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Bouman JA, Venner CM, Walker C, Arts EJ, Regoes RR. Per-pathogen virulence of HIV-1 subtypes A, C and D. Proc Biol Sci 2023; 290:20222572. [PMID: 37161335 PMCID: PMC10170192 DOI: 10.1098/rspb.2022.2572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
HIV-1 subtypes differ in their clinical manifestations and the speed in which they spread. In particular, the frequency of subtype C is increasing relative to subtypes A and D. We investigate whether HIV-1 subtypes A, C and D differ in their per-pathogen virulence and to what extend this explains the difference in spread between these subtypes. We use data from the hormonal contraception and HIV-1 genital shedding and disease progression among women with primary HIV infection study. For each study participant, we determine the set-point viral load value, CD4+ T cell level after primary infection and CD4+ T cell decline. Based on both the CD4+ T cell count after primary infection and CD4+ T cell decline, we estimate the time until AIDS. We then obtain our newly introduced measure of virulence as the inverse of the estimated time until AIDS. After fitting a model to the measured virulence and set-point viral load values, we tested if this relation varies per subtype. We found that subtype C has a significantly higher per-pathogen virulence than subtype A. Based on an evolutionary model, we then hypothesize that differences in the primary length of infection period cause the observed variation in the speed of spread of the subtypes.
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Affiliation(s)
- Judith A Bouman
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Colin M Venner
- Department of Microbiology and Immunology, Western University, London, Ontario N6A 3K7, Canada
| | - Courtney Walker
- Department of Microbiology and Immunology, Western University, London, Ontario N6A 3K7, Canada
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University, London, Ontario N6A 3K7, Canada
| | - Roland R Regoes
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
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Morrison CS, Hofmeyr GJ, Thomas KK, Rees H, Philip N, Palanee-Phillips T, Nanda K, Nair G, Onono M, Mastro TD, Lind M, Heffron R, Edward V, Deese J, Beksinska M, Beesham I, Stringer JS, Baeten JM, Ahmed K, Kiarie J, Mugo NR, Justman J, Nhlabatsi Z, Bukusi EA, Louw C, Bekker LG, Smit J, Singata-Madliki M, Sibiya S, Kasaro MP, Baron D, Donnell D, Gichangi PB, Heller KB, Mbandazayo N, Pleaner M, Scoville CW, Shears K, Steyn PS, Taylor D, Welch JD. Effects of Depot Medroxyprogesterone Acetate, Copper Intrauterine Devices, and Levonorgestrel Implants on Early HIV Disease Progression. AIDS Res Hum Retroviruses 2020; 36:632-640. [PMID: 32394723 PMCID: PMC7414801 DOI: 10.1089/aid.2020.0015] [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] [Indexed: 11/12/2022] Open
Abstract
Limited data exist on the effects of contraceptives on HIV disease progression. We studied the association between intramuscular injectable depot medroxyprogesterone acetate (DMPA-IM), the copper intrauterine device (IUD), and the levonorgestrel (LNG) implant on markers of HIV disease progression at the time of HIV detection and 3 months postdetection and time from detection to CD4 count <350 cells/mm3. Among women initiating antiretroviral therapy (ART), we studied the effect of contraceptive group on time from ART initiation to viral load (VL) <40 copies/mL. We included women 16-35 years randomized to DMPA-IM, copper IUD, or LNG implant with incident HIV infection during the Evidence for Contraceptive Options and HIV Outcomes (ECHO) trial (n = 382). We analyzed HIV VL and CD4 cell count according to participants' randomized method and also conducted a "continuous use" analysis that excluded follow-up time after method discontinuation. We used adjusted linear models to compare mean VL and CD4 cell levels by contraceptive group up to the time of ART initiation. We compared time from HIV detection to CD4 count <350 cells/mm3 and, following ART initiation, time to viral suppression (VL <40 copies/mL) using Cox proportional hazards models. At HIV detection, women allocated to DMPA-IM had lower VL relative to copper IUD (-0.28 log10 copies/mL; 95% confidence interval [CI]: -0.55 to -0.01) and LNG implant (-0.27, CI: -0.55 to 0.02) and higher mean CD4 than copper IUD users by 66 cells/mm3 (CI: 11-121). In continuous use analyses women allocated to DMPA-IM progressed to CD4 < 350 cells/mm3 slower than copper IUD users (hazard ratio [HR] = 0.6, CI: 0.3-1.1), whereas copper IUD users progressed faster than LNG implant users (HR = 1.8, CI: 1.0-3.3). Time to viral suppression was faster for DMPA-IM than copper IUD (HR = 1.5, CI: 1.0-2.3) and LNG implant 1.4 (CI: 0.9-2.2) users. We found no evidence of more rapid early HIV disease progression among women using DMPA-IM than among women using copper IUD or LNG implant. Our finding of more rapid progression among copper IUD compared with DMPA-IM users should be interpreted cautiously.
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Affiliation(s)
| | - G. Justus Hofmeyr
- Effective Care Research Unit, Department of Obstetrics and Gynaecology, University of Witwatersrand/Fort Hare/Walter Sisulu, East London, South Africa
- Department of Obstetrics and Gynaecology, University of Botswana, Gaborone, Botswana
| | | | - Helen Rees
- Wits Reproductive Health and HIV Institute (Wits RHI), University of Witswatersrand, Johannesburg, South Africa
| | - Neena Philip
- Mailman School of Public Health, ICAP at Columbia University, New York, USA
| | - Thesla Palanee-Phillips
- Wits Reproductive Health and HIV Institute (Wits RHI), University of Witswatersrand, Johannesburg, South Africa
| | | | | | | | | | - Maggie Lind
- Department of Global Health, University of Washington, Seattle, USA
| | - Renee Heffron
- Department of Global Health, University of Washington, Seattle, USA
| | - Vinodh Edward
- The Aurum Institute, Johannesburg, South Africa
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
- Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Jen Deese
- FHI 360, Durham, North Carolina, USA
| | - Mags Beksinska
- MatCH Research Unit (MRU), Faculty of Health Sciences, Department of Obstetrics and Gynecology, University of the Witwatersrand, Durban, South Africa
| | - Ivana Beesham
- MatCH Research Unit (MRU), Faculty of Health Sciences, Department of Obstetrics and Gynecology, University of the Witwatersrand, Durban, South Africa
| | - Jeffrey S.A. Stringer
- Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Jared M. Baeten
- Department of Global Health, University of Washington, Seattle, USA
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Venner CM, Nankya I, Kyeyune F, Demers K, Kwok C, Chen PL, Rwambuya S, Munjoma M, Chipato T, Byamugisha J, Van Der Pol B, Mugyenyi P, Salata RA, Morrison CS, Arts EJ. Infecting HIV-1 Subtype Predicts Disease Progression in Women of Sub-Saharan Africa. EBioMedicine 2016; 13:305-314. [PMID: 27751765 PMCID: PMC5264310 DOI: 10.1016/j.ebiom.2016.10.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/06/2016] [Accepted: 10/09/2016] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION Long-term natural history cohorts of HIV-1 in the absence of treatment provide the best measure of virulence by different viral subtypes. METHODS Newly HIV infected Ugandan and Zimbabwean women (N=303) were recruited and monitored for clinical, social, behavioral, immunological and viral parameters for 3 to 9.5years. RESULTS Ugandan and Zimbabwean women infected with HIV-1 subtype C had 2.5-fold slower rates of CD4 T-cell declines and higher frequencies of long-term non-progression than those infected with subtype A or D (GEE model, P<0.001), a difference not associated with any other clinical parameters. Relative replicative fitness and entry efficiency of HIV-1 variants directly correlated with virulence in the patients, subtype D>A>C (P<0.001, ANOVA). DISCUSSION HIV-1 subtype C was less virulent than either A or D in humans; the latter being the most virulent. Longer periods of asymptomatic HIV-1 subtype C could explain the continued expansion and dominance of subtype C in the global epidemic.
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Affiliation(s)
- Colin M Venner
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Immaculate Nankya
- Joint Clinical Research Centre, Kampala, Uganda; Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | | | - Korey Demers
- Joint Clinical Research Centre, Kampala, Uganda; Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Cynthia Kwok
- Family Health International 360, Durham, NC, USA
| | | | - Sandra Rwambuya
- Joint Clinical Research Centre, Kampala, Uganda; Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Marshall Munjoma
- Department of Obstetrics and Gynaecology, University of Zimbabwe, Harare, Zimbabwe
| | - Tsungai Chipato
- Department of Obstetrics and Gynaecology, University of Zimbabwe, Harare, Zimbabwe
| | | | - Barbara Van Der Pol
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, USA
| | | | - Robert A Salata
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | | | - Eric J Arts
- Department of Microbiology and Immunology, Western University, London, ON, Canada; Joint Clinical Research Centre, Kampala, Uganda; Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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Impact of Age and Sex on CD4+ Cell Count Trajectories following Treatment Initiation: An Analysis of the Tanzanian HIV Treatment Database. PLoS One 2016; 11:e0164148. [PMID: 27716818 PMCID: PMC5055355 DOI: 10.1371/journal.pone.0164148] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 09/20/2016] [Indexed: 12/28/2022] Open
Abstract
Objective New guidelines recommend that all HIV-infected individuals initiate antiretroviral treatment (ART) immediately following diagnosis. This study describes how immune reconstitution varies by gender and age to help identify poorly reconstituting subgroups and inform targeted testing initiatives. Design Longitudinal data from the outpatient monitoring system of the National AIDS Control Program in Tanzania. Methods An asymptotic nonlinear mixed effects model was fit to post-treatment CD4+ cell count trajectories, allowing for fixed effects of age and sex, and an age by sex interaction. Results Across 220,544 clinic visits from 32,069 HIV-infected patients, age- and sex-specific average CD4+ cell count at ART initiation ranged from 83–136 cells/mm3, long term asymptotic CD4+ cell count ranged from 301–389 cells/mm3, and time to half of maximal CD4+ reconstitution ranged from 3.57–5.68 months. CD4+ cell count at ART initiation and asymptotic CD4+ cell count were 1.28 (95% CI: 1.18–1.40) and 1.25 (95% CI: 1.20–1.31) times higher, respectively, for females compared to males in the youngest age group (19–29 years). Older patients started treatment at higher CD4+ counts but experienced slower CD4+ recovery than younger adults. Treatment initiation at greater CD4+ cell counts was correlated with greater asymptotic CD4+ cell counts within all sex and age groups. Conclusion Older adults should initiate care early in disease progression because total immune reconstitution potential and rate of reconstitution appears to decrease with age. Targeted HIV testing and care linkage remains crucial for patient populations who tend to initiate treatment at lower CD4+ cell counts, including males and younger adults.
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Population-based CD4 counts in a rural area in South Africa with high HIV prevalence and high antiretroviral treatment coverage. PLoS One 2013; 8:e70126. [PMID: 23894603 PMCID: PMC3720940 DOI: 10.1371/journal.pone.0070126] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 06/14/2013] [Indexed: 12/16/2022] Open
Abstract
Background Little is known about the variability of CD4 counts in the general population of sub-Saharan Africa countries affected by the HIV epidemic. We investigated factors associated with CD4 counts in a rural area in South Africa with high HIV prevalence and high antiretroviral treatment (ART) coverage. Methods CD4 counts, health status, body mass index (BMI), demographic characteristics and HIV status were assessed in 4990 adult resident participants of a demographic surveillance in rural KwaZulu-Natal in South Africa; antiretroviral treatment duration was obtained from a linked clinical database. Multivariable regression analysis, overall and stratified by HIV status, was performed with CD4 count levels as outcome. Results Median CD4 counts were significantly higher in women than in men overall (714 vs. 630 cells/µl, p<0.0001), both in HIV-uninfected (833 vs. 683 cells/µl, p<0.0001) and HIV-infected adults (384.5 vs. 333 cells/µl, p<0.0001). In multivariable regression analysis, women had 19.4% (95% confidence interval (CI) 16.1–22.9) higher CD4 counts than men, controlling for age, HIV status, urban/rural residence, household wealth, education, BMI, self-reported tuberculosis, high blood pressure, other chronic illnesses and sample processing delay. At ART initiation, HIV-infected adults had 21.7% (95% CI 14.6–28.2) lower CD4 counts than treatment-naive individuals; CD4 counts were estimated to increase by 9.2% (95% CI 6.2–12.4) per year of treatment. Conclusions CD4 counts are primarily determined by sex in HIV-uninfected adults, and by sex, age and duration of antiretroviral treatment in HIV-infected adults. Lower CD4 counts at ART initiation in men could be a consequence of lower CD4 cell counts before HIV acquisition.
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Pantazis N, Morrison C, Amornkul PN, Lewden C, Salata RA, Minga A, Chipato T, Jaffe H, Lakhi S, Karita E, Porter K, Meyer L, Touloumi G. Differences in HIV natural history among African and non-African seroconverters in Europe and seroconverters in sub-Saharan Africa. PLoS One 2012; 7:e32369. [PMID: 22412867 PMCID: PMC3295758 DOI: 10.1371/journal.pone.0032369] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Accepted: 01/26/2012] [Indexed: 11/18/2022] Open
Abstract
Introduction It is unknown whether HIV treatment guidelines, based on resource-rich country cohorts, are applicable to African populations. Methods We estimated CD4 cell loss in ART-naïve, AIDS-free individuals using mixed models allowing for random intercept and slope, and time from seroconversion to clinical AIDS, death and antiretroviral therapy (ART) initiation by survival methods. Using CASCADE data from 20 European and 3 sub-Saharan African (SSA) cohorts of heterosexually-infected individuals, aged ≥15 years, infected ≥2000, we compared estimates between non-African Europeans, Africans in Europe, and Africans in SSA. Results Of 1,959 (913 non-Africans, 302 Europeans - African origin, 744 SSA), two-thirds were female; median age at seroconversion was 31 years. Individuals in SSA progressed faster to clinical AIDS but not to death or non-TB AIDS. They also initiated ART later than Europeans and at lower CD4 cell counts. In adjusted models, Africans (especially from Europe) had lower CD4 counts at seroconversion and slower CD4 decline than non-African Europeans. Median (95% CI) CD4 count at seroconversion for a 15–29 year old woman was 607 (588–627) (non-African European), 469 (442–497) (European - African origin) and 570 (551–589) (SSA) cells/µL with respective CD4 decline during the first 4 years of 259 (228–289), 155 (110–200), and 199 (174–224) cells/µL (p<0.01). Discussion Despite differences in CD4 cell count evolution, death and non-TB AIDS rates were similar across study groups. It is therefore prudent to apply current ART guidelines from resource-rich countries to African populations.
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Affiliation(s)
- Nikos Pantazis
- Department of Hygiene, Epidemiology and Medical Statistics, University of Athens Medical School, Athens, Greece.
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Morrison CS, Chen PL, Nankya I, Rinaldi A, Van Der Pol B, Ma YR, Chipato T, Mugerwa R, Dunbar M, Arts E, Salata RA. Hormonal contraceptive use and HIV disease progression among women in Uganda and Zimbabwe. J Acquir Immune Defic Syndr 2011; 57:157-64. [PMID: 21358412 PMCID: PMC3164299 DOI: 10.1097/qai.0b013e318214ba4a] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND HIV-infected women need highly effective contraception to reduce unintended pregnancies and mother-to-child HIV transmission. Previous studies report conflicting results regarding the effect of hormonal contraception on HIV disease progression. METHODS HIV-infected women in Uganda and Zimbabwe were recruited immediately after seroconversion; CD4 testing and clinical examinations were conducted quarterly. The study end point was time to AIDS (two successive CD4 200 cells/mm or less or World Health Organization advanced Stage 3 or Stage 4 disease). We used marginal structural Cox survival models to estimate the effect of cumulative exposure to depot-medroxyprogesterone acetate and oral contraceptives on time to AIDS. RESULTS Three hundred three HIV-infected women contributed 1408 person-years. One hundred eleven women (37%) developed AIDS. Cumulative probability of AIDS was 50% at 7 years and did not vary by country. AIDS incidence was 6.6, 9.3, and 8.8 per 100 person-years for depot-medroxyprogesterone acetate, oral contraceptive, and nonhormonal users. Neither depot-medroxyprogesterone acetate (adjusted hazard ratio, 0.90; 95% confidence interval, 0.76-1.08) nor oral contraceptives ( adjusted hazard ratio, 1.07; 95% confidence interval, 0.89-1.29) were associated with HIV disease progression. Alternative exposure definitions of hormonal contraception use during the year before AIDS or at the time of HIV infection produced similar results. Sexually transmitted infection symptoms were associated with faster progression, whereas young age at HIV infection (18-24 years) was associated with slower progression. Adding baseline CD4 level and set point viral load to models did not change the hormonal contraception results, but Subtype D infection became associated with disease progression. CONCLUSION Hormonal contraceptive use was not associated with more rapid HIV disease progression, but older age, sexually transmitted infection symptoms, and Subtype D infection were.
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Affiliation(s)
- Charles S Morrison
- Department of Clinical Sciences, Family Health International, Research Triangle Park, NC, USA.
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