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Sheng B, Li C, Bao L, Li R. Probabilistic HIV recency classification-a logistic regression without labeled individual level training data. Ann Appl Stat 2023; 17:108-129. [PMID: 37846343 PMCID: PMC10577400 DOI: 10.1214/22-aoas1618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Accurate HIV incidence estimation based on individual recent infection status (recent vs long-term infection) is important for monitoring the epidemic, targeting interventions to those at greatest risk of new infection, and evaluating existing programs of prevention and treatment. Starting from 2015, the Population-based HIV Impact Assessment (PHIA) individual-level surveys are implemented in the most-affected countries in sub-Saharan Africa. PHIA is a nationally-representative HIV-focused survey that combines household visits with key questions and cutting-edge technologies such as biomarker tests for HIV antibody and HIV viral load which offer the unique opportunity of distinguishing between recent infection and long-term infection, and providing relevant HIV information by age, gender, and location. In this article, we propose a semi-supervised logistic regression model for estimating individual level HIV recency status. It incorporates information from multiple data sources - the PHIA survey where the true HIV recency status is unknown, and the cohort studies provided in the literature where the relationship between HIV recency status and the covariates are presented in the form of a contingency table. It also utilizes the national level HIV incidence estimates from the epidemiology model. Applying the proposed model to Malawi PHIA data, we demonstrate that our approach is more accurate for the individual level estimation and more appropriate for estimating HIV recency rates at aggregated levels than the current practice - the binary classification tree (BCT).
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Affiliation(s)
- Ben Sheng
- Department of Statistics, Penn State University, University Park, PA, USA
| | - Changcheng Li
- School of Mathematical Sciences, Dalian University of Technology Dalian, P.R. China
| | - Le Bao
- Department of Statistics, Penn State University, University Park, PA, USA
| | - Runze Li
- Department of Statistics, Penn State University, University Park, PA, USA
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Facente SN, Grebe E, Maher AD, Fox D, Scheer S, Mahy M, Dalal S, Lowrance D, Marsh K. Use of HIV Recency Assays for HIV Incidence Estimation and Other Surveillance Use Cases: Systematic Review. JMIR Public Health Surveill 2022; 8:e34410. [PMID: 35275085 PMCID: PMC8956992 DOI: 10.2196/34410] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/16/2022] [Accepted: 02/02/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND HIV assays designed to detect recent infection, also known as "recency assays," are often used to estimate HIV incidence in a specific country, region, or subpopulation, alone or as part of recent infection testing algorithms (RITAs). Recently, many countries and organizations have become interested in using recency assays within case surveillance systems and routine HIV testing services to measure other indicators beyond incidence, generally referred to as "non-incidence surveillance use cases." OBJECTIVE This review aims to identify published evidence that can be used to validate methodological approaches to recency-based incidence estimation and non-incidence use cases. The evidence identified through this review will be used in the forthcoming technical guidance by the World Health Organization (WHO) and United Nations Programme on HIV/AIDS (UNAIDS) on the use of HIV recency assays for identification of epidemic trends, whether for HIV incidence estimation or non-incidence indicators of recency. METHODS To identify the best methodological and field implementation practices for the use of recency assays to estimate HIV incidence and trends in recent infections for specific populations or geographic areas, we conducted a systematic review of the literature to (1) understand the use of recency testing for surveillance in programmatic and laboratory settings, (2) review methodologies for implementing recency testing for both incidence estimation and non-incidence use cases, and (3) assess the field performance characteristics of commercially available recency assays. RESULTS Among the 167 documents included in the final review, 91 (54.5%) focused on assay or algorithm performance or methodological descriptions, with high-quality evidence of accurate age- and sex-disaggregated HIV incidence estimation at national or regional levels in general population settings, but not at finer geographic levels for prevention prioritization. The remaining 76 (45.5%) described the field use of incidence assays including field-derived incidence (n=45), non-incidence (n=25), and both incidence and non-incidence use cases (n=6). The field use of incidence assays included integrating RITAs into routine surveillance and assisting with molecular genetic analyses, but evidence was generally weaker or only reported on what was done, without validation data or findings related to effectiveness of using non-incidence indicators calculated through the use of recency assays as a proxy for HIV incidence. CONCLUSIONS HIV recency assays have been widely validated for estimating HIV incidence in age- and sex-specific populations at national and subnational regional levels; however, there is a lack of evidence validating the accuracy and effectiveness of using recency assays to identify epidemic trends in non-incidence surveillance use cases. More research is needed to validate the use of recency assays within HIV testing services, to ensure findings can be accurately interpreted to guide prioritization of public health programming.
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Affiliation(s)
- Shelley N Facente
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States.,Facente Consulting, Richmond, CA, United States.,Vitalant Research Institute, San Francisco, CA, United States
| | - Eduard Grebe
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States.,Vitalant Research Institute, San Francisco, CA, United States.,South African Centre for Epidemiological Modeling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Andrew D Maher
- South African Centre for Epidemiological Modeling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa.,Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, United States
| | - Douglas Fox
- Facente Consulting, Richmond, CA, United States
| | | | - Mary Mahy
- Strategic Information Department, The Joint United Nations Programme on HIV/AIDS (UNAIDS), Geneva, Switzerland
| | - Shona Dalal
- Global HIV, Hepatitis and Sexually Transmitted Infections Programmes, World Health Organisation, Geneva, Switzerland
| | - David Lowrance
- Global HIV, Hepatitis and Sexually Transmitted Infections Programmes, World Health Organisation, Geneva, Switzerland
| | - Kimberly Marsh
- Strategic Information Department, The Joint United Nations Programme on HIV/AIDS (UNAIDS), Geneva, Switzerland
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Eaton JW, Brown T, Puckett R, Glaubius R, Mutai K, Bao L, Salomon JA, Stover J, Mahy M, Hallett TB. The Estimation and Projection Package Age-Sex Model and the r-hybrid model: new tools for estimating HIV incidence trends in sub-Saharan Africa. AIDS 2019; 33 Suppl 3:S235-S244. [PMID: 31800403 PMCID: PMC6919231 DOI: 10.1097/qad.0000000000002437] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 10/31/2019] [Accepted: 10/31/2019] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Improve models for estimating HIV epidemic trends in sub-Saharan Africa (SSA). DESIGN Mathematical epidemic model fit to national HIV survey and ANC sentinel surveillance (ANC-SS) data. METHODS We modified EPP to incorporate age and sex stratification (EPP-ASM) to more accurately capture the shifting demographics of maturing HIV epidemics. Secondly, we developed a new functional form for the HIV transmission rate, termed 'r-hybrid', which combines a four-parameter logistic function for the initial epidemic growth, peak, and decline followed by a first-order random walk for recent trends after epidemic stabilization. We fitted the r-hybrid model along with previously developed r-spline and r-trend models to HIV prevalence data from household surveys and ANC-SS in 177 regions in 34 SSA countries. We used leave-one-out cross validation with household survey HIV prevalence to compare model predictions. RESULTS The r-hybrid and r-spline models typically provided similar HIV prevalence trends, but sometimes qualitatively different assessments of recent incidence trends because of different structural assumptions about the HIV transmission rate. The r-hybrid model had the lowest average continuous ranked probability score, indicating the best model predictions. Coverage of 95% posterior predictive intervals was 91.5% for the r-hybrid model, versus 87.2 and 85.5% for r-spline and r-trend, respectively. CONCLUSION The EPP-ASM and r-hybrid models improve consistency of EPP and Spectrum, improve the epidemiological assumptions underpinning recent HIV incidence estimates, and improve estimates and short-term projections of HIV prevalence trends. Countries that use general population survey and ANC-SS data to estimate HIV epidemic trends should consider using these tools.
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Affiliation(s)
- Jeffrey W. Eaton
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Tim Brown
- Research Program, East-West Center, Honolulu, Hawaii
| | | | | | | | - Le Bao
- Department of Statistics, Pennsylvania State University, University Park, Pennsylvania
| | - Joshua A. Salomon
- Department of Medicine, Stanford University School of Medicine, Stanford, USA
| | - John Stover
- Avenir Health, Glastonbury, Connecticut, USA
| | - Mary Mahy
- Joint United Nations Programme on HIV/AIDS (UNAIDS), Geneva, Switzerland
| | - Timothy B. Hallett
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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Sequential immunizations with a panel of HIV-1 Env virus-like particles coach immune system to make broadly neutralizing antibodies. Sci Rep 2018; 8:7807. [PMID: 29773829 PMCID: PMC5958130 DOI: 10.1038/s41598-018-25960-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/26/2018] [Indexed: 12/24/2022] Open
Abstract
Broadly neutralizing antibodies (bnAbs) are correlated with passive HIV/SHIV protection and are desirable components of a HIV protective immunity. In the current study, we have designed a sequential-immunization strategy with a panel of envelope glycoprotein (Env)-enriched virus-like particles (VLPs) from various HIV-1 clades (A-E) to elicit bnAbs with high breadth and potency of neutralization in rabbits. We have compared this regimen with repetitive immunizations of individual Env (subtype B) VLPs or a mixture of various Env VLPs. Our results demonstrate that the sequential immunization group of animals induced significantly higher IgG endpoint titers against respective HIV Env (autologous) antigen than other control groups. Animals vaccinated sequentially showed an increase in the antibody endpoint titers and IgG antibody secreting cells (ASCs) against Con-S Env protein. Sequential immunizations with various Env VLPs promoted antibody avidity indices and enhanced bnAb responses against a panel of HIV pseudotyped virions including some of the tier 3 pseudostrains. Sequential immunizations with various VLPs displaying "native-like" HIV-1 Envs elicited bnAb responses with increased breadth and potency of neutralization.
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Updates to the Spectrum/Estimations and Projections Package model for estimating trends and current values for key HIV indicators. AIDS 2017; 31 Suppl 1:S5-S11. [PMID: 28296796 DOI: 10.1097/qad.0000000000001322] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND The Spectrum model is used by national programs and UNAIDS to prepare annual estimates of the status of the HIV epidemic in 160 countries. The model and assumptions are updated regularly under the guidance of the UNAIDS Reference Group on Estimates, Modelling and Projections in response to new data, studies, and program needs. This study describes the most recent updates for the 2016 round of estimates. METHODS Meetings of the UNAIDS Reference Group include individuals with extensive knowledge of HIV programs, research, statistics, and public policy. The Reference Group also collaborates with other institutions (such as the United Nations Population Division and the US Census Bureau) and projects (such as the ALPHA Network and IeDEA Consortium) to ensure that latest methods and data are used in the preparation of the annual estimates. In the past year new methods and data have been introduced for pediatric estimates, incidence fitting, and ART mortality (described elsewhere in this supplement). RESULTS The 2016 version of Spectrum includes a number of other enhancements, including updated demographic data from the United Nations Population Division, program options for treatment (treat all), and programs to prevent mother-to-child transmission (option B+), improved methods to aggregate uncertainty to regional and global levels, several options for generating incidence trends, adjustments to the Estimations and Projections Package model to better incorporate aging effects, adjustments to account for the changing bias in prevalence from antenatal clinic surveillance, and an option to fit incidence among all adults 15+ in addition to 15-49. CONCLUSION The new methods and data implemented in the 2016 version of Spectrum allow national programs more flexibility in describing their programs and improve the estimates of key indicators and their uncertainty.
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Buthelezi UE, Davidson CL, Kharsany ABM. Strengthening HIV surveillance: measurements to track the epidemic in real time. AFRICAN JOURNAL OF AIDS RESEARCH : AJAR 2016; 15:89-98. [PMID: 27399039 PMCID: PMC5547190 DOI: 10.2989/16085906.2016.1196223] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Surveillance for HIV as a public health initiative requires timely, detailed and robust data to systematically understand burden of infection, transmission patterns, direct prevention efforts, guide funding, identify new infections and predict future trends in the epidemic. The methods for HIV surveillance have evolved to reliably track the epidemic and identify new infections in real time. Initially HIV surveillance relied primarily on the reporting of AIDS cases followed by measuring antibodies to HIV to determine prevalence in key populations. With the roll-out of antiretroviral therapy (ART) resulting in better survival and the corresponding increase in HIV prevalence, the landscape of surveillance shifted further to track HIV prevalence and incidence within the context of programmes. Recent developments in laboratory assays that potentially measure and differentiate recent versus established HIV infection offer a cost-effective method for the rapid estimation of HIV incidence. These tests continue to be validated and are increasingly useful in informing the status of the epidemic in real time. Surveillance of heterogeneity of infections contributing to sub-epidemics requires methods to identify affected populations, density, key geographical locations and phylogenetically linked or clustered infections. Such methods could provide a nuanced understanding of the epidemic and prioritise prevention efforts to those most vulnerable. This paper brings together recent developments and challenges facing HIV surveillance, together with the application of newer assays and methods to fast-track the HIV prevention and treatment response.
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Affiliation(s)
- Usangiphile E Buthelezi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal
| | - Candace L Davidson
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal
| | - Ayesha BM Kharsany
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal
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Mumtaz GR, Weiss HA, Vickerman P, Larke N, Abu-Raddad LJ. Using hepatitis C prevalence to estimate HIV epidemic potential among people who inject drugs in the Middle East and North Africa. AIDS 2015; 29:1701-10. [PMID: 26372281 PMCID: PMC4541475 DOI: 10.1097/qad.0000000000000761] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 05/26/2015] [Accepted: 05/28/2015] [Indexed: 02/06/2023]
Abstract
OBJECTIVES The objective of this study is to understand the association between HIV and hepatitis C virus (HCV) among people who inject drugs (PWIDs) in the Middle East and North Africa (MENA), and to estimate HIV epidemic potential among PWIDs using HCV prevalence. DESIGN/METHODS Using data from a systematic review of HIV and HCV among PWID in MENA, we conducted two analyses, stratified by HIV epidemic state: a meta-analysis of the risk ratio of HCV to HIV prevalence (RRHCV/HIV) using DerSimonian-Laird random-effects models, and multivariable linear regression predicting log HIV prevalence. The HCV-HIV association from both analyses was used to estimate HIV prevalence at endemic equilibrium. We compared predicted with current HIV prevalence to classify HIV epidemic potential at country-level as low, medium or high, using predefined criteria. RESULTS The review identified 88 HCV prevalence measures among PWID in MENA, of which 54 had a paired HIV prevalence measure. The pooled RRHCV/HIV were 16, 4 and 3 in low-level, emerging and established HIV epidemics, respectively. There was a significant linear relationship between HCV and HIV at endemic equilibrium (P = 0.002). The predicted endemic HIV prevalence ranged between 8% (Tunisia) and 22% (Pakistan). Of the nine countries with data, five have high and three medium HIV epidemic potential. Only one country, Pakistan, appears to have reached saturation. CONCLUSION HCV prevalence could be a predictor of future endemic HIV prevalence. In MENA, we predict that there will be further HIV epidemic growth among PWID. The proposed methodology can identify PWID populations that should be prioritized for HIV prevention interventions.
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Affiliation(s)
- Ghina R. Mumtaz
- Infectious Disease Epidemiology Group, Weill Cornell Medical College - Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar
- MRC Tropical Epidemiology Group, Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London
| | - Helen A. Weiss
- MRC Tropical Epidemiology Group, Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London
| | - Peter Vickerman
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Natasha Larke
- MRC Tropical Epidemiology Group, Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London
| | - Laith J. Abu-Raddad
- Infectious Disease Epidemiology Group, Weill Cornell Medical College - Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar
- Department of Healthcare Policy and Research, Weill Cornell Medical College, Cornell University, Ithaca, New York
- Vaccine and Infectious Disease Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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Abstract
OBJECTIVE Describe modifications to the latest version of the Joint United Nations Programme on AIDS (UNAIDS) Estimation and Projection Package component of Spectrum (EPP 2013) to improve prevalence fitting and incidence trend estimation in national epidemics and global estimates of HIV burden. METHODS Key changes made under the guidance of the UNAIDS Reference Group on Estimates, Modelling and Projections include: availability of a range of incidence calculation models and guidance for selecting a model; a shift to reporting the Bayesian median instead of the maximum likelihood estimate; procedures for comparison and validation against reported HIV and AIDS data; incorporation of national surveys as an integral part of the fitting and calibration procedure, allowing survey trends to inform the fit; improved antenatal clinic calibration procedures in countries without surveys; adjustment of national antiretroviral therapy reports used in the fitting to include only those aged 15-49 years; better estimates of mortality among people who inject drugs; and enhancements to speed fitting. RESULTS The revised models in EPP 2013 allow closer fits to observed prevalence trend data and reflect improving understanding of HIV epidemics and associated data. CONCLUSION Spectrum and EPP continue to adapt to make better use of the existing data sources, incorporate new sources of information in their fitting and validation procedures, and correct for quantifiable biases in inputs as they are identified and understood. These adaptations provide countries with better calibrated estimates of incidence and prevalence, which increase epidemic understanding and provide a solid base for program and policy planning.
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Abstract
Background: Joint United Nations Programme on HIV/AIDS (UNAIDS) and Murray et al. have both produced sets of estimates for worldwide HIV incidence, prevalence and mortality. Understanding differences in these estimates can strengthen the interpretation of each. Methods: We describe differences in the two sets of estimates. Where possible, we have drawn on additional published data to which estimates can be compared. Findings: UNAIDS estimates that there were 6 million more people living with HIV (PLHIV) in 2013 (35 million) compared with the Murray et al. estimates (29 million). Murray et al. estimate that new infections and AIDS deaths have declined more gradually than does UNAIDS. Just under one third of the difference in PLHIV is in Africa, where Murray et al. have relied more on estimates of adult mortality trends than on data on survival times. Another third of the difference is in North America, Europe, Central Asia and Australasia. Here Murray et al. estimates of new infections are substantially lower than the number of new HIV/AIDS diagnoses reported by countries, whereas published UNAIDS estimate tend to be greater. The remaining differences are in Latin America and Asia where the data upon which the UNAIDS methods currently rely are more sparse, whereas the mortality data leveraged by Murray et al. may be stronger. In this region, however, anomalies appear to exist between the both sets of estimates and other data. Interpretation: Both estimates indicate that approximately 30 million PLHIV and that antiretroviral therapy has driven large reductions in mortality. Both estimates are useful but show instructive discrepancies with additional data sources. We find little evidence to suggest that either set of estimates can be considered systematically more accurate. Further work should seek to build estimates on as wide a base of data as possible.
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Case KK, Hallett TB, Gregson S, Porter K, Ghys PD. Development and future directions for the Joint United Nations Programme on HIV/AIDS estimates. AIDS 2014; 28 Suppl 4:S411-4. [PMID: 25406746 PMCID: PMC4247265 DOI: 10.1097/qad.0000000000000487] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 09/09/2014] [Accepted: 09/09/2014] [Indexed: 01/30/2023]
Affiliation(s)
- Kelsey K. Case
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London
| | - Timothy B. Hallett
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London
| | - Simon Gregson
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London
| | - Kholoud Porter
- MRC Clinical Trials Unit, University College London, London, UK
| | - Peter D. Ghys
- Division of Strategic Information and Monitoring, UNAIDS, Geneva, Switzerland
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