong Chen
- Department of Computer Science, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Chutong Deng
- Department of Computer Science, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Gen Zhou
- Department of Computer Science, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Pingzhao Hu
- Department of Computer Science, University of Western Ontario, London, ON N6A 3K7, Canada
- Department of Biochemistry, University of Western Ontario, London, ON N6A 3K7, Canada
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Prodger JL, Capoferri AA, Yu K, Lai J, Reynolds SJ, Kasule J, Kityamuweesi T, Buule P, Serwadda D, Kwon KJ, Schlusser K, Martens C, Scully E, Choi YH, Redd AD, Quinn TC. Reduced HIV-1 latent reservoir outgrowth and distinct immune correlates among women in Rakai, Uganda. JCI Insight 2020; 5:139287. [PMID: 32544096 DOI: 10.1172/jci.insight.139287] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/03/2020] [Indexed: 01/22/2023] Open
Abstract
HIV-1 infection remains incurable owing to the persistence of a viral reservoir that harbors integrated provirus within host cellular DNA. Increasing evidence links sex-based differences in HIV-1 immune responses and pathogenesis; however, little is known about differences in HIV-1 infection persistence. Here, we quantified persistent HIV-1 infection in 90 adults on suppressive antiretroviral therapy in Rakai, Uganda (57 female patients). Total HIV-1 DNA was quantified by PCR, and replication-competent provirus by quantitative viral outgrowth assay (QVOA). Immune phenotyping of T cell subsets and plasma biomarkers was also performed. We found that whereas both sexes had similar total HIV DNA levels, female patients had significantly fewer resting CD4+ T cells harboring replication-competent virus, as measured by viral outgrowth in the QVOA. Factors associated with viral outgrowth differed by sex; notably, frequency of programmed cell death 1 (PD1+) CD4+ T cells correlated with reservoir size in male but not female patients. The sex-based differences in HIV-1 persistence observed in this cohort warrant additional research, especially given the widespread use of the QVOA to assess reservoir size and current explorations of PD1 agonists in cure protocols. Efforts should be made to power future cure studies to assess outcomes in both male and female patients.
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Affiliation(s)
- Jessica L Prodger
- Department of Microbiology and Immunology and.,Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adam A Capoferri
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Katherine Yu
- Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Jun Lai
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Steven J Reynolds
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.,Rakai Health Sciences Program, Kalisizo, Uganda
| | | | | | - Paul Buule
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - David Serwadda
- Rakai Health Sciences Program, Kalisizo, Uganda.,Makerere University, Kampala, Uganda
| | - Kyungyoon J Kwon
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Katherine Schlusser
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Craig Martens
- Genomic Unit, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, USA
| | - Eileen Scully
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yun-Hee Choi
- Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Andrew D Redd
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Thomas C Quinn
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
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Impact of Suboptimal APOBEC3G Neutralization on the Emergence of HIV Drug Resistance in Humanized Mice. J Virol 2020; 94:JVI.01543-19. [PMID: 31801862 DOI: 10.1128/jvi.01543-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/20/2019] [Indexed: 01/05/2023] Open
Abstract
HIV diversification facilitates immune escape and complicates antiretroviral therapy. In this study, we take advantage of a humanized-mouse model to probe the contribution of APOBEC3 mutagenesis to viral evolution. Humanized mice were infected with isogenic HIV molecular clones (HIV-WT, HIV-45G, and HIV-ΔSLQ) that differ in their abilities to counteract APOBEC3G (A3G). Infected mice remained naive or were treated with the reverse transcriptase (RT) inhibitor lamivudine (3TC). Viremia, emergence of drug-resistant variants, and quasispecies diversification in the plasma compartment were determined throughout infection. While both HIV-WT and HIV-45G achieved robust infection, over time, HIV-45G replication was significantly reduced compared to that of HIV-WT in the absence of 3TC treatment. In contrast, treatment responses differed significantly between HIV-45G- and HIV-WT-infected mice. Antiretroviral treatment failed in 91% of HIV-45G-infected mice, while only 36% of HIV-WT-infected mice displayed a similar negative outcome. Emergence of 3TC-resistant variants and nucleotide diversity were determined by analyzing 155,462 single HIV reverse transcriptase gene (RT) and 6,985 vif sequences from 33 mice. Prior to treatment, variants with genotypic 3TC resistance (RT-M184I/V) were detected at low levels in over a third of all the animals. Upon treatment, the composition of the plasma quasispecies rapidly changed, leading to a majority of circulating viral variants encoding RT-184I. Interestingly, increased viral diversity prior to treatment initiation correlated with higher plasma viremia in HIV-45G-infected animals, but not in HIV-WT-infected animals. Taken together, HIV variants with suboptimal anti-A3G activity were attenuated in the absence of selection but displayed a fitness advantage in the presence of antiretroviral treatment.IMPORTANCE Both viral (e.g., RT) and host (e.g., A3G) factors can contribute to HIV sequence diversity. This study shows that suboptimal anti-A3G activity shapes viral fitness and drives viral evolution in the plasma compartment in humanized mice.
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Mohammadzadeh N, Follack TB, Love RP, Stewart K, Sanche S, Chelico L. Polymorphisms of the cytidine deaminase APOBEC3F have different HIV-1 restriction efficiencies. Virology 2018; 527:21-31. [PMID: 30448640 DOI: 10.1016/j.virol.2018.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/03/2018] [Accepted: 11/04/2018] [Indexed: 12/27/2022]
Abstract
The APOBEC3 enzyme family are host restriction factors that induce mutagenesis of HIV-1 proviral genomes through the deamination of cytosine to form uracil in nascent single-stranded (-)DNA. HIV-1 suppresses APOBEC3 activity through the HIV-1 protein Vif that induces APOBEC3 degradation. Here we compared two common polymorphisms of APOBEC3F. We found that although both polymorphisms have HIV-1 restriction activity, APOBEC3F 108 A/231V can restrict HIV-1 ΔVif up to 4-fold more than APOBEC3F 108 S/231I and is partially protected from Vif-mediated degradation. This resulted from higher levels of steady state expression of APOBEC3F 108 A/231 V. Individuals are commonly heterozygous for the APOBEC3F polymorphisms and these polymorphisms formed in cells, independent of RNA, hetero-oligomers between each other and with APOBEC3G. Hetero-oligomerization with APOBEC3F 108 A/231V resulted in partial stabilization of APOBEC3F 108 S/231I and APOBEC3G in the presence of Vif. These data demonstrate functional outcomes of APOBEC3 polymorphisms and hetero-oligomerization that affect HIV-1 restriction.
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Affiliation(s)
- Nazanin Mohammadzadeh
- University of Saskatchewan, Biochemistry, Microbiology, and Immunology, College of Medicine, Saskatoon, Saskatchewan, Canada
| | - Tyson B Follack
- University of Saskatchewan, Biochemistry, Microbiology, and Immunology, College of Medicine, Saskatoon, Saskatchewan, Canada
| | - Robin P Love
- University of Saskatchewan, Biochemistry, Microbiology, and Immunology, College of Medicine, Saskatoon, Saskatchewan, Canada
| | - Kris Stewart
- University of Saskatchewan, Department of Medicine, College of Medicine, Saskatoon, Saskatchewan Canada; Saskatchewan Infectious Disease Care Network, Saskatoon, Saskatchewan, Canada; Saskatchewan HIV/AIDS Research Endeavour, Saskatoon, Saskatchewan, Canada
| | - Stephen Sanche
- University of Saskatchewan, Department of Medicine, College of Medicine, Saskatoon, Saskatchewan Canada; Saskatchewan HIV/AIDS Research Endeavour, Saskatoon, Saskatchewan, Canada
| | - Linda Chelico
- University of Saskatchewan, Biochemistry, Microbiology, and Immunology, College of Medicine, Saskatoon, Saskatchewan, Canada; Saskatchewan HIV/AIDS Research Endeavour, Saskatoon, Saskatchewan, Canada.
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Pace of Coreceptor Tropism Switch in HIV-1-Infected Individuals after Recent Infection. J Virol 2017; 91:JVI.00793-17. [PMID: 28659473 DOI: 10.1128/jvi.00793-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 06/08/2017] [Indexed: 11/20/2022] Open
Abstract
HIV-1 entry into target cells influences several aspects of HIV-1 pathogenesis, including viral tropism, HIV-1 transmission and disease progression, and response to entry inhibitors. The evolution from CCR5- to CXCR4-using strains in a given human host is still unpredictable. Here we analyzed timing and predictors for coreceptor evolution among recently HIV-1-infected individuals. Proviral DNA was longitudinally evaluated in 66 individuals using Geno2pheno[coreceptor] Demographics, viral load, CD4+ and CD8+ T cell counts, CCR5Δ32 polymorphisms, GB virus C (GBV-C) coinfection, and HLA profiles were also evaluated. Ultradeep sequencing was performed on initial samples from 11 selected individuals. A tropism switch from CCR5- to CXCR4-using strains was identified in 9/49 (18.4%) individuals. Only a low baseline false-positive rate (FPR) was found to be a significant tropism switch predictor. No minor CXCR4-using variants were identified in initial samples of 4 of 5 R5/non-R5 switchers. Logistic regression analysis showed that patients with an FPR of >40.6% at baseline presented a stable FPR over time whereas lower FPRs tend to progressively decay, leading to emergence of CXCR4-using strains, with a mean evolution time of 27.29 months (range, 8.90 to 64.62). An FPR threshold above 40.6% determined by logistic regression analysis may make it unnecessary to further determine tropism for prediction of disease progression related to emergence of X4 strains or use of CCR5 antagonists. The detection of variants with intermediate FPRs and progressive FPR decay over time not only strengthens the power of Geno2pheno in predicting HIV tropism but also indirectly confirms a continuous evolution from earlier R5 variants toward CXCR4-using strains.IMPORTANCE The introduction of CCR5 antagonists in the antiretroviral arsenal has sparked interest in coreceptors utilized by HIV-1. Despite concentrated efforts, viral and human host features predicting tropism switch are still poorly understood. Limited longitudinal data are available to assess the influence that these factors have on predicting tropism switch and disease progression. The present study describes longitudinal tropism evolution in a group of recently HIV-infected individuals to determine the prevalence and potential correlates of tropism switch. We demonstrated here that a low baseline FPR determined by the Geno2pheno[coreceptor] algorithm can predict tropism evolution from CCR5 to CXCR4 coreceptor use.
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