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Winslow DL. Is early initiation of antiretroviral therapy important? AIDS 2024; 38:1263-1264. [PMID: 38814713 DOI: 10.1097/qad.0000000000003898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Affiliation(s)
- Dean L Winslow
- Stanford University School of Medicine, Stanford, CA, USA
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Romero EV, Feder AF. Elevated HIV Viral Load is Associated with Higher Recombination Rate In Vivo. Mol Biol Evol 2024; 41:msad260. [PMID: 38197289 PMCID: PMC10777272 DOI: 10.1093/molbev/msad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 01/11/2024] Open
Abstract
HIV's exceptionally high recombination rate drives its intrahost diversification, enabling immune escape and multidrug resistance within people living with HIV. While we know that HIV's recombination rate varies by genomic position, we have little understanding of how recombination varies throughout infection or between individuals as a function of the rate of cellular coinfection. We hypothesize that denser intrahost populations may have higher rates of coinfection and therefore recombination. To test this hypothesis, we develop a new approach (recombination analysis via time series linkage decay or RATS-LD) to quantify recombination using autocorrelation of linkage between mutations across time points. We validate RATS-LD on simulated data under short read sequencing conditions and then apply it to longitudinal, high-throughput intrahost viral sequencing data, stratifying populations by viral load (a proxy for density). Among sampled viral populations with the lowest viral loads (<26,800 copies/mL), we estimate a recombination rate of 1.5×10-5 events/bp/generation (95% CI: 7×10-6 to 2.9×10-5), similar to existing estimates. However, among samples with the highest viral loads (>82,000 copies/mL), our median estimate is approximately 6 times higher. In addition to co-varying across individuals, we also find that recombination rate and viral load are associated within single individuals across different time points. Our findings suggest that rather than acting as a constant, uniform force, recombination can vary dynamically and drastically across intrahost viral populations and within them over time. More broadly, we hypothesize that this phenomenon may affect other facultatively asexual populations where spatial co-localization varies.
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Affiliation(s)
- Elena V Romero
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Alison F Feder
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Herbold Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
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Romero EV, Feder AF. Elevated HIV viral load is associated with higher recombination rate in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539643. [PMID: 37873119 PMCID: PMC10592651 DOI: 10.1101/2023.05.05.539643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
HIV's exceptionally high recombination rate drives its intra-host diversification, enabling immune escape and multi-drug resistance within people living with HIV. While we know that HIV's recombination rate varies by genomic position, we have little understanding of how recombination varies throughout infection or between individuals as a function of the rate of cellular coinfection. We hypothesize that denser intra-host populations may have higher rates of coinfection and therefore recombination. To test this hypothesis, we develop a new approach (Recombination Analysis via Time Series Linkage Decay, or RATS-LD) to quantify recombination using autocorrelation of linkage between mutations across time points. We validate RATS-LD on simulated data under short read sequencing conditions and then apply it to longitudinal, high-throughput intra-host viral sequencing data, stratifying populations by viral load (a proxy for density). Among sampled viral populations with the lowest viral loads (< 26,800 copies/mL), we estimate a recombination rate of 1.5 × 10-5 events/bp/generation (95% CI: 7 × 10-6 - 2.9 × 10-5), similar to existing estimates. However, among samples with the highest viral loads (> 82,000 copies/mL), our median estimate is approximately 6 times higher. In addition to co-varying across individuals, we also find that recombination rate and viral load are associated within single individuals across different time points. Our findings suggest that rather than acting as a constant, uniform force, recombination can vary dynamically and drastically across intra-host viral populations and within them over time. More broadly, we hypothesize that this phenomenon may affect other facultatively asexual populations where spatial co-localization varies.
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Affiliation(s)
- Elena V. Romero
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Alison F. Feder
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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Maddox V, Vallely P, Brailsford SR, Harvala H. Virological safety of the UK blood supply in the era of individual risk assessments and HIV PrEP. Transfus Med 2023; 33:372-378. [PMID: 37668150 DOI: 10.1111/tme.12993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/06/2023]
Abstract
A more individualised donor selection policy was implemented in the UK in 2021, which replaced the previous 3-month deferral for men who have sex with men (MSM). Other blood services have a variety of policies in place to ensure the virological safety of blood components, ranging from an indefinite ban on MSM, to a defined period of exclusion, or to an individualised risk assessment that is not based on gender or sexual orientation. Justification of these policies should be based on scientific evidence including assessment of lengths of virological window periods, infectious disease epidemiology within donor populations and donation screening assay sensitivities. Developments in molecular technology and assays which can detect both antibodies and antigens in the very early stages of infection have significantly reduced the risk in most developed countries. However, the increasing usage of pre-exposure prophylaxis (PrEP) to prevent acquisition of HIV infection after possible high-risk sexual contact within the UK blood donor population has been recently noted. It has brought with it new diagnostic challenges within blood screening, notably possible non-detection of HIV RNA and serological markers following PrEP use despite potential infectivity. The use of other testing strategies such as detection of HIV DNA and screening for non-declared PrEP usage should be investigated further.
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Affiliation(s)
| | - Pamela Vallely
- Division of Evolution, Infection and Genomics Science, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | - Heli Harvala
- Microbiology Services, NHS Blood and Transplant, London, UK
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Universal Repeat Screening for Human Immunodeficiency Virus in the Third Trimester of Pregnancy: A Cost-Effectiveness Analysis. Obstet Gynecol 2023; 141:535-543. [PMID: 36800852 DOI: 10.1097/aog.0000000000005086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/01/2022] [Indexed: 02/18/2023]
Abstract
OBJECTIVE To assess the cost effectiveness of universal repeat screening for human immunodeficiency virus (HIV) infection in the third trimester of pregnancy. METHODS A decision-analytic model was constructed to compare two strategies: screening for HIV infection in the first trimester alone compared with the addition of repeat screening in the third trimester. Probabilities, costs, and utilities were derived from the literature and varied in sensitivity analyses. The assumed incidence of HIV infection in pregnancy was 0.0145% or 14.5 per 100,000. Outcomes included costs (in 2022 U.S. dollars), maternal and neonatal quality-adjusted life-years (QALYs), and cases of neonatal HIV infection. Our theoretical cohort contained 3.8 million pregnant individuals, the approximate number of births per year in the United States. The willingness-to-pay threshold was set at $100,000/QALY. We performed univariable and multivariable sensitivity analyses to determine inputs that most influenced the model. RESULTS Universal third-trimester screening prevented 133 cases of neonatal HIV infection in this theoretical cohort. Universal third-trimester screening led to an increased cost of $17.54 million and 2,732 increased QALYs, with an incremental cost-effectiveness ratio of $6,418.56 per QALY, less than the willingness-to-pay threshold. In a univariate sensitivity analysis, third-trimester screening remained cost effective with variation of HIV incidence in pregnancy to as low as 0.0052%. CONCLUSION In a theoretical U.S.-based cohort of pregnant individuals, universal repeat screening for HIV infection in the third trimester was found to be cost effective and to reduce vertical transmission of HIV. These results merit consideration of a broader HIV-screening program in the third trimester.
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Validation of Promoters and Codon Optimization on CRISPR/Cas9-Engineered Jurkat Cells Stably Expressing αRep4E3 for Interfering with HIV-1 Replication. Int J Mol Sci 2022; 23:ijms232315049. [PMID: 36499376 PMCID: PMC9738563 DOI: 10.3390/ijms232315049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/15/2022] [Accepted: 11/27/2022] [Indexed: 12/05/2022] Open
Abstract
Persistent and efficient therapeutic protein expression in the specific target cell is a significant concern in gene therapy. The controllable integration site, suitable promoter, and proper codon usage influence the effectiveness of the therapeutic outcome. Previously, we developed a non-immunoglobulin scaffold, alpha repeat protein (αRep4E3), as an HIV-1 RNA packaging interference system in SupT1 cells using the lentiviral gene transfer. Although the success of anti-HIV-1 activity was evidenced, the integration site is uncontrollable and may not be practical for clinical translation. In this study, we use the CRISPR/Cas9 gene editing technology to precisely knock-in αRep4E3 genes into the adeno-associated virus integration site 1 (AAVS1) safe harbor locus of the target cells. We compare the αRep4E3 expression under the regulation of three different promoters, including cytomegalovirus (CMV), human elongation factor-1 alpha (EF1α), and ubiquitin C (UbC) promoters with and without codon optimization in HEK293T cells. The results demonstrated that the EF1α promoter with codon-optimized αRep4E3mCherry showed higher protein expression than other promoters with non-optimized codons. We then performed a proof-of-concept study by knocking in the αRep4E3mCherry gene at the AAVS1 locus of the Jurkat cells. The results showed that the αRep4E3mCherry-expressing Jurkat cells exhibited anti-HIV-1 activities against HIV-1NL4-3 strain as evidenced by decreased capsid (p24) protein levels and viral genome copies as compared to the untransfected Jurkat control cells. Altogether, our study demonstrates that the αRep4E3 could interfere with the viral RNA packaging and suggests that the αRep4E3 scaffold protein could be a promising anti-viral molecule that offers a functional cure for people living with HIV-1.
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Orser L, O'Byrne P, Holmes D. AIDS cases in Ottawa: A review of simultaneous HIV and AIDS diagnoses. Public Health Nurs 2022; 39:909-916. [PMID: 35305282 PMCID: PMC9544046 DOI: 10.1111/phn.13065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVES In Canada, HIV diagnoses continue unabated, with many of these cases being identified at a late stage of infection. While current public health surveillance data does not capture timing of diagnoses, locally, we identified a number of patients concurrently diagnosed with AIDS and HIV. DESIGN To understand the key characteristics, presenting symptoms, and risk factors associated with an AIDS diagnosis, we undertook a prospective chart review of HIV and AIDS diagnoses in Ottawa, Canada. SAMPLE Sixty seven charts of persons diagnosed with HIV and AIDS between 2015 and 2021 were reviewed. MEASUREMENTS Data were analyzed using descriptive statistics. RESULTS Results show some inconsistencies regarding HIV risk factors identified in published literature compared to those for persons diagnosed with AIDS in this study. Namely, patients in this review were more likely to be male, Black (from HIV-endemic regions), and heterosexual, and were diagnosed at critical stage in infection (total average CD4+ count of 92.9 cells/mm3 ) with 44.8% of patients concurrently diagnosed with one or more AIDS-related opportunistic infections. CONCLUSIONS The findings can be applied to strengthen HIV screening efforts in primary care settings, particularly among patients who present with persistent symptoms or illnesses related to chronic HIV infection. Additional considerations should be made for public health nurses to provide counseling and linkage to HIV testing/prevention services for patients at the time of an STI or Tuberculosis diagnosis and to increase AIDS-specific data collection.
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Affiliation(s)
- Lauren Orser
- University of OttawaSchool of NursingOttawaCanada,Ottawa Public HealthSexual Health ClinicOttawaCanada
| | - Patrick O'Byrne
- University of OttawaSchool of NursingOttawaCanada,Ottawa Public HealthSexual Health ClinicOttawaCanada
| | - Dave Holmes
- University of OttawaSchool of NursingOttawaCanada
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Gilbertson A, Tucker JD, Dubé K, Dijkstra M, Rennie S. Ethical considerations for HIV remission clinical research involving participants diagnosed during acute HIV infection. BMC Med Ethics 2021; 22:169. [PMID: 34961509 PMCID: PMC8714439 DOI: 10.1186/s12910-021-00716-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/20/2021] [Indexed: 11/16/2022] Open
Abstract
HIV remission clinical researchers are increasingly seeking study participants who are diagnosed and treated during acute HIV infection—the brief period between infection and the point when the body creates detectable HIV antibodies. This earliest stage of infection is often marked by flu-like illness and may be an especially tumultuous period of confusion, guilt, anger, and uncertainty. Such experiences may present added ethical challenges for HIV research recruitment, participation, and retention. The purpose of this paper is to identify potential ethical challenges associated with involving acutely diagnosed people living with HIV in remission research and considerations for how to mitigate them. We identify three domains of potential ethical concern for clinicians, researchers, and ethics committee members to consider: 1) Recruitment and informed consent; (2) Transmission risks and partner protection; and (3) Ancillary and continuing care. We discuss each of these domains with the aim of inspiring further work to advance the ethical conduct of HIV remission research. For example, experiences of confusion and uncertainty regarding illness and diagnosis during acute HIV infection may complicate informed consent procedures in studies that seek to recruit directly after diagnosis. To address this, it may be appropriate to use staged re-consent procedures or comprehension assessment. Responsible conduct of research requires a broad understanding of acute HIV infection that encompasses its biomedical, psychological, social, and behavioral dimensions. We argue that the lived experience of acute HIV infection may introduce ethical concerns that researchers and reviewers should address during study design and ethical approval.
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Affiliation(s)
- Adam Gilbertson
- Pacific Institute for Research and Evaluation, Chapel Hill Center, 101 Conner Drive, Suite 200, Chapel Hill, NC, 27514-7038, USA. .,UNC Center for Bioethics, Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Joseph D Tucker
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WCE1, UK.,UNC Project-China, 2 Lujing Road, Guangzhou, China
| | - Karine Dubé
- Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Maartje Dijkstra
- Department of Infectious Diseases, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, The Netherlands
| | - Stuart Rennie
- UNC Center for Bioethics, Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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Tchiakpe E, Keke RK, Vidal N, Bachabi M, Gangbo FA, Diop‑Ndiaye H, Toure‑Kane C, Yessoufou A. Contribution of the classical polymerase chain reaction in the diagnosis of a HIV-1 infected patient in Benin: a case report. AIDS Res Ther 2021; 18:18. [PMID: 33882959 PMCID: PMC8059016 DOI: 10.1186/s12981-021-00342-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/08/2021] [Indexed: 11/26/2022] Open
Abstract
Background First ambitious target by 2020 of UNAIDS is that 90% of people living with HIV know their HIV status. In people older than 18 months of age, serological confirmation test is recommended to confirm HIV infection. Case presentation Here we report the case of a patient tested positive with HIV-1, ELISA, Murex® Ag⁄Ab Combination assay (OD450 = 0.802 and cutoff-OD = 0.279) and negative by using FIRST RESPONSE HIV1-2.O CARD TEST (version 2.0) RAPID HIV CARD TEST. Viral load performed with Cobas® TaqMan® 96/Cobas® Ampliprep® was 6.49log10. The virus could be sequenced in partial gag and pol genes and belonged to CRF02_AG clade. Conclusion Conventional PCR is a complementary method for the diagnosis of inconclusive HIV-1 serologies by antibodies.
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Ali Z, Waseem S, Anis RA, Anees M. Assessment of cell free mitochondrial DNA as a biomarker of disease severity in different viral infections. Pak J Med Sci 2020; 36:860-866. [PMID: 32704253 PMCID: PMC7372646 DOI: 10.12669/pjms.36.5.2476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Objective: Cell Free mitochondrial DNA (CF mt-DNA) has emerged as a novel biomarker to investigate disease pathophysiology of different infections. The present study was designed to elucidate the association between CF mt-DNA, IL-6 and viral load in HIV, HBV and HCV infections and predict its role as a potential biomarker to assess the disease severity in viral infections. Methods: Total 120 blood samples were collected from January 2018 to December 2018 of HIV, HBV and HCV patients and healthy controls (30 samples in each group). DNA and RNA were extracted from the serum to determine the levels of CF mt-DNA and viral load, respectively. IL-6 from the serum of infected individuals was quantified with ELISA. Results: HCV patients showed the highest levels of CF mt-DNA, IL-6 and viral load, followed by HBV and HIV. Significant correlation was found between CF mt-DNA and IL-6 among the HBV patients (p=0.017). However, no significant correlation of CF mt-DNA was observed with IL-6 in HIV and HCV or with the viral load in any of the three infections. Conclusion: Elevated CF mt-DNA indicates its role in severity of viral infections. Independence of CF mt-DNA expression from viral load and IL-6 in case of HIV and HCV suggests involvement of other inflammatory pathways regulating CF mt-DNA elevation.
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Affiliation(s)
- Zain Ali
- Zain Ali, MPhil. Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shahid Waseem
- Shahid Waseem, Ph.D. Alpha Genomics Private Limited, Islamabad, Pakistan
| | - Riffat Aysha Anis
- Riffat Aysha Anis, Ph.D. Institute of Diet and Nutritional Sciences, The University of Lahore, Islamabad Campus, Pakistan
| | - Mariam Anees
- Mariam Anees, Ph.D. Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
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In vitro replicative fitness of early Transmitted founder HIV-1 variants and sensitivity to Interferon alpha. Sci Rep 2020; 10:2747. [PMID: 32066770 PMCID: PMC7026412 DOI: 10.1038/s41598-020-59596-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 01/14/2020] [Indexed: 01/10/2023] Open
Abstract
Type I interferons, particularly interferon-alpha (IFN-α), play a vital role in the host's anti-viral defenses by interfering with viral replication. However, the virus rapidly evolves to exploit the IFN-α response for its replication, spread, and pathogenic function. In this study, we attempted to determine IFN-α susceptibility and productivity of infectious transmitted/founder (TF) (n = 8) and non-transmitted (NT) viruses (n = 8) derived from HIV-1 infected infants. Independent experiments were carried out to determine IFN-α resistance, replication fitness, and viral productivity in CD4+ T cells over a short period. In vitro studies showed that TF viruses were resistant to IFN-α during the very near moment of transmission, but in the subsequent time points, they became susceptible to IFN-α. We did not observe much difference in replicative fitness of the TF viruses in cultures treated with and without IFN-α, but the difference was significant in the case of NT viruses obtained from the same individual. Despite increased susceptibility to IFN-α, NT viruses produced more viral particles than TF viruses. Similar results were also obtained in cultures treated with maraviroc (MVC). The study identified unique characteristics of TF viruses thus prompting further investigation into virus-host interaction occurring during the early stages of HIV infection.
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