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Mainou E, Berendam SJ, Obregon-Perko V, Uffman EA, Phan CT, Shaw GM, Bar KJ, Kumar MR, Fray EJ, Siliciano JM, Siliciano RF, Silvestri G, Permar SR, Fouda GG, McCarthy J, Chahroudi A, Chan C, Conway JM. Comparative analysis of within-host dynamics of acute infection and viral rebound dynamics in postnatally SHIV-infected ART-treated infant rhesus macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595130. [PMID: 38826467 PMCID: PMC11142125 DOI: 10.1101/2024.05.21.595130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Viral dynamics of acute HIV infection and HIV rebound following suspension of antiretroviral therapy may be qualitatively similar but must differ given, for one, development of adaptive immune responses. Understanding the differences of acute HIV infection and viral rebound dynamics in pediatric populations may provide insights into the mechanisms of viral control with potential implications for vaccine design and the development of effective targeted therapeutics for infants and children. Mathematical models have been a crucial tool to elucidate the complex processes driving viral infections within the host. Traditionally, acute HIV infection has been modeled with a standard model of viral dynamics initially developed to explore viral decay during treatment, while viral rebound has necessitated extensions of that standard model to incorporate explicit immune responses. Previous efforts to fit these models to viral load data have underscored differences between the two infection stages, such as increased viral clearance rate and increased death rate of infected cells during rebound. However, these findings have been predicated on viral load measurements from disparate adult individuals. In this study, we aim to bridge this gap, in infants, by comparing the dynamics of acute infection and viral rebound within the same individuals by leveraging an infant nonhuman primate Simian/Human Immunodeficiency Virus (SHIV) infection model. Ten infant Rhesus macaques (RMs) orally challenged with SHIV.C.CH505 375H dCT and given ART at 8 weeks post-infection. These infants were then monitored for up to 60 months post-infection with serial viral load and immune measurements. We use the HIV standard viral dynamics model fitted to viral load measurements in a nonlinear mixed effects framework. We find that the primary difference between acute infection and rebound is the increased death rate of infected cells during rebound. We use these findings to generate hypotheses on the effects of adaptive immune responses. We leverage these findings to formulate hypotheses to elucidate the observed results and provide arguments to support the notion that delayed viral rebound is characterized by a stronger CD8+ T cell response.
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Affiliation(s)
- Ellie Mainou
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Emilie A Uffman
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Caroline T Phan
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - George M Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katharine J Bar
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mithra R Kumar
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emily J Fray
- Department of Biochemistry and Molecular Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Janet M Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guido Silvestri
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Sallie R Permar
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | | | - Janice McCarthy
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Jessica M Conway
- Department of Mathematics, Pennsylvania State University, University Park, PA, USA
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2
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Van Rompay KK, Coffey LL, Yee JL, Singapuri A, Stuart J, Lanteri MC, Maria FS, Lu K, Singh I, Bakkour S, Stone M, Williamson PC, Muench MO, Busch MP, Simmons G. Plasma transfusion-transmission of Zika virus in mice and macaques. Transfusion 2023; 63:574-585. [PMID: 36621777 PMCID: PMC10134791 DOI: 10.1111/trf.17243] [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: 10/10/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 01/10/2023]
Abstract
BACKGROUND Zika virus (ZIKV) epidemics with infections in pregnant women are associated with severe neurological disease in newborns. Although an arbovirus, ZIKV is also blood transfusion-transmitted (TT). Greater knowledge of the efficiency of ZIKV TT would aid decisions on testing and pathogen reduction technologies (PRT). STUDY DESIGN AND METHODS Plasma units from ZIKV RNA-reactive blood donors were used to study infectivity in vitro, in mice, and in macaques. Furthermore, plasma units were subjected to PRT using amotosalen/ultraviolet light A (A/UVA) before transfusion. RESULTS In vitro infectivity of ZIKV RNA-reactive plasma varied between 100 and 1000 international units (IU) of ZIKV RNA. Immunodeficient mice were more sensitive with as low as 32 IU sufficient to infect 50% of mice. 50-5500 IU of RNA led to TT in macaques using dose escalation of three different RNA-positive, seronegative plasma units. In contrast, RNA-reactive units collected postseroconversion were not infectious in macaques, even at a dose of 9 million IU RNA. After A/UVA PRT, transfusion of plasma containing up to 18 million IU was no longer infectious in vitro and did not result in ZIKV TT in macaques. CONCLUSION Significant risks of ZIKV TT are likely confined to a relatively short viremic window before seroconversion, and that sensitive nucleic acid amplification testing likely identifies the majority of infectious plasma. PRT was demonstrated to be effective at preventing ZIKV TT. Considering that there is no approved ZIKV vaccine, these data are relevant to mitigate the risk of TT during the future ZIKV outbreaks.
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Affiliation(s)
- Koen K.A. Van Rompay
- California National Primate Research Center, University of California, Davis, CA, United States of America
- Department of Pathology, Microbiology and Immunology, University of California, Davis, CA, United States of America
| | - Lark L. Coffey
- Department of Pathology, Microbiology and Immunology, University of California, Davis, CA, United States of America
| | - JoAnn L. Yee
- California National Primate Research Center, University of California, Davis, CA, United States of America
| | - Anil Singapuri
- Department of Pathology, Microbiology and Immunology, University of California, Davis, CA, United States of America
| | - Jackson Stuart
- Department of Pathology, Microbiology and Immunology, University of California, Davis, CA, United States of America
| | | | | | - Kai Lu
- Vitalant Research Institute, San Francisco, California, United States of America
| | - Inderdeep Singh
- Vitalant Research Institute, San Francisco, California, United States of America
| | - Sonia Bakkour
- Vitalant Research Institute, San Francisco, California, United States of America
| | - Mars Stone
- Vitalant Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States of America
| | | | - Marcus O. Muench
- Vitalant Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States of America
| | - Michael P. Busch
- Vitalant Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States of America
| | - Graham Simmons
- Vitalant Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States of America
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3
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Modeling the Risk of HIV Transfusion Transmission. J Acquir Immune Defic Syndr 2023; 92:173-179. [PMID: 36219691 DOI: 10.1097/qai.0000000000003115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 09/19/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND Blood donations are routinely screened for HIV to prevent an infectious unit from being released to the blood supply. Despite improvements to blood screening assays, donations from infected donors remain undetectable during the window period (WP), when the virus has not yet replicated above the lower limit of detection (LOD) of a screening assay. To aid in the quantitative risk assessments of WP donations, a dose-response model describing the probability of transfusion-transmission of HIV over a range of viral RNA copies was developed. METHODS An exponential model was chosen based on data fit and parsimony. A data set from a HIV challenge study using a nonhuman primate model and another data set from reported human blood transfusions associated with HIV infected donors were separately fit to the model to generate parameter estimates. A Bayesian framework using No-U-Turn Sampling (NUTS) and Monte Carlo simulations was performed to generate posterior distributions quantifying uncertainty in parameter estimation and model predictions. RESULTS The parameters of the exponential model for both nonhuman primate and human data were estimated with a mean (95% credible intervals) of 2.70 × 10 -2 (7.74 × 10 -3 , 6.06 × 10 -2 ) and 7.56 × 10 -4 (3.68 × 10 -4 , 1.31 × 10 -3 ), respectively. The predicted ID 50 for the animal and human models was 26 (12, 90) and 918 (529, 1886) RNA copies transfused, respectively. CONCLUSION This dose-response model can be used in a quantitative framework to estimate the probability of transfusion-transmission of HIV through WP donations. These models can be especially informative when assessing risk from blood components with low viral load.
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A More Comprehensive Clinical and Laboratory Characterization of 61 Acute HIV Infection Patients in Southwest China. Pathogens 2023; 12:pathogens12010142. [PMID: 36678489 PMCID: PMC9864376 DOI: 10.3390/pathogens12010142] [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: 10/25/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/18/2023] Open
Abstract
Acute HIV infection (AHI), i.e., the early stage of HIV infection, plays an important role in immune system failure and HIV transmission, but most AHI patients are missed due to their non-specific symptoms. To facilitate the identification of patients with high AHI risk and reduction of missed diagnosis, we characterized 61 AHI patients in a Southwest China hospital with 4300 beds; specifically, we characterized their general clinical characteristics, evolution in results of a novel HIV screening assay called Elecsys® HIV Duo, and by programming, we analyzed the ability of all routine laboratory tests (e.g., routine blood analysis) to identify AHI patients. Among 61 AHI patients, 85.2% were male and the median age was 42 (interquartile range, 25-62) years. A total of 61.9% of patients visit the emergency department first during AHI. Clinical presentation of AHI patients included fever, fatigue, chills, rash, and various respiratory, digestive, and nervous system symptoms. Two of three results from Elecsys® HIV Duo show clear evolution trends: HIV P24 antigen decreased while HIV antibody increased in consecutive samples of nearly all patients. High fluorescence lymphocytes have a very high positive likelihood ratio (LR+) of 10.33 and a relatively high "rate of out-of-range tests" of 56.8% (21 in 37 patients who received this test had a result outside the reference range). In addition, we identified more than ten tests with LR+ greater than two. In summary, the emergency department is important for AHI screening. The evolution of HIV P24 Ag and HIV Ab and those laboratory tests with a high "rate of out-of-range tests" or high LR+ may aid the AHI identification and missed diagnosis reduction.
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The Impact of Early Antiretroviral Treatment (ART) for HIV on the Sensitivity of the Latest Generation of Blood Screening and Point of Care Assays. Viruses 2022; 14:v14071426. [PMID: 35891406 PMCID: PMC9324335 DOI: 10.3390/v14071426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 12/04/2022] Open
Abstract
Introduction: Rapid initiation of antiretroviral therapy (ART) in early HIV infection is important to limit seeding of the viral reservoir. A number of studies have shown that if ART is commenced prior to seroconversion, the seroconversion may, or may not, occur. We aimed to assess whether seroreversion or no seroconversion occurs using samples collected during an early treatment study in South Africa. Methods: We tested 10 longitudinal samples collected over three years from 70 blood donors who initiated ART after detection of acute or early HIV infection during donation screening on fourth- and fifth-generation HIV antibody and RNA assays, and three point of care (POC) rapid tests. Donors were allocated to three treatment groups: (1) very early, (2) early, and (3) later. Longitudinal samples were grouped into time bins post-treatment initiation. Results: On all three high-throughput HIV antibody assays, no clear pattern of declining signal intensity was observed over time after ART initiation in any of the treatment initiation groups and 100% detection was obtained. The Abbott Determine POC assay showed 100% detection at all time points with no seroreversion. However, the Abbott ABON HIV1 and OraSure OraQuick POC assays showed lower proportions of detection in all time bins in the very early treated group, ranging from 50.0% (95% CI: 26.8–73.2%) to 83.1% (95% CI: 64.2–93.0%), and moderate detection rates in the early and later-treated groups. Conclusion: While our findings are generally reassuring for HIV detection when high-throughput serological screening assays are used, POC assays may have lower sensitivity for detection of HIV infection after early treatment. Findings are relevant for blood safety and other settings where POC assays are used.
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Vaidya NK, Bloomquist A, Perelson AS. Modeling Within-Host Dynamics of SARS-CoV-2 Infection: A Case Study in Ferrets. Viruses 2021; 13:1635. [PMID: 34452499 PMCID: PMC8402735 DOI: 10.3390/v13081635] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/27/2021] [Accepted: 08/09/2021] [Indexed: 12/26/2022] Open
Abstract
The pre-clinical development of antiviral agents involves experimental trials in animals and ferrets as an animal model for the study of SARS-CoV-2. Here, we used mathematical models and experimental data to characterize the within-host infection dynamics of SARS-CoV-2 in ferrets. We also performed a global sensitivity analysis of model parameters impacting the characteristics of the viral infection. We provide estimates of the viral dynamic parameters in ferrets, such as the infection rate, the virus production rate, the infectious virus proportion, the infected cell death rate, the virus clearance rate, as well as other related characteristics, including the basic reproduction number, pre-peak infectious viral growth rate, post-peak infectious viral decay rate, pre-peak infectious viral doubling time, post-peak infectious virus half-life, and the target cell loss in the respiratory tract. These parameters and indices are not significantly different between animals infected with viral strains isolated from the environment and isolated from human hosts, indicating a potential for transmission from fomites. While the infection period in ferrets is relatively short, the similarity observed between our results and previous results in humans supports that ferrets can be an appropriate animal model for SARS-CoV-2 dynamics-related studies, and our estimates provide helpful information for such studies.
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Affiliation(s)
- Naveen K. Vaidya
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182, USA;
- Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA
- Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Angelica Bloomquist
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182, USA;
- Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA
- Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Alan S. Perelson
- Los Alamos National Laboratory, Theoretical Biology and Biophysics Group, Los Alamos, NM 87545, USA;
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Modeling Intracellular Delay in Within-Host HIV Dynamics Under Conditioning of Drugs of Abuse. Bull Math Biol 2021; 83:81. [PMID: 34061253 DOI: 10.1007/s11538-021-00908-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 05/05/2021] [Indexed: 10/21/2022]
Abstract
Drugs of abuse, such as opiates, have been widely associated with the enhancement of HIV replication, the acceleration of disease progression, and severe neuropathogenesis. Specifically, the presence of drugs of abuse (morphine) switches target cells (CD4[Formula: see text] T cells) from lower-to-higher susceptibility to HIV infection. The effect of such switching behaviors on viral dynamics may be altered due to the intracellular delay (the replication time between viral entry into a target cell and the production of new viruses by the infected cell). In this study, we develop, for the first time, a viral dynamics model that includes an intracellular delay under the conditioning of drugs of abuse. We parameterize the model using experimental data from simian immunodeficiency virus infection of morphine-addicted macaques. Results from thorough mathematical analyses and numerical simulations of our model show that the intracellular delay can play a significant role in HIV dynamics under the conditioning of drugs of abuse, particularly during the acute phase of infection. Our model and the related results provide new insights into the HIV dynamics and may help develop strategies to control HIV infections in drug abusers.
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8
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Williamson PC, Biggerstaff BJ, Simmons G, Stone M, Winkelman V, Latoni G, Alsina J, Bakkour S, Newman C, Pate LL, Galel SA, Kleinman S, Busch MP. Evolving viral and serological stages of Zika virus RNA-positive blood donors and estimation of incidence of infection during the 2016 Puerto Rican Zika epidemic: an observational cohort study. THE LANCET. INFECTIOUS DISEASES 2020; 20:1437-1445. [PMID: 32673594 DOI: 10.1016/s1473-3099(19)30706-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/31/2019] [Accepted: 11/14/2019] [Indexed: 01/11/2023]
Abstract
BACKGROUND Puerto Rico began screening blood donations for Zika virus RNA with nucleic acid amplification tests (NAATs) on April 3, 2016, because of an emerging Zika virus outbreak. We followed up positive donors to assess the dynamics of viral and serological markers during the early stages of Zika virus infection and update the estimate of infection incidence in the Puerto Rican population during the outbreak. METHODS Blood donations from volunteer donors in Puerto Rico were screened for the presence of Zika virus RNA using the cobas Zika NAAT. Positive donations were further tested to confirm infection, estimate viral load, and identify Zika virus-specific IgM antibodies. Individuals with positive blood donations were invited to attend follow-up visits. Donations with confirmed infection (defined as detection of Zika virus RNA or IgM on additional testing of index or follow-up samples) were assessed for stage of infection according to Zika virus RNA detectability in simulated minipools, viral load, and Zika virus IgM status. A three-step process was used to estimate the mean duration of NAAT reactivity of Zika virus in human plasma from individuals identified pre-seroconversion with at least one follow up visit and to update the 2016 incidence estimate of Zika virus infection. FINDINGS Between April 3 and Dec 31, 2016, 53 112 blood donations were screened for Zika virus, of which 351 tested positive, 339 had confirmed infections, and 319 could be staged. Compared with IgM-positive index donations (n=110), IgM-negative index donations (n=209) had higher mean viral loads (1·1 × 106vs 8·3 × 104 international units per mL) and were more likely to be detected in simulated minipools (93% [n=194] vs 26% [n=29]). The proportions of donations with confirmed infections that had viral RNA detected only in individual-donation NAATs (ie, not in simulated minipools) and were IgM positive increased as the epidemic evolved. The estimated mean duration of NAAT detectability in the 140 donors included in the follow-up study was 11·70 days (95% CI 10·06-14·36). Applying this detection period to the observed proportion of donations that were confirmed NAAT positive yielded a Zika virus seasonal incidence estimate of 21·1% (95% CI 18·1-24·1); 768 101 infections in a population of 3 638 773 in 2016. INTERPRETATION Characterisation of early Zika virus infection has implications for blood safety because infectivity of blood donations and utility of screening methods likely correlate with viral load and serological stage of infection. Our findings also have implications for diagnostic testing, public health surveillance, and epidemiology, and we estimate that around 21% of the Puerto Rican population was infected during the 2016 outbreak. FUNDING Biomedical Advanced Research and Development Authority, National Heart, Lung, and Blood Institute.
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Affiliation(s)
| | | | | | - Mars Stone
- Vitalant Research Institute, San Francisco, CA, USA
| | | | | | - Jose Alsina
- Banco de Sangre Servicios Mutuos, Guaynabo, PR, USA
| | | | - Christina Newman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Lisa L Pate
- Roche Molecular Systems, Pleasanton, CA, USA
| | | | - Steven Kleinman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
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de Oliveira Garcia Mateos S, Preiss L, Gonçalez TT, Di Lorenzo Oliveira C, Grebe E, Di Germanio C, Stone M, Amorim Filho L, Carneiro Proietti AB, Belisario AR, de Almeida-Neto C, Mendrone-Junior A, Loureiro P, Busch MP, Custer B, Cerdeira Sabino E. 10-year analysis of human immunodeficiency virus incidence in first-time and repeat donors in Brazil. Vox Sang 2020; 116:207-216. [PMID: 32996602 DOI: 10.1111/vox.13002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND OBJECTIVES Incidence in first-time and repeat blood donors is an important measure of transfusion-transmitted HIV infection (TT-HIV) risk. This study assessed HIV incidence over time at four large blood centres in Brazil. MATERIALS AND METHODS Donations were screened and confirmed using serological assays for HIV from 2007 to 2016, and additionally screened by nucleic acid testing from 2011 forward. Limiting antigen (LAg) avidity testing was conducted on HIV seroreactive samples from first-time donors to classify whether an infection was recently acquired. We calculated incidence in first-time donors using the mean duration of recent infection and in repeat donors using classical methods. Time and demographic trends were assessed using Poisson regression. RESULTS Over the 10-year period, HIV incidence in first-time donors was highest in Recife (45·1/100 000 person-years (105 py)) followed by São Paulo (32·2/105 py) and then Belo Horizonte (23·3/105 py), and in repeat donors was highest in Recife (33·2/105 py), Belo Horizonte (27·5/105 py) and São Paulo (17·0/105 py). Results from Rio de Janeiro were available from 2013 to 2016 with incidence in first-time donors of 35·9/105 py and repeat donors from 2011 to 2016 of 29·2/105 py. Incidence varied by other donor demographics. When incidence was considered in 2-year intervals, no significant trend was evident. Overall residual risk of TT-HIV was 5·46 and 7·41 per million units of pRBC and FFP transfused, respectively. CONCLUSION HIV incidence in both first-time and repeat donors varied by region in Brazil. Clear secular trends were not evident.
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Affiliation(s)
- Sheila de Oliveira Garcia Mateos
- Departamento de Moléstias Infecciosas e Parasitárias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Department of Hemotherapy, Hemorio, Rio de Janeiro, Brazil
| | - Liliana Preiss
- Division of Biostatistics and Epidemiology, RTI International, Rockville, MD, USA
| | | | | | - Eduard Grebe
- Vitalant Research Institute, San Francisco, CA, USA.,University of California San Francisco, San Francisco, CA, USA
| | | | - Mars Stone
- Vitalant Research Institute, San Francisco, CA, USA
| | | | | | - Andre Rolim Belisario
- Department GDTC (Technical-Scientific Development Management), Hemominas, Minas Gerais, Brazil
| | - Cesar de Almeida-Neto
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil.,Disciplina de Ciências Médicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | - Paula Loureiro
- Pernambuco University, Recife, Brazil.,Fundação Hemope/Hemocentro de Pernambuco, Recife, Brazil
| | - Michael P Busch
- Vitalant Research Institute, San Francisco, CA, USA.,University of California San Francisco, San Francisco, CA, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA.,University of California San Francisco, San Francisco, CA, USA
| | - Ester Cerdeira Sabino
- Departamento de Moléstias Infecciosas e Parasitárias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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10
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Raehtz KD, Barrenäs F, Xu C, Busman-Sahay K, Valentine A, Law L, Ma D, Policicchio BB, Wijewardana V, Brocca-Cofano E, Trichel A, Gale M, Keele BF, Estes JD, Apetrei C, Pandrea I. African green monkeys avoid SIV disease progression by preventing intestinal dysfunction and maintaining mucosal barrier integrity. PLoS Pathog 2020; 16:e1008333. [PMID: 32119719 PMCID: PMC7077871 DOI: 10.1371/journal.ppat.1008333] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 03/17/2020] [Accepted: 01/18/2020] [Indexed: 12/12/2022] Open
Abstract
Unlike HIV infection, SIV infection is generally nonpathogenic in natural hosts, such as African green monkeys (AGMs), despite life-long high viral replication. Lack of disease progression was reportedly based on the ability of SIV-infected AGMs to prevent gut dysfunction, avoiding microbial translocation and the associated systemic immune activation and chronic inflammation. Yet, the maintenance of gut integrity has never been documented, and the mechanism(s) by which gut integrity is preserved are unknown. We sought to investigate the early events of SIV infection in AGMs, specifically examining the impact of SIVsab infection on the gut mucosa. Twenty-nine adult male AGMs were intrarectally infected with SIVsab92018 and serially sacrificed at well-defined stages of SIV infection, preramp-up (1-3 days post-infection (dpi)), ramp-up (4-6 dpi), peak viremia (9-12 dpi), and early chronic SIV infection (46-55 dpi), to assess the levels of immune activation, apoptosis, epithelial damage and microbial translocation in the GI tract and peripheral lymph nodes. Tissue viral loads, plasma cytokines and plasma markers of gut dysfunction were also measured throughout the course of early infection. While a strong, but transient, interferon-based inflammatory response was observed, the levels of plasma markers linked to enteropathy did not increase. Accordingly, no significant increases in apoptosis of either mucosal enterocytes or lymphocytes, and no damage to the mucosal epithelium were documented during early SIVsab infection of AGMs. These findings were supported by RNAseq of the gut tissue, which found no significant alterations in gene expression that would indicate microbial translocation. Thus, for the first time, we confirmed that gut epithelial integrity is preserved, with no evidence of microbial translocation, in AGMs throughout early SIVsab infection. This might protect AGMs from developing intestinal dysfunction and the subsequent chronic inflammation that drives both HIV disease progression and HIV-associated comorbidities.
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Affiliation(s)
- Kevin D. Raehtz
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Fredrik Barrenäs
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Cuiling Xu
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, United States of America
- Oregon National Primate Research Center, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Audrey Valentine
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Lynn Law
- Department of Immunology, University of Washington, Seattle, Washington, United States of America
- Center for Innate Immunity and Immune Diseases, University of Washington, Washington, United States of America
| | - Dongzhu Ma
- Department of Orthopedic Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Benjamin B. Policicchio
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Viskam Wijewardana
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Egidio Brocca-Cofano
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Anita Trichel
- Division of Laboratory Animal Resources, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael Gale
- Department of Immunology, University of Washington, Seattle, Washington, United States of America
- Center for Innate Immunity and Immune Diseases, University of Washington, Washington, United States of America
- Washington National Primate Research Center, University of Washington, Seattle, Washington, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory of Cancer Research, Frederick, Maryland, United States of America
| | - Jacob D. Estes
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, United States of America
- Oregon National Primate Research Center, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Cristian Apetrei
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ivona Pandrea
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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11
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Dimitrov D, Wood D, Ulrich A, Swan DA, Adamson B, Lama JR, Sanchez J, Duerr A. Projected effectiveness of HIV detection during early infection and rapid ART initiation among MSM and transgender women in Peru: A modeling study. Infect Dis Model 2019; 4:73-82. [PMID: 31025025 PMCID: PMC6475714 DOI: 10.1016/j.idm.2019.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 12/01/2022] Open
Abstract
Background The Sabes study, a treatment as prevention intervention in Peru, tested the hypothesis that initiating antiretroviral therapy (ART) early in HIV infection when viral load is high, would markedly reduce onward HIV transmission among high-risk men who have sex with men (MSM) and transgender women (TW). We investigated the potential population-level benefits of detection of HIV early after acquisition and rapid initiation of ART. Methods We designed a transmission dynamic model to simulate the HIV epidemic among MSM and TW in Peru, calibrated to data on HIV prevalence and ART coverage from 2004 to 2011. We assessed the impact of an intervention starting in 2018 in which up to 50% of the new infections were diagnosed within three months of acquisition and initiated on ART within 1 month of diagnosis. We estimated the impact of the intervention over 20 years using the cumulative prevented fraction of new HIV infections compared to scenarios without intervention. Findings Our model suggests that only 19% of the infected MSM and TW are virally suppressed in 2018 and 35%-40% of the new HIV infections are transmitted from contacts with acutely-infected partners. An intervention reaching 10% of all acutely infected MSM and TW is projected to prevent 13.3% [Uncertainty interval: 11.9%-14.3%] of the new infections over 20 years and reduce HIV incidence in 2038 by 24%. Reaching 50% of all acutely infected MSM and TW will increase the prevalence of viral suppression in 2038 to 59% and prevent 41% of expected infections over 20 years. Reaching 50% of the high-risk MSM and TW in acute phase would reduce HIV incidence in 2038 by 60% and prevent 36% of new infections between 2018 and 2038. Conclusions Early detection of HIV infections and rapid initiation of ART among MSM is desirable as it would increase the effectiveness of the HIV prevention program in Peru. Targeting high-risk MSM and TW will be highly efficient.
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Affiliation(s)
- Dobromir Dimitrov
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daniel Wood
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Angela Ulrich
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Global Health, University of Washington, Seattle, WA, USA
| | - David A Swan
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Blythe Adamson
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Comparative Health Outcomes, Policy, & Economics (CHOICE) Institute, University of Washington, Seattle, WA, USA
| | - Javier R Lama
- Asociación Civil Impacta Salud y Educación, Lima, Peru
| | - Jorge Sanchez
- Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales, Universidad Mayor de San Marcos, Lima, Peru
| | - Ann Duerr
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Global Health, University of Washington, Seattle, WA, USA
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12
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Modeling the Effects of Morphine-Altered Virus Specific Antibody Responses on HIV/SIV Dynamics. Sci Rep 2019; 9:5423. [PMID: 30931971 PMCID: PMC6443976 DOI: 10.1038/s41598-019-41751-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 03/14/2019] [Indexed: 11/24/2022] Open
Abstract
Drugs of abuse, such as opiates, have been widely associated with enhancing HIV replication, accelerating disease progression and diminishing host-immune responses, thereby making it harder to effectively manage HIV infection. It is thus important to study the effects of drugs of abuse on HIV-infection and immune responses. Here, we develop mathematical models that incorporate the effects of morphine-altered antibody responses on HIV/SIV dynamics. Based on fitting the model to experimental data from simian immunodeficiency virus (SIV) infections in control and morphine-addicted macaques, we found that two of the most significant effects of virus specific antibodies are neutralizing viral particles and enhancing viral clearance. Using our model, we quantified how morphine alters virus-specific antibody responses, and how this alteration affects the key components of virus dynamics such as infection rate, virus clearance, viral load, CD4+ T cell count, and CD4+ T cell loss in SIV-infected macaques under conditioning with morphine. We found that in a subpopulation of SIV-infected morphine addicted macaques, the presence of drugs of abuse may cause significantly diminished antibody responses, resulting in more severe infection with increased SIV infectivity, a decreased viral clearance rate, increased viral load, and higher CD4+ T cell loss.
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13
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Stansfield SE, Mittler JE, Gottlieb GS, Murphy JT, Hamilton DT, Detels R, Wolinsky SM, Jacobson LP, Margolick JB, Rinaldo CR, Herbeck JT, Goodreau SM. Sexual role and HIV-1 set point viral load among men who have sex with men. Epidemics 2019; 26:68-76. [PMID: 30193771 PMCID: PMC6538391 DOI: 10.1016/j.epidem.2018.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 07/12/2018] [Accepted: 08/28/2018] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND HIV-1 set point viral load (SPVL) is a highly variable trait that influences disease progression and transmission risk. Men who are exclusively insertive (EI) during anal intercourse require more sexual contacts to become infected than exclusively receptive (ER) men. Thus, we hypothesize that EIs are more likely to acquire their viruses from highly infectious partners (i.e., with high SPVLs) and to have higher SPVLs than infected ERs. METHODS We used a one-generation Bernoulli model, a dynamic network model, and data from the Multicenter AIDS Cohort Study (MACS) to examine whether and under what circumstances MSM differ in SPVL by sexual role. RESULTS Both models predicted higher SPVLs in EIs than role versatile (RV) or ER men, but only in scenarios where longer-term relationships predominated. ER and RV men displayed similar SPVLs. EI men remained far less likely than ER men to become infected, however. When the MACS data were limited by some estimates of lower sex partner counts (a proxy for longer relationships), EI men had higher SPVLs; these differences were clinically relevant (>0.3 log10 copies/mL) and statistically significant (p < 0.05). CONCLUSIONS Mode of acquisition may be an important aspect of SPVL evolution in MSM, with clinical implications.
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Affiliation(s)
- Sarah E Stansfield
- Departments of Anthropology & Epidemiology, University of Washington, 314 Denny Hall, Box 353100, Seattle, WA 98195-3100, USA.
| | - John E Mittler
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Geoffrey S Gottlieb
- Departments of Medicine & Global Health, University of Washington, Seattle, WA 98195, USA
| | - James T Murphy
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Deven T Hamilton
- Center for Studies in Demography and Ecology, University of Washington, Seattle, WA 98195, USA
| | - Roger Detels
- Department of Epidemiology, University of California School of Public Health, Los Angeles, CA, 90024, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Lisa P Jacobson
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Joseph B Margolick
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Charles R Rinaldo
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, 15261, USA
| | - Joshua T Herbeck
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Steven M Goodreau
- Department of Anthropology, University of Washington, Seattle, WA 98195, USA
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14
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Cappy P, Barlet V, Lucas Q, Tinard X, Pillonel J, Gross S, Tiberghien P, Laperche S. Transfusion of HIV-infected blood products despite highly sensitive nucleic acid testing. Transfusion 2019; 59:2046-2053. [PMID: 30784073 DOI: 10.1111/trf.15203] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/18/2019] [Accepted: 01/20/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND In France, the risk of HIV transmission by transfusion was reduced by implementing pooled nucleic acid testing (NAT) in 2001 and individual NAT in 2010. We report here the first case in France of transfusion of human immunodeficiency virus (HIV)-infected blood donated during HIV pre-ramp-up phase that tested individual NAT negative. METHODS Blood donations are screened for HIV antibodies and HIV RNA (ProcleixUltrio, Grifols; limit of detection at 95%, 23 copies/mL). When a repeat donor tests positive for HIV, a repository sample from the previous donation is tested with the Cobas Taqman HIV-1 test (CTM, Roche; limit of detection at 95%, 17 copies/mL). RESULTS In August 2017, a 57-year-old male repeat donor was screened positive for HIV antibodies and RNA (plasma viral load, 11,599 copies/mL). The previous donation had tested negative with Ultrio in March 2017 but was positive with an unquantifiable plasma viral load when tested with CTM. Sequencing showed no mismatch between Ultrio primers/probes and the target sequence. HIV transmission was excluded by lookback studies in the recipient of platelets, which had been pathogen reduced, but not in the recipient of RBCs due to premature death. CONCLUSION This case demonstrates that the risk of contaminated donations due to the early HIV infection phase going undetected by highly sensitive NAT is real but exceptional. The absence of transmission to the platelets recipient could be due to the very low viral inoculum and/or to the efficacy of the viral inactivation. This case also highlights the additional value of a systematic donation archiving and the importance of donor education and predonation selection.
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Affiliation(s)
- Pierre Cappy
- Département des Agents Transmissibles par le Sang, Centre National de Référence Risques Infectieux Transfusionnels, Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Valérie Barlet
- ETS Auvergne Rhône Alpes, Laboratoire de qualification biologique des dons Est, Etablissement Français du Sang, Metz-Tessy, France
| | - Quentin Lucas
- Département des Agents Transmissibles par le Sang, Centre National de Référence Risques Infectieux Transfusionnels, Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Xavier Tinard
- ETS grand est, Pôle des vigilances, Etablissement Français du Sang, Nancy, France
| | - Josiane Pillonel
- Département des maladies infectieuses, Santé publique France, Saint-Maurice, France
| | - Sylvie Gross
- Etablissement Français du Sang, Saint Denis, France
| | - Pierre Tiberghien
- Etablissement Français du Sang, Saint Denis, France.,Unité mixte de recherche 1098 INSERM, Université de Franche-Comté, Etablissement Français du Sang, Besançon, France
| | - Syria Laperche
- Département des Agents Transmissibles par le Sang, Centre National de Référence Risques Infectieux Transfusionnels, Institut National de la Transfusion Sanguine (INTS), Paris, France
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15
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Selik RM, Linley L. Viral Loads Within 6 Weeks After Diagnosis of HIV Infection in Early and Later Stages: Observational Study Using National Surveillance Data. JMIR Public Health Surveill 2018; 4:e10770. [PMID: 30401660 PMCID: PMC6246969 DOI: 10.2196/10770] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/10/2018] [Accepted: 07/18/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Early (including acute) HIV infection is associated with viral loads higher than those in later stages. OBJECTIVE This study aimed to examine the association between acute infection and viral loads near the time of diagnosis using data reported to the US National HIV Surveillance System. METHODS We analyzed data on infections diagnosed in 2012-2016 and reported through December 2017. Diagnosis and staging were based on the 2014 US surveillance case definition for HIV infection. We divided early HIV-1 infection (stage 0) into two subcategories. Subcategory 0α: a negative or indeterminate HIV-1 antibody test was ≤60 days after the first confirmed positive HIV-1 test or a negative or indeterminate antibody test or qualitative HIV-1 nucleic acid test (NAT) was ≤180 days before the first positive test, the latter being a NAT or detectable viral load. Subcategory 0β: a negative or indeterminate antibody or qualitative NAT was ≤180 days before the first positive test, the latter being an HIV antibody or antigen/antibody test. We compared median earliest viral loads for each stage and subcategory in each of the first 6 weeks after diagnosis using only the earliest viral load for each individual. RESULTS Of 203,392 infections, 56.69% (115,297/203,392) were reported with a quantified earliest viral load within 6 weeks after diagnosis and criteria sufficient to determine the stage at diagnosis. Among 5081 infections at stage 0, the median earliest viral load fell from 694,000 copies/mL in week 1 to 125,022 in week 2 and 43,473 by week 6. Among 30,910 infections in stage 1, the median earliest viral load ranged 15,412-17,495. Among 42,784 infections in stage 2, the median viral load declined from 44,973 in week 1 to 38,497 in week 6. Among 36,522 infections in stage 3 (AIDS), the median viral load dropped from 205,862 in week 1 to 119,000 in week 6. The median earliest viral load in stage 0 subcategory 0α fell from 1,344,590 copies/mL in week 1 to 362,467 in week 2 and 47,320 in week 6, while that in subcategory 0β was 70,114 copies/mL in week 1 and then 32,033 to 44,067 in weeks 2-6. The median viral load in subcategory 0α was higher than that in subcategory 0β in each of the first 6 weeks after diagnosis (P<.001). CONCLUSIONS In the 1st week after diagnosis, viral loads in early infections are generally several times higher than those in later stages at diagnosis. By the 3rd week, however, most are lower than those in stage 3. High viral loads in early infection are much more common in subcategory 0α than in subcategory 0β, consistent with 0α comprising mostly acute infections and 0β comprising mostly postacute early infections. These findings may inform the prioritization of interventions for prevention.
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Affiliation(s)
- Richard M Selik
- Division of HIV/AIDS and Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Laurie Linley
- Division of HIV/AIDS and Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
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16
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Comparison of Detection Limits of Fourth- and Fifth-Generation Combination HIV Antigen-Antibody, p24 Antigen, and Viral Load Assays on Diverse HIV Isolates. J Clin Microbiol 2018; 56:JCM.02045-17. [PMID: 29793968 DOI: 10.1128/jcm.02045-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/04/2018] [Indexed: 12/18/2022] Open
Abstract
Detection of acute HIV infection is critical for HIV public health and diagnostics. Clinical fourth-generation antigen (Ag)/antibody (Ab) combination (combo) and p24 Ag immunoassays have enhanced detection of acute infection compared to Ab-alone assays but require ongoing evaluation with currently circulating diverse subtypes. Genetically and geographically diverse HIV clinical isolates were used to assess clinical HIV diagnostic, blood screening, and next-generation assays. Three-hundred-member panels of 20 serially diluted well-characterized antibody-negative HIV isolates for which the researchers were blind to the results (blind panels) were distributed to manufacturers and end-user labs to assess the relative analytic sensitivity of currently approved and preapproved clinical HIV fourth-generation Ag/Ab combo or p24 Ag-alone immunoassays for the detection of diverse subtypes. The limits of detection (LODs) of virus were estimated for different subtypes relative to confirmed viral loads. Analysis of immunoassay sensitivity was benchmarked against confirmed viral load measurements on the blind panel. On the basis of the proportion of positive results on 300 observations, all Ag/Ab combo and standard sensitivity p24 Ag assays performed similarly and within half-log LODs, illustrating the similar breadth of reactivity and diagnostic utility. Ultrasensitive p24 Ag assays achieved dramatically increased sensitivities, while the rapid combo assays performed poorly. The similar performance of the different commercially available fourth-generation assays on diverse subtypes supports their use in broad geographic settings with locally circulating HIV clades and recombinant strains. Next-generation preclinical ultrasensitive p24 Ag assays achieved dramatically improved sensitivity, while rapid fourth-generation assays performed poorly for p24 Ag detection.
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17
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Conway JM, Perelson AS. Early HIV infection predictions: role of viral replication errors. SIAM JOURNAL ON APPLIED MATHEMATICS 2018; 78:1863-1890. [PMID: 31231142 PMCID: PMC6588189 DOI: 10.1137/17m1134019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In order to prevent and/or control infections it is necessary to understand their early-time dynamics. However this is precisely the phase of HIV about which the least is known. To investigate the initial stages of HIV infection within a host we have developed a multi-type, continuous-time branching process model. This model is a stochastic extension of the standard viral dynamics model, under the assumption that the number of cell targets for viral infection is constant, biologically reasonable since, during the earliest stages of HIV infection, very few cells are infected relative to their total population size. We use our model to investigate three important clinical characteristics of early HIV infection following intravenous challenge: risk of infection, time to infection clearance (assuming failed infection), and time to infection detection. Our focus is on the impact of errors in viral replication that result in non-infectious virus production on these characteristics. Only a small fraction of circulating virus in any chronically infected individual is capable of infecting susceptible cells: estimates range from 1/104 - 1/103. Characterization and quantification of the processes by which virus becomes defective remains incomplete. We consider two mechanisms that result in defective virus: (1) Copying errors, i.e., lethal errors in reverse transcription, which introduce mutations into the HIV-1 proviral genome, some of which may cripple the viral genome produced, and (2) Packaging errors, i.e., errors during viral packaging, at the end of the viral replication cycle, which cause defective virus by packaging new virions without, for example, viral RNA or key proteins required for infectivity. We show that assumptions on mechanisms of defective virus production can significantly impact early HIV infection model predictions. For example, the risk of infection is orders of magnitude higher if all defective virus is associated with packaging errors, but infection is predicted to be detectable sooner following HIV exposure if all defective virus is associated with copying errors. Thus, in order to make reliable predictions of risk, clearance time, and detection time, better characterization of viral replication is required.
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Affiliation(s)
- Jessica M Conway
- Department of Mathematics and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
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18
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Vaidya NK, Ribeiro RM, Liu P, Haynes BF, Tomaras GD, Perelson AS. Correlation Between Anti-gp41 Antibodies and Virus Infectivity Decay During Primary HIV-1 Infection. Front Microbiol 2018; 9:1326. [PMID: 29973924 PMCID: PMC6019451 DOI: 10.3389/fmicb.2018.01326] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 05/30/2018] [Indexed: 12/14/2022] Open
Abstract
Recent experiments have suggested that the infectivity of simian immunodeficiency virus (SIV) and human immunodeficiency virus type-1 (HIV-1) in plasma decreases over time during primary infection. Because anti-gp41 antibodies are produced early during HIV-1 infection and form antibody-virion complexes, we studied if such early HIV-1 specific antibodies are correlated with the decay in HIV-1 infectivity. Using a viral dynamic model that allows viral infectivity to decay and frequent early viral load data obtained from 6 plasma donors we estimate that HIV-1 infectivity begins to decay after about 2 weeks of infection. The length of this delay is consistent with the time before antibody-virion complexes were detected in the plasma of these donors and is correlated (p = 0.023, r = 0.87) with the time for antibodies to be first detected in plasma. Importantly, we identify that the rate of infectivity decay is significantly correlated with the rate of increase in plasma anti-gp41 IgG concentration (p = 0.046, r = 0.82) and the increase in IgM+IgG anti-gp41 concentration (p = 8.37 × 10−4, r = 0.98). Furthermore, we found that the viral load decay after the peak did not have any significant correlation with the rate of anti-gp41 IgM or IgG increase. These results indicate that early anti-gp41 antibodies may cause viral infectivity decay, but may not contribute significantly to controlling post-peak viral load, likely due to insufficient quantity or affinity. Our findings may be helpful to devise strategies, including antibody-based vaccines, to control acute HIV-1 infection.
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Affiliation(s)
- Naveen K Vaidya
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, United States
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics Group, MS K710, Los Alamos National Laboratory, Los Alamos, NM, United States.,Laboratório de Biomatemática, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Pinghuang Liu
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Barton F Haynes
- Duke University School of Medicine, Durham, NC, United States
| | | | - Alan S Perelson
- Theoretical Biology and Biophysics Group, MS K710, Los Alamos National Laboratory, Los Alamos, NM, United States
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19
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Ciupe SM, Miller CJ, Forde JE. A Bistable Switch in Virus Dynamics Can Explain the Differences in Disease Outcome Following SIV Infections in Rhesus Macaques. Front Microbiol 2018; 9:1216. [PMID: 29930544 PMCID: PMC6001289 DOI: 10.3389/fmicb.2018.01216] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 05/18/2018] [Indexed: 12/22/2022] Open
Abstract
Experimental studies have shown that the size and infectious-stage of viral inoculum influence disease outcomes in rhesus macaques infected with simian immunodeficiency virus. The possible contribution to disease outcome of antibody developed after transmission and/or present in the inoculum in free or bound form is not understood. In this study, we develop a mathematical model of virus-antibody immune complex formation and use it to predict their role in transmission and protection. The model exhibits a bistable switch between clearance and persistence states. We fitted it to temporal virus data and estimated the parameter values for free virus infectivity rate and antibody carrying capacity for which the model transitions between virus clearance and persistence when the initial conditions (in particular the ratio of immune complexes to free virus) vary. We used these results to quantify the minimum virus amount in the inoculum needed to establish persistent infections in the presence and absence of protective antibodies.
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Affiliation(s)
- Stanca M Ciupe
- Department of Mathematics, Virginia Tech, Blacksburg, VA, United States
| | - Christopher J Miller
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, Center for Comparative Medicine and California National Primate Research Center, University of California, Davis, Davis, CA, United States
| | - Jonathan E Forde
- Department of Mathematics and Computer Science, Hobart and Williams Smith Colleges, Geneva, NY, United States
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20
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Toussova OV, Kozlov AP, Verevochkin SV, Lancaster KE, Shaboltas AV, Masharsky A, Dukhovlinova E, Miller WC, Hoffman IF. A Cohort Approach to Real-Time Detection of Acute HIV Infections Among People Who Inject Drugs in St. Petersburg, Russia. AIDS Res Hum Retroviruses 2018; 34:261-268. [PMID: 29145741 DOI: 10.1089/aid.2017.0076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
To detect acute HIV infections (AHIs) in real time among people who inject drugs (PWID) in St. Petersburg, Russia and to test the feasibility of this approach. Prospective cohort study. One hundred seronegative or acutely HIV-infected at screening PWID were enrolled and followed until the end of the 12-month pilot period. Each participant was evaluated, tested, and counseled for HIV monthly. Two HIV tests were used: HIV antibody and HIV RNA PCR. If diagnosed with AHI, participants were followed weekly for a month; then, monthly for 3 months; and then, quarterly for the duration of the follow-up period. HIV risk behavior was assessed at each study visit. Most enrolled PWID were 30-39 years old, male, completed high school or more, not employed full-time, heroin users, and frequently shared injection paraphernalia. AHI prevalence at screening was 1.8% [95% confidence interval (CI): 0.4, 5.5]. Three participants with AHI at enrollment represented 3% (95% CI: 0.6, 8.5) of the 100 participants who consented to enroll. Among the HIV-uninfected participants (n = 97), the AHI incidence over time was 9.3 per 100 person-years. Persons with AHI were more likely to report alcohol intoxication within the prior 30 days. This was the first study to detect AHI using a cohort approach. The approach proved to be feasible: recruitment, retention, AHI detection, and virological endpoints were successfully reached. A cost analysis in a real-world setting would be required to determine if this strategy could be brought to scale. The study revealed continued high HIV incidence rate among PWID in St. Petersburg, Russia and the importance of prevention and treatment programs for this group.
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Affiliation(s)
- Olga V. Toussova
- Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
| | - Andrei P. Kozlov
- The Biomedical Center, St. Petersburg, Russia
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Sergei V. Verevochkin
- The Biomedical Center, St. Petersburg, Russia
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Kathryn E. Lancaster
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | | | | | - Elena Dukhovlinova
- The Biomedical Center, St. Petersburg, Russia
- University of North Carolina, Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina
| | - William C. Miller
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Irving F. Hoffman
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina
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21
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Kosaka PM, Pini V, Calleja M, Tamayo J. Ultrasensitive detection of HIV-1 p24 antigen by a hybrid nanomechanical-optoplasmonic platform with potential for detecting HIV-1 at first week after infection. PLoS One 2017; 12:e0171899. [PMID: 28199410 PMCID: PMC5310927 DOI: 10.1371/journal.pone.0171899] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 01/27/2017] [Indexed: 01/03/2023] Open
Abstract
Early detection of HIV infection is the best way to prevent spread of the disease and to improve the efficiency of the antiretroviral therapy. Nucleic acid amplification tests (NAAT) have become the gold-standard for detecting low-concentrations of the virus in blood. However, these methods are technically demanding and cost-prohibitive in developing countries. Immunoassays are more affordable and can be more easily adapted for point-of-care diagnosis. However, the sensitivity so far of these methods has been too low. We here report the development of a sandwich immunoassay that combines nanomechanical and optoplasmonic transduction methods for detecting the HIV-1 capsid antigen p24 in human serum. The immunoreactions take place on the surface of a compliant microcantilever where gold nanoparticles are used as both mechanical and plasmonic labels. The microcantilever acts as both a mechanical resonator and an optical cavity for the transduction of the mechanical and plasmonic signals. The limit of detection of the immunoassay is 10−17 g/mL that is equivalent to one virion in 10 mL of plasma. This is 5 orders of magnitude better than last generation of approved immunoassays and 2 orders of magnitude better than NAAT. This technology meets the demands to be produced en masse at low cost and the capability for miniaturization to be used at the point-of-care.
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Affiliation(s)
- Priscila M. Kosaka
- IMM–Instituto de Microelectrónica de Madrid (CNM-CSIC), Isaac Newton, 8, PTM, Tres Cantos, Madrid, Spain
- * E-mail: (JT); (PMK)
| | - Valerio Pini
- IMM–Instituto de Microelectrónica de Madrid (CNM-CSIC), Isaac Newton, 8, PTM, Tres Cantos, Madrid, Spain
| | - Montserrat Calleja
- IMM–Instituto de Microelectrónica de Madrid (CNM-CSIC), Isaac Newton, 8, PTM, Tres Cantos, Madrid, Spain
| | - Javier Tamayo
- IMM–Instituto de Microelectrónica de Madrid (CNM-CSIC), Isaac Newton, 8, PTM, Tres Cantos, Madrid, Spain
- * E-mail: (JT); (PMK)
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Abstract
In this chapter, we will review recent research on the virology of HIV-1 transmission and the impact of the transmitted virus genotype on subsequent disease progression. In most instances of HIV-1 sexual transmission, a single genetic variant, or a very limited number of variants from the diverse viral quasi-species present in the transmitting partner establishes systemic infection. Transmission involves both stochastic and selective processes, such that in general a minority variant in the donor is transmitted. While there is clear evidence for selection, the biological properties that mediate transmission remain incompletely defined. Nevertheless, the genotype of the transmitted founder virus, which reflects prior exposure to and escape from host immune responses, clearly influences disease progression. Some escape mutations impact replicative capacity, while others effectively cloak the virus from the newly infected host's immune response by preventing recognition. It is the balance between the impact of escape mutations on viral fitness and susceptibility to the host immunogenetics that defines HIV-1 disease progression.
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Little SJ. Treatment of Acute HIV Infection and the Potential Role of Acutely HIV-Infected Persons in Cure Studies. TOPICS IN ANTIVIRAL MEDICINE 2016; 23:156-160. [PMID: 27398768 PMCID: PMC6148942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Diagnosis of acute HIV infection is important for accurate estimation of HIV incidence, identifying persons who are unaware of their HIV infection, and offering immediate treatment and risk-reduction strategies. The higher viral loads associated with acute HIV infection are associated with an increased risk of transmission. Current treatment recommendations are the same for acute and established infections. Studies of acute HIV infection indicate that initiation of antiretroviral therapy during this period may allow greater recovery of CD4+ T-cell count and function and may result in a smaller latent viral reservoir and a skewing of infection away from central memory CD4+ T cells toward shorter-lived transitional memory CD4+ T cells. This article summarizes a presentation by Susan J. Little, MD, at the IAS-USA continuing education program, Improving the Management of HIV Disease, held in Los Angeles, California, in April 2015.
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Monitoring Integration over Time Supports a Role for Cytotoxic T Lymphocytes and Ongoing Replication as Determinants of Reservoir Size. J Virol 2016; 90:10436-10445. [PMID: 27630237 DOI: 10.1128/jvi.00242-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/15/2016] [Indexed: 01/30/2023] Open
Abstract
The dynamics of HIV reservoir accumulation off antiretroviral therapy (ART) is underexplored. Levels of integrated HIV DNA in peripheral blood mononuclear cells (PBMCs) were longitudinally monitored before and after antiviral therapy. HIV integration increased over time in both elite controllers (ECs; n = 8) and noncontrollers (NCs; n = 6) before ART, whereas integration remained stable in patients on ART (n = 4). The median annual fold change was higher in NCs than in ECs and negatively correlated with CD4/CD8 T-cell ratio. Cytotoxic T lymphocyte (CTL) function as assessed by infected CD4 T-cell elimination (ICE) and granzyme B activity did not significantly change over time in ECs, suggesting that the gradual increase in integrated HIV DNA observed in ECs was not a result of progressive loss of immune-mediated control. Also, acutely infected (n = 7) but not chronically infected (n = 6) patients exhibited a significant drop in integrated HIV DNA 12 months after ART initiation. In conclusion, in the absence of ART, integrated HIV accumulates over time both in NCs and in ECs, at variable individual rates. Starting ART early in infection leads to a greater drop in integrated HIV DNA than does initiating treatment after years of infection. The increase in integrated HIV DNA over time suggests that early treatment may be of benefit in limiting HIV reservoirs. IMPORTANCE The establishment of a latent reservoir represents a barrier to cure among HIV-infected individuals. The dynamics of HIV reservoir accumulation over time in patients before antiviral therapy is underexplored, in large part because it is difficult to accurately and reproducibly measure the size of HIV reservoir in this setting. In our study, we compared the dynamics of integrated HIV DNA over time in ECs and NCs before and after ART was initiated. We found that integrated HIV DNA levels progressively increase over time in the absence of ART, but with a higher, albeit variable, rate in NCs compared to ECs. In addition, integrated HIV DNA declines more dramatically when ART is initiated in acute rather than chronic HIV infection, suggesting important differences between acute and chronic infection. Our study highlights the role of HIV replication and CTL control in reservoir accumulation in sanctuary sites and why ART appears to be more effective in acute infection.
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Vaidya NK, Ribeiro RM, Perelson AS, Kumar A. Modeling the Effects of Morphine on Simian Immunodeficiency Virus Dynamics. PLoS Comput Biol 2016; 12:e1005127. [PMID: 27668463 PMCID: PMC5036892 DOI: 10.1371/journal.pcbi.1005127] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 08/25/2016] [Indexed: 12/20/2022] Open
Abstract
Complications of HIV-1 infection in individuals who utilize drugs of abuse is a significant problem, because these drugs have been associated with higher virus replication and accelerated disease progression as well as severe neuropathogenesis. To gain further insight it is important to quantify the effects of drugs of abuse on HIV-1 infection dynamics. Here, we develop a mathematical model that incorporates experimentally observed effects of morphine on inducing HIV-1 co-receptor expression. For comparison we also considered viral dynamic models with cytolytic or noncytolytic effector cell responses. Based on the small sample size Akaike information criterion, these models were inferior to the new model based on changes in co-receptor expression. The model with morphine affecting co-receptor expression agrees well with the experimental data from simian immunodeficiency virus infections in morphine-addicted macaques. Our results show that morphine promotes a target cell subpopulation switch from a lower level of susceptibility to a state that is about 2-orders of magnitude higher in susceptibility to SIV infection. As a result, the proportion of target cells with higher susceptibility remains extremely high in morphine conditioning. Such a morphine-induced population switch not only has adverse effects on the replication rate, but also results in a higher steady state viral load and larger CD4 count drops. Moreover, morphine conditioning may pose extra obstacles to controlling viral load during antiretroviral therapy, such as pre-exposure prophylaxis and post infection treatments. This study provides, for the first time, a viral dynamics model, viral dynamics parameters, and related analytical and simulation results for SIV dynamics under drugs of abuse.
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Affiliation(s)
- Naveen K. Vaidya
- Department of Mathematics and Statistics, University of Missouri-Kansas City, Missouri, United States of America
- Division of Pharmacology, School of Pharmacy, University of Missouri-Kansas City, Missouri, United States of America
| | - Ruy M. Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alan S. Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Anil Kumar
- Division of Pharmacology, School of Pharmacy, University of Missouri-Kansas City, Missouri, United States of America
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Incorporating Acute HIV Screening into Routine HIV Testing at Sexually Transmitted Infection Clinics, and HIV Testing and Counseling Centers in Lilongwe, Malawi. J Acquir Immune Defic Syndr 2016; 71:272-80. [PMID: 26428231 PMCID: PMC4752378 DOI: 10.1097/qai.0000000000000853] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Background and Objectives: Integrating acute HIV-infection (AHI) testing into clinical settings is critical to prevent transmission, and realize potential treatment-as-prevention benefits. We evaluated acceptability of AHI testing and compared AHI prevalence at sexually transmitted infection (STI) clinics and HIV testing and counseling (HTC) clinics in Lilongwe, Malawi. Methods: We conducted HIV RNA testing for HIV-seronegative patients visiting STI and HTC clinics. AHI was defined as positive RNA and negative/discordant rapid antibody tests. We evaluated demographic, behavioral, and transmission-risk differences between STI and HTC patients and assessed performance of a risk-score for targeted screening. Results: Nearly two-thirds (62.8%, 9280/14,755) of eligible patients consented to AHI testing. We identified 59 persons with AHI (prevalence = 0.64%)–a 0.9% case-identification increase. Prevalence was higher at STI [1.03% (44/4255)] than at HTC clinics [0.3% (15/5025), P < 0.01], accounting for 2.3% of new diagnoses vs 0.3% at HTC clinic. Median viral load (VL) was 758,050 copies per milliliter; 25% (15/59) had VL ≥10,000,000 copies per milliliter. Median VL was higher at STI (1,000,000 copies/mL) compared with HTC (153,125 copies/mL, P = 0.2). Among persons with AHI, those tested at STI clinics were more likely to report genital sores compared with those tested at HTC clinics (54.6% vs 6.7%, P < 0.01). The risk score algorithm performed well in identifying persons with AHI at HTC clinics (sensitivity = 73%, specificity = 89%). Conclusions: The majority of patients consented to AHI testing. AHI prevalence was substantially higher in STI clinics than HTC clinics. Remarkably high VLs and concomitant genital scores demonstrate the potential for transmission. Universal AHI screening at STI clinics, and targeted screening at HTC centers, should be considered.
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Li H, Stoddard MB, Wang S, Giorgi EE, Blair LM, Learn GH, Hahn BH, Alter HJ, Busch MP, Fierer DS, Ribeiro RM, Perelson AS, Bhattacharya T, Shaw GM. Single-Genome Sequencing of Hepatitis C Virus in Donor-Recipient Pairs Distinguishes Modes and Models of Virus Transmission and Early Diversification. J Virol 2016; 90:152-66. [PMID: 26468546 PMCID: PMC4702571 DOI: 10.1128/jvi.02156-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/02/2015] [Indexed: 01/06/2023] Open
Abstract
UNLABELLED Despite the recent development of highly effective anti-hepatitis C virus (HCV) drugs, the global burden of this pathogen remains immense. Control or eradication of HCV will likely require the broad application of antiviral drugs and development of an effective vaccine. A precise molecular identification of transmitted/founder (T/F) HCV genomes that lead to productive clinical infection could play a critical role in vaccine research, as it has for HIV-1. However, the replication schema of these two RNA viruses differ substantially, as do viral responses to innate and adaptive host defenses. These differences raise questions as to the certainty of T/F HCV genome inferences, particularly in cases where multiple closely related sequence lineages have been observed. To clarify these issues and distinguish between competing models of early HCV diversification, we examined seven cases of acute HCV infection in humans and chimpanzees, including three examples of virus transmission between linked donors and recipients. Using single-genome sequencing (SGS) of plasma vRNA, we found that inferred T/F sequences in recipients were identical to viral sequences in their respective donors. Early in infection, HCV genomes generally evolved according to a simple model of random evolution where the coalescent corresponded to the T/F sequence. Closely related sequence lineages could be explained by high multiplicity infection from a donor whose viral sequences had undergone a pretransmission bottleneck due to treatment, immune selection, or recent infection. These findings validate SGS, together with mathematical modeling and phylogenetic analysis, as a novel strategy to infer T/F HCV genome sequences. IMPORTANCE Despite the recent development of highly effective, interferon-sparing anti-hepatitis C virus (HCV) drugs, the global burden of this pathogen remains immense. Control or eradication of HCV will likely require the broad application of antiviral drugs and the development of an effective vaccine, which could be facilitated by a precise molecular identification of transmitted/founder (T/F) viral genomes and their progeny. We used single-genome sequencing to show that inferred HCV T/F sequences in recipients were identical to viral sequences in their respective donors and that viral genomes generally evolved early in infection according to a simple model of random sequence evolution. Altogether, the findings validate T/F genome inferences and illustrate how T/F sequence identification can illuminate studies of HCV transmission, immunopathogenesis, drug resistance development, and vaccine protection, including sieving effects on breakthrough virus strains.
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Affiliation(s)
- Hui Li
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mark B Stoddard
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shuyi Wang
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elena E Giorgi
- T-Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Lily M Blair
- T-Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA Department of Biology, Stanford University, Stanford, California, USA
| | - Gerald H Learn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Harvey J Alter
- Department of Transfusion Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael P Busch
- Blood Systems Research Institute, University of California San Francisco, San Francisco, California, USA
| | - Daniel S Fierer
- Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ruy M Ribeiro
- T-Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Tanmoy Bhattacharya
- T-Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA Santa Fe Institute, Santa Fe, New Mexico, USA
| | - George M Shaw
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Suthar AB, Granich RM, Kato M, Nsanzimana S, Montaner JSG, Williams BG. Programmatic Implications of Acute and Early HIV Infection. J Infect Dis 2015; 212:1351-60. [PMID: 26310309 DOI: 10.1093/infdis/jiv430] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/18/2015] [Indexed: 02/01/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection includes acute, early, chronic, and late stages. Acute HIV infection lasts approximately 3 weeks and early HIV infection, which includes acute HIV infection, lasts approximately 7 weeks. Many testing and blood screening algorithms detect HIV antibodies about 3 weeks after HIV infection. Incidence estimates are based on results of modeling, cohort studies, surveillance, and/or assays. Viral load is the key modifiable risk factor for HIV transmission and peaks during acute and early HIV infection. Empirical evidence characterizing the impact of acute and early HIV infection on the spread of the HIV epidemic are limited. Time trends of HIV prevalence collected from concentrated and generalized epidemics suggest that acute and early HIV infection may have a limited role in population HIV transmission. Collectively, these data suggest that acute and early HIV infection is relatively short and does not currently require fundamentally different programmatic approaches to manage the HIV/AIDS epidemic in most settings. Research and surveillance will inform which epidemic contexts and phases may require tailored strategies for these stages of HIV infection.
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Affiliation(s)
- Amitabh B Suthar
- South African Centre for Epidemiological Modelling and Analysis, University of Stellenbosch, South Africa
| | - Reuben M Granich
- International Association of Providers of AIDS Care, Washington D.C
| | - Masaya Kato
- World Health Organization Vietnam Country Office, Hanoi
| | | | | | - Brian G Williams
- Wits Reproductive Health Institute, University of the Witwatersrand, Johannesburg, South Africa
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Caro-Vega Y, del Rio C, Dias Lima V, Lopez-Cervantes M, Crabtree-Ramirez B, Bautista-Arredondo S, Colchero MA, Sierra-Madero J. Estimating the Impact of Earlier ART Initiation and Increased Testing Coverage on HIV Transmission among Men Who Have Sex with Men in Mexico using a Mathematical Model. PLoS One 2015; 10:e0136534. [PMID: 26302044 PMCID: PMC4547810 DOI: 10.1371/journal.pone.0136534] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 08/04/2015] [Indexed: 12/26/2022] Open
Abstract
Objective To estimate the impact of late ART initiation on HIV transmission among men who have sex with men (MSM) in Mexico. Methods An HIV transmission model was built to estimate the number of infections transmitted by HIV-infected men who have sex with men (MSM-HIV+) MSM-HIV+ in the short and long term. Sexual risk behavior data were estimated from a nationwide study of MSM. CD4+ counts at ART initiation from a representative national cohort were used to estimate time since infection. Number of MSM-HIV+ on treatment and suppressed were estimated from surveillance and government reports. Status quo scenario (SQ), and scenarios of early ART initiation and increased HIV testing were modeled. Results We estimated 14239 new HIV infections per year from MSM-HIV+ in Mexico. In SQ, MSM take an average 7.4 years since infection to initiate treatment with a median CD4+ count of 148 cells/mm3(25th-75th percentiles 52–266). In SQ, 68% of MSM-HIV+ are not aware of their HIV status and transmit 78% of new infections. Increasing the CD4+ count at ART initiation to 350 cells/mm3 shortened the time since infection to 2.8 years. Increasing HIV testing to cover 80% of undiagnosed MSM resulted in a reduction of 70% in new infections in 20 years. Initiating ART at 500 cells/mm3 and increasing HIV testing the reduction would be of 75% in 20 years. Conclusion A substantial number of new HIV infections in Mexico are transmitted by undiagnosed and untreated MSM-HIV+. An aggressive increase in HIV testing coverage and initiating ART at a CD4 count of 500 cells/mm3 in this population would significantly benefit individuals and decrease the number of new HIV infections in Mexico.
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Affiliation(s)
- Yanink Caro-Vega
- Faculty of Medicine, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubiran, Mexico City, Mexico
| | - Carlos del Rio
- Hubert Department of Global Health, Rollins School of Public Health & Emory Center for AIDS Research, Atlanta, Georgia, United States of America
| | - Viviane Dias Lima
- Division of AIDS, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Brenda Crabtree-Ramirez
- Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubiran, Mexico City, Mexico
| | - Sergio Bautista-Arredondo
- Division of Health Economics and Health Systems Innovations, National Institute of Public Health, Cuernavaca, Morelos, Mexico
| | - M. Arantxa Colchero
- Division of Health Economics and Health Systems Innovations, National Institute of Public Health, Cuernavaca, Morelos, Mexico
| | - Juan Sierra-Madero
- Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubiran, Mexico City, Mexico
- * E-mail:
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Reassessment of HIV-1 acute phase infectivity: accounting for heterogeneity and study design with simulated cohorts. PLoS Med 2015; 12:e1001801. [PMID: 25781323 PMCID: PMC4363602 DOI: 10.1371/journal.pmed.1001801] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 02/04/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The infectivity of the HIV-1 acute phase has been directly measured only once, from a retrospectively identified cohort of serodiscordant heterosexual couples in Rakai, Uganda. Analyses of this cohort underlie the widespread view that the acute phase is highly infectious, even more so than would be predicted from its elevated viral load, and that transmission occurring shortly after infection may therefore compromise interventions that rely on diagnosis and treatment, such as antiretroviral treatment as prevention (TasP). Here, we re-estimate the duration and relative infectivity of the acute phase, while accounting for several possible sources of bias in published estimates, including the retrospective cohort exclusion criteria and unmeasured heterogeneity in risk. METHODS AND FINDINGS We estimated acute phase infectivity using two approaches. First, we combined viral load trajectories and viral load-infectivity relationships to estimate infectivity trajectories over the course of infection, under the assumption that elevated acute phase infectivity is caused by elevated viral load alone. Second, we estimated the relative hazard of transmission during the acute phase versus the chronic phase (RHacute) and the acute phase duration (dacute) by fitting a couples transmission model to the Rakai retrospective cohort using approximate Bayesian computation. Our model fit the data well and accounted for characteristics overlooked by previous analyses, including individual heterogeneity in infectiousness and susceptibility and the retrospective cohort's exclusion of couples that were recorded as serodiscordant only once before being censored by loss to follow-up, couple dissolution, or study termination. Finally, we replicated two highly cited analyses of the Rakai data on simulated data to identify biases underlying the discrepancies between previous estimates and our own. From the Rakai data, we estimated RHacute = 5.3 (95% credibility interval [95% CrI]: 0.79-57) and dacute = 1.7 mo (95% CrI: 0.55-6.8). The wide credibility intervals reflect an inability to distinguish a long, mildly infectious acute phase from a short, highly infectious acute phase, given the 10-mo Rakai observation intervals. The total additional risk, measured as excess hazard-months attributable to the acute phase (EHMacute) can be estimated more precisely: EHMacute = (RHacute - 1) × dacute, and should be interpreted with respect to the 120 hazard-months generated by a constant untreated chronic phase infectivity over 10 y of infection. From the Rakai data, we estimated that EHMacute = 8.4 (95% CrI: -0.27 to 64). This estimate is considerably lower than previously published estimates, and consistent with our independent estimate from viral load trajectories, 5.6 (95% confidence interval: 3.3-9.1). We found that previous overestimates likely stemmed from failure to account for risk heterogeneity and bias resulting from the retrospective cohort study design. Our results reflect the interaction between the retrospective cohort exclusion criteria and high (47%) rates of censorship amongst incident serodiscordant couples in the Rakai study due to loss to follow-up, couple dissolution, or study termination. We estimated excess physiological infectivity during the acute phase from couples data, but not the proportion of transmission attributable to the acute phase, which would require data on the broader population's sexual network structure. CONCLUSIONS Previous EHMacute estimates relying on the Rakai retrospective cohort data range from 31 to 141. Our results indicate that these are substantial overestimates of HIV-1 acute phase infectivity, biased by unmodeled heterogeneity in transmission rates between couples and by inconsistent censoring. Elevated acute phase infectivity is therefore less likely to undermine TasP interventions than previously thought. Heterogeneity in infectiousness and susceptibility may still play an important role in intervention success and deserves attention in future analyses.
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Sterrett S, Learn GH, Edlefsen PT, Haynes BF, Hahn BH, Shaw GM, Bar KJ. Low Multiplicity of HIV-1 Infection and No Vaccine Enhancement in VAX003 Injection Drug Users. Open Forum Infect Dis 2014; 1:ofu056. [PMID: 25734126 PMCID: PMC4281816 DOI: 10.1093/ofid/ofu056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 06/23/2014] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND We performed human immunodeficiency virus type 1 (HIV-1) transmitted/founder (T/F) virus analysis of the VAX003 vaccine efficacy trial participants to characterize the transmission bottleneck and test for vaccine-associated reduction or enhancement of infection in this injection drug user (IDU) cohort. METHODS We performed single genome sequencing of plasma vRNA from 50 subjects sampled in early HIV infection. Sequences were analyzed phylogenetically, T/F viruses enumerated, and a sieve analysis performed. RESULTS Eight of 19 (42%) placebo recipients were productively infected by more than 1 virus (range 1-5, median 1, mean 1.7). This frequency of multiple virus transmission was greater than reported for heterosexual cohorts (19%, P = .03) but not statistically different from vaccine recipients (22.6%, P > .05), where the range was 1-3, median 1, and mean 1.3 (P > .05 for all comparisons). An atypical sieve effect was detected in Env V2 but was not associated with reduction or enhancement of virus acquisition. CONCLUSIONS The number of T/F viruses in IDUs was surprising low, with 95% of individuals infected by only 1-3 viruses. This finding suggests that a successful vaccine or other prevention modality generally needs to protect against only one or a few viruses regardless of risk behavior. T/F analysis identified an atypical genetic sieve in the V2 region of Envelope and found no evidence for vaccine-mediated enhancement in VAX003.
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Affiliation(s)
| | - Gerald H Learn
- Perelman School of Medicine , University of Pennsylvania , Philadelphia
| | - Paul T Edlefsen
- Fred Hutchinson Cancer Research Center , Seattle, Washington
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University Medical Center , Durham, North Carolina
| | - Beatrice H Hahn
- Perelman School of Medicine , University of Pennsylvania , Philadelphia
| | - George M Shaw
- Perelman School of Medicine , University of Pennsylvania , Philadelphia
| | - Katharine J Bar
- Perelman School of Medicine , University of Pennsylvania , Philadelphia
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Prevention of HIV-1 transmission with postexposure prophylaxis after inadvertent infected blood transfusion. AIDS 2014; 28:1539-41. [PMID: 24896805 DOI: 10.1097/qad.0000000000000268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Impact of viral load and the duration of primary infection on HIV transmission: systematic review and meta-analysis. AIDS 2014; 28:1021-9. [PMID: 24691205 DOI: 10.1097/qad.0000000000000135] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
OBJECTIVES HIV 'treatment as prevention' (TasP) describes early treatment of HIV-infected patients intended to reduce viral load and transmission. Crucial assumptions for estimating TasP's effectiveness are the underlying estimates of transmission risk. We aimed to determine transmission risk during primary infection, and describe the relation of HIV transmission risk to viral load. DESIGN A systematic review and meta-analysis. METHODS We searched PubMed and Embase databases for studies that established a relationship between viral load and transmission risk, or primary infection and transmission risk, in serodiscordant couples. We analysed assumptions about the relationship between viral load and transmission risk, and between duration of primary infection and transmission risk. RESULTS We found 36 eligible articles, based on six different study populations. Studies consistently found that higher viral loads lead to higher HIV transmission rates, but assumptions about the shape of this increase varied from exponential increase to saturation. The assumed duration of primary infection ranged from 1.5 to 12 months; for each additional month, the log10 transmission rate ratio between primary and asymptomatic infection decreased by 0.40. CONCLUSION Assumptions and estimates of the relationship between viral load and transmission risk, and the relationship between primary infection and transmission risk, vary substantially and predictions of TasP's effectiveness should take this uncertainty into account.
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Abstract
PURPOSE OF REVIEW The development of a preventive HIV vaccine remains an unresolved challenge. Animal models that can predict the results of HIV vaccine efficacy trials and identify the immune mechanisms responsible for vaccine protection would be most useful for HIV vaccine development. The purpose of the current review is to critique recent developments in the use of animal models of HIV infection in preclinical studies of AIDS vaccines and to describe how the use of improved animal models can inform the development of an HIV vaccine. RECENT FINDINGS The results of preclinical experiments with candidate HIV vaccines can vary with the SIV challenge virus used. It is now known that there is considerable variability in the neutralization sensitivity and that the level of viral sequence diversity within the challenge stocks varies. This has allowed more realistic preclinical vaccine studies with heterologous vaccine antigens and challenge viruses. Further, the dose of challenge virus and the route of virus challenge can modify the efficacy of candidate vaccines in preclinical studies. SUMMARY Recent experiments demonstrate that nonhuman primate models of AIDS can reproduce the complex biology of HIV transmission, recapitulate the results of HIV vaccine efficacy trials in humans and be used to identify correlates of protection.
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Wang X, Liu S, Rong L. Permanence and extinction of a non-autonomous HIV-1
model with time delays. ACTA ACUST UNITED AC 2014. [DOI: 10.3934/dcdsb.2014.19.1783] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Cohen MS, Smith MK, Muessig KE, Hallett TB, Powers KA, Kashuba AD. Antiretroviral treatment of HIV-1 prevents transmission of HIV-1: where do we go from here? Lancet 2013; 382:1515-24. [PMID: 24152938 PMCID: PMC3880570 DOI: 10.1016/s0140-6736(13)61998-4] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Antiretroviral drugs that inhibit viral replication were expected to reduce transmission of HIV by lowering the concentration of HIV in the genital tract. In 11 of 13 observational studies, antiretroviral therapy (ART) provided to an HIV-infected index case led to greatly reduced transmission of HIV to a sexual partner. In the HPTN 052 randomised controlled trial, ART used in combination with condoms and counselling reduced HIV transmission by 96·4%. Evidence is growing that wider, earlier initiation of ART could reduce population-level incidence of HIV. However, the full benefits of this strategy will probably need universal access to very early ART and excellent adherence to treatment. Challenges to this approach are substantial. First, not all HIV-infected individuals can be located, especially people with acute and early infection who are most contagious. Second, the ability of ART to prevent HIV transmission in men who have sex with men (MSM) and people who use intravenous drugs has not been shown. Indeed, the stable or increased incidence of HIV in MSM in some communities where widespread use of ART has been established emphasises the concern that not enough is known about treatment as prevention for this crucial population. Third, although US guidelines call for immediate use of ART, such guidelines have not been embraced worldwide. Some experts do not believe that immediate or early ART is justified by present evidence, or that health-care infrastructure for this approach is sufficient. These concerns are very difficult to resolve. Ongoing community-based prospective trials of early ART are likely to help to establish the population-level benefit of ART, and-if successful-to galvanise treatment as prevention.
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Affiliation(s)
- Myron S Cohen
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA; Department of Microbiology, University of North Carolina, Chapel Hill, NC, USA; Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA.
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Bruhn R, Lelie N, Custer B, Busch M, Kleinman S. Prevalence of human immunodeficiency virus RNA and antibody in first-time, lapsed, and repeat blood donations across five international regions and relative efficacy of alternative screening scenarios. Transfusion 2013; 53:2399-412. [DOI: 10.1111/trf.12299] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 04/17/2013] [Accepted: 04/17/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Roberta Bruhn
- Blood Systems Research Institute; Lelie Research; San Francisco California Paris France
- University of British Columbia; Canada
| | - Nico Lelie
- Blood Systems Research Institute; Lelie Research; San Francisco California Paris France
- University of British Columbia; Canada
| | - Brian Custer
- Blood Systems Research Institute; Lelie Research; San Francisco California Paris France
- University of British Columbia; Canada
| | - Michael Busch
- Blood Systems Research Institute; Lelie Research; San Francisco California Paris France
- University of British Columbia; Canada
| | - Steven Kleinman
- Blood Systems Research Institute; Lelie Research; San Francisco California Paris France
- University of British Columbia; Canada
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Vermeulen M, Coleman C, Mitchel J, Reddy R, van Drimmelen H, Fickett T, Busch M, Lelie N. Comparison of human immunodeficiency virus assays in window phase and elite controller samples: viral load distribution and implications for transmission risk. Transfusion 2013; 53:2384-98. [PMID: 23445273 PMCID: PMC5061040 DOI: 10.1111/trf.12117] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 12/04/2012] [Accepted: 12/04/2012] [Indexed: 01/02/2023]
Abstract
BACKGROUND After 3 years of individual-donation nucleic acid test (ID-NAT) screening by the South African National Blood Service (SANBS), a repository of 73 human immunodeficiency virus antibody (anti-HIV)-negative window period (WP)-yield samples and 28 anti-HIV-positive, HIV-RNA-negative elite controllers (ECs) became available for comparison of a p24 antigen (p24 Ag) assay (Innogenetics), two viral load assays (Siemens branch DNA [bDNA] 3.0 and Abbott real-time polymerase chain reaction [RT-PCR]), and three triplex NAT assays (Novartis Diagnostics Ultrio and Ultrio-Plus and Roche TaqScreen) by replicate testing of dilutions. STUDY DESIGN AND METHODS Viral loads were assessed by bDNA and RT-PCR assays and if below 100 copies (cps)/mL, by Ultrio limiting dilution probit analysis. The probability of virus transmission by WP and EC donations was estimated for different levels of the 50% minimum infectious dose (ID50 ) using Poisson distribution statistics. RESULTS The equal distribution of WP donations plotted by log HIV-RNA levels indicated a random appearance of donors in the ramp-up phase. The HIV p24 Ag assay detected 45% of WP samples and the cutoff crossing point was estimated at 8140 (bDNA)/22,710 (RT-PCR) cps/mL. On replicate retesting of 40 HIV p24 Ag-negative ID-NAT WP-yield samples Ultrio minipool (MP)8, Ultrio-Plus MP8, and TaqScreen MP6 detected 79, 81, and 78%, respectively. Modeling with an estimated ID50 of 31.6 virions/RBC indicated that 15% of p24 Ag-negative ID-NAT WP-yield donations would have transmitted HIV if MP6-8 NAT had been used. Only 2% of RBC transfusions from ECs are estimated to be infectious with a worst-case ID50 estimate of 316 virions. CONCLUSION Our analysis of viremia and infectivity of WP and EC donations enables comparison of the efficacy of NAT options in preventing HIV transmission risk.
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Affiliation(s)
- Marion Vermeulen
- South African National Blood Service (SANBS), Johannesburg, South Africa; BioQControl, DDL Laboratories, Rijswijk, Netherlands; Creative Testing Solutions, Tampa, Florida; Blood Systems Research Institute, San Francisco, California; Lelie Research Paris, Paris, France
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41
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Perelson AS, Ribeiro RM. Modeling the within-host dynamics of HIV infection. BMC Biol 2013; 11:96. [PMID: 24020860 PMCID: PMC3765939 DOI: 10.1186/1741-7007-11-96] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 09/02/2013] [Indexed: 02/07/2023] Open
Abstract
The new field of viral dynamics, based on within-host modeling of viral infections, began with models of human immunodeficiency virus (HIV), but now includes many viral infections. Here we review developments in HIV modeling, emphasizing quantitative findings about HIV biology uncovered by studying acute infection, the response to drug therapy and the rate of generation of HIV variants that escape immune responses. We show how modeling has revealed many dynamical features of HIV infection and how it may provide insight into the ultimate cure for this infection.
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Affiliation(s)
- Alan S Perelson
- MS K710, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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42
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Ramos EM, Harb S, Dragavon J, Swenson P, Stekler JD, Coombs RW. Performance of an alternative HIV diagnostic algorithm using the ARCHITECT HIV Ag/Ab Combo assay and potential utility of sample-to-cutoff ratio to discriminate primary from established infection. J Clin Virol 2013; 58 Suppl 1:e38-43. [PMID: 24029686 DOI: 10.1016/j.jcv.2013.08.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 08/13/2013] [Accepted: 08/17/2013] [Indexed: 01/01/2023]
Abstract
BACKGROUND The ARCHITECT HIV Ag/Ab Combo assay has a wide dynamic range for determining the sample-to-cutoff ratio (S/CO) values compared to other diagnostic HIV antibody assays. OBJECTIVES Determine the performance of an HIV testing algorithm that uses the ARCHITECT combo assay in the clinical setting and explore the utility of the signal-to-cutoff (S/CO) ratio to predict acute HIV-1 infection status. STUDY DESIGN A retrospective analysis of clinical samples from a hospital and referral population screened for HIV-1 infection between May 2011 and March 2013. Repeatedly reactive samples were tested using the Multispot HIV-1/HIV-2 rapid test and depending on that result, confirmatory orthogonal testing used the Western blot (WB) for HIV-1, Immunoblot for HIV-2 and nucleic acid amplification testing (NAAT) for HIV RNA. RESULTS A total of 21,317 test results were evaluated of which 509 were ARCHITECT repeatedly reactive; of these, 422 were Multispot-reactive only for HIV-1 (413 WB-positive; 9 indeterminate), 4 were Multispot-reactive for both HIV-1 and HIV-2 (one HIV-2 immunoblot-positive with 17 HIV-2 RNA copies/mL) and 83 were Multispot-non-reactive of which 15 were HIV-1 RNA positive and represented acute HIV-1 infection. There was an association among the ARCHITECT S/CO (median; IQR) values for antibody-negative (0.14; 0.11-0.16), acute infection (33; 2.1-76) and established HIV-1 infection (794; 494-1,029) (Kruskal-Wallis, p<0.0001). CONCLUSIONS The ARCHITECT combo assay with Multispot confirmation and reserved use of HIV-1 WB, HIV-2 Immunoblot and HIV NAAT for Multispot dual HIV-1/2 infection, and NAAT alone for Multispot-negative specimens, had a suitable test performance for detecting acute and established HIV infection.
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Affiliation(s)
- Eric M Ramos
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States.
| | - Socorro Harb
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States
| | - Joan Dragavon
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States
| | - Paul Swenson
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States; Public Health - Seattle and King County, United States
| | - Joanne D Stekler
- Public Health - Seattle and King County, United States; Department of Medicine, University of Washington, Seattle, WA, United States
| | - Robert W Coombs
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States; Department of Medicine, University of Washington, Seattle, WA, United States
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Smith MK, Rutstein SE, Powers KA, Fidler S, Miller WC, Eron JJ, Cohen MS. The detection and management of early HIV infection: a clinical and public health emergency. J Acquir Immune Defic Syndr 2013; 63 Suppl 2:S187-99. [PMID: 23764635 PMCID: PMC4015137 DOI: 10.1097/qai.0b013e31829871e0] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
This review considers the detection and management of early HIV infection (EHI), defined here as the first 6 months of infection. This phase is clinically important because a reservoir of infected cells formed in the individual renders HIV incurable, and the magnitude of viremia at the end of this period predicts the natural history of disease. Epidemiologically, it is critical because the very high viral load that typically accompanies early infection also makes infected individuals maximally contagious to their sexual partners. Future efforts to prevent HIV transmission with expanded testing and treatment may be compromised by elevated transmission risk earlier in the course of HIV infection, although the extent of this impact is yet unknown. Treatment as prevention efforts will nevertheless need to develop strategies to address testing, linkage to care, and treatment of EHI. Cost-effective and efficient identification of more persons with early HIV will depend on advancements in diagnostic technology and strengthened symptom-based screening strategies. Treatment for persons with EHI must balance individual health benefits and reduction of the risk of onward viral transmission. An increasing body of evidence supports the use of immediate antiretroviral therapy to treat EHI to maintain CD4 count and functionality, limit the size of the HIV reservoir, and reduce the risk of onward viral transmission. Although we can anticipate considerable challenges in identifying and linking to care persons in the earliest phases of HIV infection, there are many reasons to pursue this strategy.
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Affiliation(s)
- M Kumi Smith
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Petrie SM, Guarnaccia T, Laurie KL, Hurt AC, McVernon J, McCaw JM. Reducing uncertainty in within-host parameter estimates of influenza infection by measuring both infectious and total viral load. PLoS One 2013; 8:e64098. [PMID: 23691157 PMCID: PMC3655064 DOI: 10.1371/journal.pone.0064098] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 04/08/2013] [Indexed: 11/19/2022] Open
Abstract
For in vivo studies of influenza dynamics where within-host measurements are fit with a mathematical model, infectivity assays (e.g. 50% tissue culture infectious dose; TCID50) are often used to estimate the infectious virion concentration over time. Less frequently, measurements of the total (infectious and non-infectious) viral particle concentration (obtained using real-time reverse transcription-polymerase chain reaction; rRT-PCR) have been used as an alternative to infectivity assays. We investigated the degree to which measuring both infectious (via TCID50) and total (via rRT-PCR) viral load allows within-host model parameters to be estimated with greater consistency and reduced uncertainty, compared with fitting to TCID50 data alone. We applied our models to viral load data from an experimental ferret infection study. Best-fit parameter estimates for the “dual-measurement” model are similar to those from the TCID50-only model, with greater consistency in best-fit estimates across different experiments, as well as reduced uncertainty in some parameter estimates. Our results also highlight how variation in TCID50 assay sensitivity and calibration may hinder model interpretation, as some parameter estimates systematically vary with known uncontrolled variations in the assay. Our techniques may aid in drawing stronger quantitative inferences from in vivo studies of influenza virus dynamics.
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Affiliation(s)
- Stephen M. Petrie
- Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Teagan Guarnaccia
- Monash University, Churchill, Victoria, Australia
- World Health Organization Collaborating Centre for Reference and Research on Influenza, North Melbourne, Victoria, Australia
| | - Karen L. Laurie
- World Health Organization Collaborating Centre for Reference and Research on Influenza, North Melbourne, Victoria, Australia
| | - Aeron C. Hurt
- Monash University, Churchill, Victoria, Australia
- World Health Organization Collaborating Centre for Reference and Research on Influenza, North Melbourne, Victoria, Australia
| | - Jodie McVernon
- Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Vaccine and Immunisation Research Group, Murdoch Childrens Research Institute, Royal Childrens Hospital, Parkville, Victoria, Australia
| | - James M. McCaw
- Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Vaccine and Immunisation Research Group, Murdoch Childrens Research Institute, Royal Childrens Hospital, Parkville, Victoria, Australia
- * E-mail:
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Abstract
Defining the virus-host interactions responsible for HIV-1 transmission, including the phenotypic requirements of viruses capable of establishing de novo infections, could be important for AIDS vaccine development. Previous analyses have failed to identify phenotypic properties other than chemokine receptor 5 (CCR5) and CD4+ T-cell tropism that are preferentially associated with viral transmission. However, most of these studies were limited to examining envelope (Env) function in the context of pseudoviruses. Here, we generated infectious molecular clones of transmitted founder (TF; n = 27) and chronic control (CC; n = 14) viruses of subtypes B (n = 18) and C (n = 23) and compared their phenotypic properties in assays specifically designed to probe the earliest stages of HIV-1 infection. We found that TF virions were 1.7-fold more infectious (P = 0.049) and contained 1.9-fold more Env per particle (P = 0.048) compared with CC viruses. TF viruses were also captured by monocyte-derived dendritic cells 1.7-fold more efficiently (P = 0.035) and more readily transferred to CD4+ T cells (P = 0.025). In primary CD4+ T cells, TF and CC viruses replicated with comparable kinetics; however, when propagated in the presence of IFN-α, TF viruses replicated to higher titers than CC viruses. This difference was significant for subtype B (P = 0.000013) but not subtype C (P = 0.53) viruses, possibly reflecting demographic differences of the respective patient cohorts. Together, these data indicate that TF viruses are enriched for higher Env content, enhanced cell-free infectivity, improved dendritic cell interaction, and relative IFN-α resistance. These viral properties, which likely act in concert, should be considered in the development and testing of AIDS vaccines.
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Community viral load as a measure for assessment of HIV treatment as prevention. THE LANCET. INFECTIOUS DISEASES 2013; 13:459-64. [PMID: 23537801 DOI: 10.1016/s1473-3099(12)70314-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Community viral load, defined as an aggregation of individual viral loads of people infected with HIV in a specific community, has been proposed as a useful measure to monitor HIV treatment uptake and quantify its effect on transmission. The first reports of community viral load were published in 2009, and the measure was subsequently incorporated into the US National HIV/AIDS Strategy. Although intuitively an appealing strategy, measurement of community viral load has several theoretical limitations and biases that need further assessment, which can be grouped into four categories: issues of selection and measurement, the importance of HIV prevalence in determining the potential for ongoing HIV transmission, interpretation of community viral load and its effect on ongoing HIV transmission in a community, and the ecological fallacy (ie, ecological bias). These issues need careful assessment as community viral load is being considered as a public health measurement to assess the effect of HIV care on prevention.
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47
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48
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Goodreau SM, Carnegie NB, Vittinghoff E, Lama JR, Sanchez J, Grinsztejn B, Koblin BA, Mayer KH, Buchbinder SP. What drives the US and Peruvian HIV epidemics in men who have sex with men (MSM)? PLoS One 2012; 7:e50522. [PMID: 23209768 PMCID: PMC3510067 DOI: 10.1371/journal.pone.0050522] [Citation(s) in RCA: 257] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Accepted: 10/23/2012] [Indexed: 01/17/2023] Open
Abstract
In this work, we estimate the proportions of transmissions occurring in main vs. casual partnerships, and by the sexual role, infection stage, and testing and treatment history of the infected partner, for men who have sex with men (MSM) in the US and Peru. We use dynamic, stochastic models based in exponential random graph models (ERGMs), obtaining inputs from multiple large-scale MSM surveys. Parallel main partnership and casual sexual networks are simulated. Each man is characterized by age, race, circumcision status, sexual role behavior, and propensity for unprotected anal intercourse (UAI); his history is modeled from entry into the adult population, with potential transitions including HIV infection, detection, treatment, AIDS diagnosis, and death. We implemented two model variants differing in assumptions about acute infectiousness, and assessed sensitivity to other key inputs. Our two models suggested that only 4–5% (Model 1) or 22–29% (Model 2) of HIV transmission results from contacts with acute-stage partners; the plurality (80–81% and 49%, respectively) stem from chronic-stage partners and the remainder (14–16% and 27–35%, respectively) from AIDS-stage partners. Similar proportions of infections stem from partners whose infection is undiagnosed (24–31%), diagnosed but untreated (36–46%), and currently being treated (30–36%). Roughly one-third of infections (32–39%) occur within main partnerships. Results by country were qualitatively similar, despite key behavioral differences; one exception was that transmission from the receptive to insertive partner appears more important in Peru (34%) than the US (21%). The broad balance in transmission contexts suggests that education about risk, careful assessment, pre-exposure prophylaxis, more frequent testing, earlier treatment, and risk-reduction, disclosure, and adherence counseling may all contribute substantially to reducing the HIV incidence among MSM in the US and Peru.
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Affiliation(s)
- Steven M Goodreau
- Department of Anthropology, University of Washington, Seattle, Washington, United States of America.
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49
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Goodreau SM, Carnegie NB, Vittinghoff E, Lama JR, Sanchez J, Grinsztejn B, Koblin BA, Mayer KH, Buchbinder SP. What drives the US and Peruvian HIV epidemics in men who have sex with men (MSM)? PLoS One 2012; 7:e50522. [PMID: 23209768 DOI: 10.1371/joumal.pone.0050522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Accepted: 10/23/2012] [Indexed: 05/26/2023] Open
Abstract
In this work, we estimate the proportions of transmissions occurring in main vs. casual partnerships, and by the sexual role, infection stage, and testing and treatment history of the infected partner, for men who have sex with men (MSM) in the US and Peru. We use dynamic, stochastic models based in exponential random graph models (ERGMs), obtaining inputs from multiple large-scale MSM surveys. Parallel main partnership and casual sexual networks are simulated. Each man is characterized by age, race, circumcision status, sexual role behavior, and propensity for unprotected anal intercourse (UAI); his history is modeled from entry into the adult population, with potential transitions including HIV infection, detection, treatment, AIDS diagnosis, and death. We implemented two model variants differing in assumptions about acute infectiousness, and assessed sensitivity to other key inputs. Our two models suggested that only 4-5% (Model 1) or 22-29% (Model 2) of HIV transmission results from contacts with acute-stage partners; the plurality (80-81% and 49%, respectively) stem from chronic-stage partners and the remainder (14-16% and 27-35%, respectively) from AIDS-stage partners. Similar proportions of infections stem from partners whose infection is undiagnosed (24-31%), diagnosed but untreated (36-46%), and currently being treated (30-36%). Roughly one-third of infections (32-39%) occur within main partnerships. Results by country were qualitatively similar, despite key behavioral differences; one exception was that transmission from the receptive to insertive partner appears more important in Peru (34%) than the US (21%). The broad balance in transmission contexts suggests that education about risk, careful assessment, pre-exposure prophylaxis, more frequent testing, earlier treatment, and risk-reduction, disclosure, and adherence counseling may all contribute substantially to reducing the HIV incidence among MSM in the US and Peru.
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Affiliation(s)
- Steven M Goodreau
- Department of Anthropology, University of Washington, Seattle, Washington, United States of America.
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50
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Abstract
HIV-1 is transmitted by sexual contact across mucosal surfaces, by maternal-infant exposure, and by percutaneous inoculation. For reasons that are still incompletely understood, CCR5-tropic viruses (R5 viruses) are preferentially transmitted by all routes. Transmission is followed by an orderly appearance of viral and host markers of infection in the blood plasma. In the acute phase of infection, HIV-1 replicates exponentially and diversifies randomly, allowing for an unambiguous molecular identification of transmitted/founder virus genomes and a precise characterization of the population bottleneck to virus transmission. Sexual transmission of HIV-1 most often results in productive clinical infection arising from a single virus, highlighting the extreme bottleneck and inherent inefficiency in virus transmission. It remains to be determined if HIV-1 transmission is largely a stochastic process whereby any reasonably fit R5 virus can be transmitted or if there are features of transmitted/founder viruses that facilitate their transmission in a biologically meaningful way. Human tissue explant models of HIV-1 infection and animal models of SIV/SHIV/HIV-1 transmission, coupled with new challenge virus strains that more closely reflect transmitted/founder viruses, have the potential to elucidate fundamental mechanisms in HIV-1 transmission relevant to vaccine design and other prevention strategies.
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Affiliation(s)
- George M Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104, USA
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