scholarly journals Use of HIV Recency Assays for HIV Incidence Estimation and Non-Incidence Surveillance Use Cases: A systematic review

2021 ◽  
Author(s):  
Shelley N. Facente ◽  
Lillian Agyei ◽  
Andrew D. Maher ◽  
Mary Mahy ◽  
Shona Dalal ◽  
...  
Keyword(s):  
Systematic Review ◽  
Molecular Genetic ◽  
Field Performance ◽  
Use Cases ◽  
Surveillance Systems ◽  
Hiv Incidence ◽  
Recent Infection ◽  
Validation Data ◽  
Incidence Estimation ◽  
Age And Sex

ABSTRACTIntroductionHIV 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, and in measuring other indicators beyond incidence, generally referred to as “non-incidence surveillance use cases.”MethodsTo identify best methodological and field implementation practices for the use of recency assays to estimate HIV incidence and trends in recent infections for key populations or specific geographic areas, we undertook: 1) a global Call for Information released from WHO/UNAIDS; and 2) a systematic review of the literature to: (a) assess the field performance characteristics of commercially available recency assays, (b) understand the use of recency testing for surveillance in programmatic and laboratory settings, and (c) review methodologies for implementing recency testing for both incidence estimation and non-incidence use cases.Results and discussionAmong the 90 documents ultimately reviewed, 65 (88%) focused on assay/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 25 documents described field-derived incidence (n=14) and non-incidence (n=11) use cases, including 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 recency assays when used for these purposes.ConclusionsHIV recency assays have been widely validated for estimating HIV incidence in age- and sex-specific populations at national and sub-national regional levels; however, there was a lack of evidence validating the accuracy and effectiveness of using recency assays for non-incidence surveillance use cases. The evidence identified through this review will be used in forthcoming technical guidance on the use of HIV recency assays for surveillance use cases by WHO and UNAIDS; further evidence on methodologies and effectiveness of non-incidence use cases is needed.

scholarly journals Principles and uses of HIV incidence estimation from recent infection testing - a review

2008 ◽  
Vol 13 (36) ◽  
Author(s):  
S Le Vu ◽  
J Pillonel ◽  
C Semaille ◽  
P Bernillon ◽  
Y Le Strat ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Hiv Infections ◽  
Specific Aspect ◽  
Surveillance Systems ◽  
Hiv Incidence ◽  
Recent Infection ◽  
Immunodeficiency Virus ◽  
Period Estimation ◽  
Incidence Estimation ◽  
The Relationship

Since the 1990s, the development of laboratory-based methods has allowed to estimate incidence of human immunodeficiency virus (HIV) infections on single samples. The tests aim to differentiate recent from established HIV infection. Incidence estimates are obtained by using the relationship between prevalence, incidence and duration of recent infection. We describe the principle of the methods and typical uses of these tests to characterise recent infection and derive incidence. We discuss the challenges in interpreting estimates and we consider the implications for surveillance systems. Overall, these methods can add remarkable value to surveillance systems based on prevalence surveys as well as HIV case reporting. The assumptions that must be fulfilled to correctly interpret the estimates are mostly similar to those required in prevalence measurement. However, further research on the specific aspect of window period estimation is needed in order to generalise these methods in various population settings.

scholarly journals Optimal accounting for age and time structure of HIV incidence estimates based on cross-sectional survey data with ascertainment of ‘recent infection’

2021 ◽  
Author(s):  
Laurette Mhlanga ◽  
Grebe Eduard ◽  
Alex Welte
Keyword(s):  
Survey Data ◽  
Age Structure ◽  
Estimation Procedure ◽  
Time Dependent ◽  
Data Sets ◽  
Hiv Incidence ◽  
Recent Infection ◽  
Cross Sectional ◽  
Incidence Estimation ◽  
Dependent Mortality

Abstract BackgroundMany surveys have attempted to estimate HIV incidence from cross-sectional data which includes ascertainment of ‘recent infection’, but the inevitable age and time structure of this data has never been systematically explored – no doubt partly because statistical precision in such estimates is often insufficient to allow for satisfactory disaggregation. Given the non-trivial age structure of HIV incidence and prevalence, and the enormous investments that have been made in such data sets, it is important to understand effective ways to extract valid age structure from these precious data sets. MethodsUsing a comprehensive demographic/epidemiological simulation platform developed for this, and some wider, purposes (documented in more detail separately) we simulated a complex ‘South Africa inspired’ HIV epidemic, with explicitly specified 1) age/time dependent incidence, 2) age/time dependent mortality for uninfected individuals, and 3) age/time/time-since-infection dependent mortality for infected individuals. In this simulated world, we conducted cross-sectional surveys at various times, and applied variants of the recent infection based incidence estimation methodology of Kassanjee et al. We analysed in considerable detail how to smooth, and average over, the age structure in these surveys to produce the incidence estimates, paying attention to the fundamental trade-off between bias and statistical error.ResultsWe summarise our detailed observations about incidence estimates, generated by various age smoothing or age disaggregation procedures, into a straightforward fully specified ‘one size fits most’ algorithm for processing the survey data into age-specific incidence estimates: 1) generalised linear regression to turn observations into ‘prevalence’ of ‘infection’ and ‘recent infection’ (logit, and complementary log log, link functions, respectively; fitting coefficients of up to cubic terms in age/time); 2) a ‘moving window’ data inclusion recipe which handles each age/time point of interest separately; 3) post hoc age averaging of resulting pseudo continuously fitted incidence; 4) bootstrapping as a generic variance/significance estimation procedure.ConclusionsAs far as we are aware, this is the first analysis of several fine details of how age structure in cross-sectional surveys interacts with recency-based incidence estimation. Our proposed default estimation procedure generates incidence estimates with negligible bias and near-optimal precision, and can be readily applied to complex survey data sets by any group in possession of such data. Our code is available, in part freely through the R computing platform, and in part upon request.

scholarly journals Optimal accounting for age and time structure of HIV incidence estimates based on cross-sectional survey data with ascertainment of ‘recent infection’

2021 ◽  
Author(s):  
Laurette Mhlanga ◽  
Grebe Eduard ◽  
Alex Welte
Keyword(s):  
Survey Data ◽  
Age Structure ◽  
Estimation Procedure ◽  
Time Dependent ◽  
Data Sets ◽  
Hiv Incidence ◽  
Recent Infection ◽  
Cross Sectional ◽  
Incidence Estimation ◽  
Dependent Mortality

Abstract BackgroundMany surveys have attempted to estimate HIV incidence from cross-sectional data which includes ascertainment of ‘recent infection’, but the inevitable age and time structure of this data has never been systematically explored – no doubt partly because statistical precision in such estimates is often insufficient to allow for satisfactory disaggregation. Given the non-trivial age structure of HIV incidence and prevalence, and the enormous investments that have been made in such data sets, it is important to understand effective ways to extract valid age structure from these precious data sets. MethodsUsing a comprehensive demographic/epidemiological simulation platform developed for this, and some wider, purposes (documented in more detail separately) we simulated a complex ‘South Africa inspired’ HIV epidemic, with explicitly specified 1) age/time dependent incidence, 2) age/time dependent mortality for uninfected individuals, and 3) age/time/time-since-infection dependent mortality for infected individuals. In this simulated world, we conducted cross-sectional surveys at various times, and applied variants of the recent infection based incidence estimation methodology of Kassanjee et al. We analysed in considerable detail how to smooth, and average over, the age structure in these surveys to produce the incidence estimates, paying attention to the fundamental trade-off between bias and statistical error.ResultsWe summarise our detailed observations about incidence estimates, generated by various age smoothing or age disaggregation procedures, into a straightforward fully specified ‘one size fits most’ algorithm for processing the survey data into age-specific incidence estimates: 1) generalised linear regression to turn observations into ‘prevalence’ of ‘infection’ and ‘recent infection’ (logit, and complementary log log, link functions, respectively; fitting coefficients of up to cubic terms in age/time); 2) a ‘moving window’ data inclusion recipe which handles each age/time point of interest separately; 3) post hoc age averaging of resulting pseudo continuously fitted incidence; 4) bootstrapping as a generic variance/significance estimation procedure.ConclusionsAs far as we are aware, this is the first analysis of several fine details of how age structure in cross-sectional surveys interacts with recency-based incidence estimation. Our proposed default estimation procedure generates incidence estimates with negligible bias and near-optimal precision, and can be readily applied to complex survey data sets by any group in possession of such data. Our code is available, in part freely through the R computing platform, and in part upon request.

scholarly journals Systematic Review of Hepatitis E Virus in Brazil: A One-Health Approach of the Human-Animal-Environment Triad

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2290
Author(s):  
Danny Franciele da Silva Dias Moraes ◽  
João R. Mesquita ◽  
Valéria Dutra ◽  
Maria São José Nascimento
Keyword(s):  
Systematic Review ◽  
One Health ◽  
Hepatitis E ◽  
Published Data ◽  
Surveillance Systems ◽  
Industrialized Countries ◽  
Genotype 3 ◽  
The World ◽  
Waterborne Transmission ◽  
Sanitary Conditions

Brazil is the fifth largest country in the world with diverse socioeconomic and sanitary conditions, also being the fourth largest pig producer in the world. The aim of the present systematic review was to collect and summarize all HEV published data from Brazil (from 1995 to October 2020) performed in humans, animals, and the environment, in a One Health perspective. A total of 2173 papers were retrieved from five search databases (LILACs, Mendeley, PubMed, Scopus, and Web of Science) resulting in 71 eligible papers after application of exclusion/inclusion criteria. Data shows that HEV genotype 3 (HEV-3) was the only retrieved genotype in humans, animals, and environment in Brazil. The South region showed the highest human seroprevalence and also the highest pig density and industry, suggesting a zoonotic link. HEV-1 and 2 were not detected in Brazil, despite the low sanitary conditions of some regions. From the present review we infer that HEV epidemiology in Brazil is similar to that of industrialized countries (only HEV-3, swine reservoirs, no waterborne transmission, no association with low sanitary conditions). Hence, we alert for the implementation of HEV surveillance systems in swine and for the consideration of HEV in the diagnostic routine of acute and chronic hepatitis in humans.

scholarly journals HIV Diversity as a Biomarker for HIV Incidence Estimation: Including a High-Resolution Melting Diversity Assay in a Multiassay Algorithm

2013 ◽  
Vol 52 (1) ◽  
pp. 115-121 ◽  
Author(s):  
M. M. Cousins ◽  
J. Konikoff ◽  
O. Laeyendecker ◽  
C. Celum ◽  
S. P. Buchbinder ◽  
...  
Keyword(s):  
High Resolution ◽  
High Resolution Melting ◽  
Hiv Incidence ◽  
Incidence Estimation ◽  
Hiv Diversity

scholarly journals Measuring energy, macro and micronutrient intake in UK children and adolescents: a comparison of validated dietary assessment tools

BMC Nutrition ◽  
2019 ◽  
Vol 5 (1) ◽  
Author(s):  
Linda A. Bush ◽  
Jayne Hutchinson ◽  
Jozef Hooson ◽  
Marisol Warthon-Medina ◽  
Neil Hancock ◽  
...  
Keyword(s):  
Systematic Review ◽  
Children And Adolescents ◽  
Validation Studies ◽  
Dietary Assessment ◽  
Assessment Tools ◽  
Food Diary ◽  
Doubly Labelled Water ◽  
Validation Data ◽  
Review Of Reviews ◽  
The Uk

Abstract Background Measuring dietary intake in children and adolescents can be challenging due to misreporting, difficulties in establishing portion size and reliance on recording dietary data via proxy reporters. The aim of this review was to present results from a recent systematic review of reviews reporting and comparing validated dietary assessment tools used in younger populations in the UK. Methods Validation data for dietary assessment tools used in younger populations (≤18 years) were extracted and summarised using results from a systematic review of reviews of validated dietary assessment tools. Mean differences and Bland-Altman limits of agreement (LOA) between the test and reference tool were extracted or calculated and compared for energy, macronutrients and micronutrients. Results Seventeen studies which reported validation of 14 dietary assessment tools (DATs) were identified with relevant nutrition information. The most commonly validated nutrients were energy, carbohydrate, protein, fat, calcium, iron, folate and vitamin C. There were no validated DATs reporting assessment of zinc, iodine or selenium intake. The most frequently used reference method was the weighed food diary, followed by doubly labelled water and 24 h recall. Summary plots were created to facilitate comparison between tools. On average, the test tools reported higher mean intakes than the reference methods with some studies consistently reporting wide LOA. Out of the 14 DATs, absolute values for LOA and mean difference were obtained for 11 DATs for EI. From the 24 validation results assessing EI, 16 (67%) reported higher mean intakes than the reference. Of the seven (29%) validation studies using doubly labelled water (DLW) as the reference, results for the test DATs were not substantially better or worse than those using other reference measures. Further information on the studies from this review is available on the www.nutritools.org website. Conclusions Validated dietary assessment tools for use with children and adolescents in the UK have been identified and compared. Whilst tools are generally validated for macronutrient intakes, micronutrients are poorly evaluated. Validation studies that include estimates of zinc, selenium, dietary fibre, sugars and sodium are needed.

scholarly journals Moving towards a reliable HIV incidence test – current status, resources available, future directions and challenges ahead

2016 ◽  
Vol 145 (5) ◽  
pp. 925-941 ◽  
Author(s):  
G. MURPHY ◽  
C. D. PILCHER ◽  
S. M. KEATING ◽  
R. KASSANJEE ◽  
S. N. FACENTE ◽  
...  
Keyword(s):  
Performance Metrics ◽  
Critical Path ◽  
Population Level ◽  
Current Status ◽  
Hiv Incidence ◽  
Recent Infection ◽  
Novel Approach ◽  
Product Profile ◽  
And Performance ◽  
The Impact

SUMMARYIn 2011 the Incidence Assay Critical Path Working Group reviewed the current state of HIV incidence assays and helped to determine a critical path to the introduction of an HIV incidence assay. At that time the Consortium for Evaluation and Performance of HIV Incidence Assays (CEPHIA) was formed to spur progress and raise standards among assay developers, scientists and laboratories involved in HIV incidence measurement and to structure and conduct a direct independent comparative evaluation of the performance of 10 existing HIV incidence assays, to be considered singly and in combinations as recent infection test algorithms. In this paper we report on a new framework for HIV incidence assay evaluation that has emerged from this effort over the past 5 years, which includes a preliminary target product profile for an incidence assay, a consensus around key performance metrics along with analytical tools and deployment of a standardized approach for incidence assay evaluation. The specimen panels for this evaluation have been collected in large volumes, characterized using a novel approach for infection dating rules and assembled into panels designed to assess the impact of important sources of measurement error with incidence assays such as viral subtype, elite host control of viraemia and antiretroviral treatment. We present the specific rationale for several of these innovations, and discuss important resources for assay developers and researchers that have recently become available. Finally, we summarize the key remaining steps on the path to development and implementation of reliable assays for monitoring HIV incidence at a population level.

scholarly journals Effect of syphilis infection on HIV acquisition: a systematic review and meta-analysis

2020 ◽  
pp. sextrans-2020-054706
Author(s):  
Meng Yin Wu ◽  
Hui Zi Gong ◽  
Kui Ru Hu ◽  
He-yi Zheng ◽  
Xia Wan ◽  
...  
Keyword(s):  
Systematic Review ◽  
Relative Risk ◽  
High Risk ◽  
Meta Analysis ◽  
Risk Groups ◽  
Hiv Incidence ◽  
Syphilis Infection ◽  
High Risk Populations ◽  
Hiv Acquisition ◽  
Risk Of Hiv Acquisition

ObjectivesCo-infection of syphilis and HIV remains hard to manage and its morbidity shows a rising tendency. Syphilis has been associated with increased risk of HIV acquisition in high-risk groups, especially in men who have sex with men (MSM). This systematic review and meta-analysis estimates the effect of syphilis infection on subsequent HIV acquisition, and assesses its difference between MSM and other high-risk populations.MethodsFive electronic databases were searched for literature published to 21 September 2019 without language restrictions. Longitudinal studies that enrolled key populations to compare the incidence of HIV with and without syphilis exposure were included. We used a random-effects model to estimate the effect of syphilis infection on HIV acquisition among high-risk populations, which include MSM, sex workers, serodiscordant couples, people who inject drugs and attendees of STD clinics.ResultsA total of 17 cohorts and 5 case-control studies involving 65 232 participants were included. HIV incidence showed a two-time increase after syphilis exposure, compared with a control group (relative risk (RR) 2.67 (95% CI 2.05 to 3.47); p<0.05 for prevalence; RR 3.21 (95% CI 2.26 to 4.57); p=0.419 for incidence). No significant differences were observed between MSM and other high-risk groups in syphilis infection prevalence (RR 2.60 (95% CI 1.78 to 3.80); p<0.05 vs RR, 2.98 (95% CI 2.15 to 4.14); p<0.05; ratio of relative risk 0.76 (95% CI 0.49 to 1.17)).ConclusionsSyphilis infection increases the risk of HIV acquisition in high-risk populations. There is no evidence to suggest MSM are at greater risk than other high-risk populations. Prompt diagnosis, timely treatment, preventive interventions against syphilis infection would be a worthwhile investment for reducing HIV incidence. Strategies to combat stigma and discrimination targeted at MSM are pragmatically needed.

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