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  1. Artikel ; Online: Multi-arm multi-stage (MAMS) randomised selection designs: impact of treatment selection rules on the operating characteristics.

    Choodari-Oskooei, Babak / Blenkinsop, Alexandra / Handley, Kelly / Pinkney, Thomas / Parmar, Mahesh K B

    BMC medical research methodology

    2024  Band 24, Heft 1, Seite(n) 124

    Abstract: Background: Multi-arm multi-stage (MAMS) randomised trial designs have been proposed to evaluate multiple research questions in the confirmatory setting. In designs with several interventions, such as the 8-arm 3-stage ROSSINI-2 trial for preventing ... ...

    Abstract Background: Multi-arm multi-stage (MAMS) randomised trial designs have been proposed to evaluate multiple research questions in the confirmatory setting. In designs with several interventions, such as the 8-arm 3-stage ROSSINI-2 trial for preventing surgical wound infection, there are likely to be strict limits on the number of individuals that can be recruited or the funds available to support the protocol. These limitations may mean that not all research treatments can continue to accrue the required sample size for the definitive analysis of the primary outcome measure at the final stage. In these cases, an additional treatment selection rule can be applied at the early stages of the trial to restrict the maximum number of research arms that can progress to the subsequent stage(s). This article provides guidelines on how to implement treatment selection within the MAMS framework. It explores the impact of treatment selection rules, interim lack-of-benefit stopping boundaries and the timing of treatment selection on the operating characteristics of the MAMS selection design.
    Methods: We outline the steps to design a MAMS selection trial. Extensive simulation studies are used to explore the maximum/expected sample sizes, familywise type I error rate (FWER), and overall power of the design under both binding and non-binding interim stopping boundaries for lack-of-benefit.
    Results: Pre-specification of a treatment selection rule reduces the maximum sample size by approximately 25% in our simulations. The familywise type I error rate of a MAMS selection design is smaller than that of the standard MAMS design with similar design specifications without the additional treatment selection rule. In designs with strict selection rules - for example, when only one research arm is selected from 7 arms - the final stage significance levels can be relaxed for the primary analyses to ensure that the overall type I error for the trial is not underspent. When conducting treatment selection from several treatment arms, it is important to select a large enough subset of research arms (that is, more than one research arm) at early stages to maintain the overall power at the pre-specified level.
    Conclusions: Multi-arm multi-stage selection designs gain efficiency over the standard MAMS design by reducing the overall sample size. Diligent pre-specification of the treatment selection rule, final stage significance level and interim stopping boundaries for lack-of-benefit are key to controlling the operating characteristics of a MAMS selection design. We provide guidance on these design features to ensure control of the operating characteristics.
    Mesh-Begriff(e) Humans ; Randomized Controlled Trials as Topic/methods ; Research Design ; Sample Size ; Patient Selection
    Sprache Englisch
    Erscheinungsdatum 2024-06-03
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2041362-2
    ISSN 1471-2288 ; 1471-2288
    ISSN (online) 1471-2288
    ISSN 1471-2288
    DOI 10.1186/s12874-024-02247-w
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Treatment selection in multi-arm multi-stage designs: With application to a postpartum haemorrhage trial.

    Choodari-Oskooei, Babak / Thwin, Soe Soe / Blenkinsop, Alexandra / Widmer, Mariana / Althabe, Fernando / Parmar, Mahesh Kb

    Clinical trials (London, England)

    2023  Band 20, Heft 1, Seite(n) 71–80

    Abstract: Background: Multi-arm multi-stage trials are an efficient, adaptive approach for testing many treatments simultaneously within one protocol. In settings where numbers of patients available to be entered into trials and resources might be limited, such ... ...

    Abstract Background: Multi-arm multi-stage trials are an efficient, adaptive approach for testing many treatments simultaneously within one protocol. In settings where numbers of patients available to be entered into trials and resources might be limited, such as primary postpartum haemorrhage, it may be necessary to select a pre-specified subset of arms at interim stages even if they are all showing some promise against the control arm. This will put a limit on the maximum number of patients required and reduce the associated costs. Motivated by the World Health Organization Refractory HaEmorrhage Devices trial in postpartum haemorrhage, we explored the properties of such a selection design in a randomised phase III setting and compared it with other alternatives. The objectives are: (1) to investigate how the timing of treatment selection affects the operating characteristics; (2) to explore the use of an information-rich (continuous) intermediate outcome to select the best-performing arm, out of four treatment arms, compared with using the primary (binary) outcome for selection at the interim stage; and (3) to identify factors that can affect the efficiency of the design.
    Methods: We conducted simulations based on the refractory haemorrhage devices multi-arm multi-stage selection trial to investigate the impact of the timing of treatment selection and applying an adaptive allocation ratio on the probability of correct selection, overall power and familywise type I error rate. Simulations were also conducted to explore how other design parameters will affect both the maximum sample size and trial timelines.
    Results: The results indicate that the overall power of the trial is bounded by the probability of 'correct' selection at the selection stage. The results showed that good operating characteristics are achieved if the treatment selection is conducted at around 17% of information time. Our results also showed that although randomising more patients to research arms before selection will increase the probability of selecting correctly, this will not increase the overall efficiency of the (selection) design compared with the fixed allocation ratio of 1:1 to all arms throughout.
    Conclusions: Multi-arm multi-stage selection designs are efficient and flexible with desirable operating characteristics. We give guidance on many aspects of these designs including selecting the intermediate outcome measure, the timing of treatment selection, and choosing the operating characteristics.
    Mesh-Begriff(e) Female ; Humans ; Research Design ; Postpartum Hemorrhage/therapy ; Sample Size ; Patient Selection ; Outcome Assessment, Health Care
    Sprache Englisch
    Erscheinungsdatum 2023-01-17
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2138796-5
    ISSN 1740-7753 ; 1740-7745
    ISSN (online) 1740-7753
    ISSN 1740-7745
    DOI 10.1177/17407745221136527
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: List child dependents on death certificates.

    Flaxman, Seth / Kasonka, Lackson / Cluver, Lucie / Souza, Andrea Santos / Nelson, Charles A / Blenkinsop, Alexandra / Unwin, H Juliette T / Hillis, Susan

    Science (New York, N.Y.)

    2023  Band 380, Heft 6644, Seite(n) 467

    Mesh-Begriff(e) Child ; Humans ; Child, Orphaned ; COVID-19/mortality ; Death Certificates ; Models, Statistical ; Cause of Death
    Sprache Englisch
    Erscheinungsdatum 2023-05-04
    Erscheinungsland United States
    Dokumenttyp Letter
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.adh8784
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Assessing the impact of efficacy stopping rules on the error rates under the multi-arm multi-stage framework.

    Blenkinsop, Alexandra / Parmar, Mahesh Kb / Choodari-Oskooei, Babak

    Clinical trials (London, England)

    2019  Band 16, Heft 2, Seite(n) 132–141

    Abstract: Background: The multi-arm multi-stage framework uses intermediate outcomes to assess lack-of-benefit of research arms at interim stages in randomised trials with time-to-event outcomes. However, the design lacks formal methods to evaluate early evidence ...

    Abstract Background: The multi-arm multi-stage framework uses intermediate outcomes to assess lack-of-benefit of research arms at interim stages in randomised trials with time-to-event outcomes. However, the design lacks formal methods to evaluate early evidence of overwhelming efficacy on the definitive outcome measure. We explore the operating characteristics of this extension to the multi-arm multi-stage design and how to control the pairwise and familywise type I error rate. Using real examples and the updated nstage program, we demonstrate how such a design can be developed in practice.
    Methods: We used the Dunnett approach for assessing treatment arms when conducting comprehensive simulation studies to evaluate the familywise error rate, with and without interim efficacy looks on the definitive outcome measure, at the same time as the planned lack-of-benefit interim analyses on the intermediate outcome measure. We studied the effect of the timing of interim analyses, allocation ratio, lack-of-benefit boundaries, efficacy rule, number of stages and research arms on the operating characteristics of the design when efficacy stopping boundaries are incorporated. Methods for controlling the familywise error rate with efficacy looks were also addressed.
    Results: Incorporating Haybittle-Peto stopping boundaries on the definitive outcome at the interim analyses will not inflate the familywise error rate in a multi-arm design with two stages. However, this rule is conservative; in general, more liberal stopping boundaries can be used with minimal impact on the familywise error rate. Efficacy bounds in trials with three or more stages using an intermediate outcome may inflate the familywise error rate, but we show how to maintain strong control.
    Conclusion: The multi-arm multi-stage design allows stopping for both lack-of-benefit on the intermediate outcome and efficacy on the definitive outcome at the interim stages. We provide guidelines on how to control the familywise error rate when efficacy boundaries are implemented in practice.
    Mesh-Begriff(e) Bias ; Computer Simulation ; Data Interpretation, Statistical ; Endpoint Determination ; Humans ; Randomized Controlled Trials as Topic/methods ; Randomized Controlled Trials as Topic/standards ; Reproducibility of Results ; Research Design ; Time Factors
    Sprache Englisch
    Erscheinungsdatum 2019-01-16
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2138796-5
    ISSN 1740-7753 ; 1740-7745
    ISSN (online) 1740-7753
    ISSN 1740-7745
    DOI 10.1177/1740774518823551
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: Assessment of COVID-19 as the Underlying Cause of Death Among Children and Young People Aged 0 to 19 Years in the US.

    Flaxman, Seth / Whittaker, Charles / Semenova, Elizaveta / Rashid, Theo / Parks, Robbie M / Blenkinsop, Alexandra / Unwin, H Juliette T / Mishra, Swapnil / Bhatt, Samir / Gurdasani, Deepti / Ratmann, Oliver

    JAMA network open

    2023  Band 6, Heft 1, Seite(n) e2253590

    Abstract: Importance: COVID-19 was the underlying cause of death for more than 940 000 individuals in the US, including at least 1289 children and young people (CYP) aged 0 to 19 years, with at least 821 CYP deaths occurring in the 1-year period from August 1, ... ...

    Abstract Importance: COVID-19 was the underlying cause of death for more than 940 000 individuals in the US, including at least 1289 children and young people (CYP) aged 0 to 19 years, with at least 821 CYP deaths occurring in the 1-year period from August 1, 2021, to July 31, 2022. Because deaths among US CYP are rare, the mortality burden of COVID-19 in CYP is best understood in the context of all other causes of CYP death.
    Objective: To determine whether COVID-19 is a leading (top 10) cause of death in CYP in the US.
    Design, setting, and participants: This national population-level cross-sectional epidemiological analysis for the years 2019 to 2022 used data from the US Centers for Disease Control and Prevention Wide-Ranging Online Data for Epidemiologic Research (WONDER) database on underlying cause of death in the US to identify the ranking of COVID-19 relative to other causes of death among individuals aged 0 to 19 years. COVID-19 deaths were considered in 12-month periods between April 1, 2020, and August 31, 2022, compared with deaths from leading non-COVID-19 causes in 2019, 2020, and 2021.
    Main outcomes and measures: Cause of death rankings by total number of deaths, crude rates per 100 000 population, and percentage of all causes of death, using the National Center for Health Statistics 113 Selected Causes of Death, for ages 0 to 19 and by age groupings (<1 year, 1-4 years, 5-9 years, 10-14 years, 15-19 years).
    Results: There were 821 COVID-19 deaths among individuals aged 0 to 19 years during the study period, resulting in a crude death rate of 1.0 per 100 000 population overall; 4.3 per 100 000 for those younger than 1 year; 0.6 per 100 000 for those aged 1 to 4 years; 0.4 per 100 000 for those aged 5 to 9 years; 0.5 per 100 000 for those aged 10 to 14 years; and 1.8 per 100 000 for those aged 15 to 19 years. COVID-19 mortality in the time period of August 1, 2021, to July 31, 2022, was among the 10 leading causes of death in CYP aged 0 to 19 years in the US, ranking eighth among all causes of deaths, fifth in disease-related causes of deaths (excluding unintentional injuries, assault, and suicide), and first in deaths caused by infectious or respiratory diseases when compared with 2019. COVID-19 deaths constituted 2% of all causes of death in this age group.
    Conclusions and relevance: The findings of this study suggest that COVID-19 was a leading cause of death in CYP. It caused substantially more deaths in CYP annually than any vaccine-preventable disease historically in the recent period before vaccines became available. Various factors, including underreporting and not accounting for COVID-19's role as a contributing cause of death from other diseases, mean that these estimates may understate the true mortality burden of COVID-19. The findings of this study underscore the public health relevance of COVID-19 to CYP. In the likely future context of sustained SARS-CoV-2 circulation, appropriate pharmaceutical and nonpharmaceutical interventions (eg, vaccines, ventilation, air cleaning) will continue to play an important role in limiting transmission of the virus and mitigating severe disease in CYP.
    Mesh-Begriff(e) Child ; Humans ; Adolescent ; Cause of Death ; COVID-19 ; Cross-Sectional Studies ; SARS-CoV-2 ; Communicable Diseases
    Sprache Englisch
    Erscheinungsdatum 2023-01-03
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2574-3805
    ISSN (online) 2574-3805
    DOI 10.1001/jamanetworkopen.2022.53590
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Buch ; Online: Sources of HIV infections among MSM with a migration background

    Blenkinsop, Alexandra / Pantazis, Nikos / Kostaki, Evangelia Georgia / Sofocleous, Lysandros / van Sighem, Ard / Bezemer, Daniela / van de Laar, Thijs / van der Valk, Marc / Reiss, Peter / de Bree, Godelieve / Ratmann, Oliver

    a viral phylogenetic case study in Amsterdam, the Netherlands

    2024  

    Abstract: Background: Men and women with a migration background comprise an increasing proportion of incident HIV cases across Western Europe. Several studies indicate a substantial proportion acquire HIV post-migration. Methods: We used partial HIV consensus ... ...

    Abstract Background: Men and women with a migration background comprise an increasing proportion of incident HIV cases across Western Europe. Several studies indicate a substantial proportion acquire HIV post-migration. Methods: We used partial HIV consensus sequences with linked demographic and clinical data from the opt-out ATHENA cohort of people with HIV in the Netherlands to quantify population-level sources of transmission to Dutch-born and foreign-born Amsterdam men who have sex with men (MSM) between 2010-2021. We identified phylogenetically and epidemiologically possible transmission pairs in local transmission chains and interpreted these in the context of estimated infection dates, quantifying transmission dynamics between sub-populations by world region of birth. Results: We estimate the majority of Amsterdam MSM who acquired their infection locally had a Dutch-born Amsterdam MSM source (56% [53-58%]). Dutch-born MSM were the predominant source population of infections among almost all foreign-born Amsterdam MSM sub-populations. Stratifying by two-year intervals indicated shifts in transmission dynamics, with a majority of infections originating from foreign-born MSM since 2018, although uncertainty ranges remained wide. Conclusions: In the context of declining HIV incidence among Amsterdam MSM, our data suggest whilst native-born MSM have predominantly driven transmissions in 2010-2021, the contribution from foreign-born MSM living in Amsterdam is increasing.
    Schlagwörter Quantitative Biology - Populations and Evolution
    Erscheinungsdatum 2024-01-16
    Erscheinungsland us
    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel: Age and gender profiles of HIV infection burden and viraemia: novel metrics for HIV epidemic control in African populations with high antiretroviral therapy coverage.

    Brizzi, Andrea / Kagaayi, Joseph / Ssekubugu, Robert / Abeler-Dörner, Lucie / Blenkinsop, Alexandra / Bonsall, David / Chang, Larry W / Fraser, Christophe / Galiwango, Ronald M / Kigozi, Godfrey / Kyle, Imogen / Monod, Mélodie / Nakigozi, Gertrude / Nalugoda, Fred / Rosen, Joseph G / Laeyendecker, Oliver / Quinn, Thomas C / Grabowski, M Kate / Reynolds, Steven J /
    Ratmann, Oliver

    medRxiv : the preprint server for health sciences

    2024  

    Abstract: Introduction: To prioritize and tailor interventions for ending AIDS by 2030 in Africa, it is important to characterize the population groups in which HIV viraemia is concentrating.: Methods: We analysed HIV testing and viral load data collected ... ...

    Abstract Introduction: To prioritize and tailor interventions for ending AIDS by 2030 in Africa, it is important to characterize the population groups in which HIV viraemia is concentrating.
    Methods: We analysed HIV testing and viral load data collected between 2013-2019 from the open, population-based Rakai Community Cohort Study (RCCS) in Uganda, to estimate HIV seroprevalence and population viral suppression over time by gender, one-year age bands and residence in inland and fishing communities. All estimates were standardized to the underlying source population using census data. We then assessed 95-95-95 targets in their ability to identify the populations in which viraemia concentrates.
    Results: Following the implementation of Universal Test and Treat, the proportion of individuals with viraemia decreased from 4.9% (4.6%-5.3%) in 2013 to 1.9% (1.7%-2.2%) in 2019 in inland communities and from 19.1% (18.0%-20.4%) in 2013 to 4.7% (4.0%-5.5%) in 2019 in fishing communities. Viraemia did not concentrate in the age and gender groups furthest from achieving 95-95-95 targets. Instead, in both inland and fishing communities, women aged 25-29 and men aged 30-34 were the 5-year age groups that contributed most to population-level viraemia in 2019, despite these groups being close to or had already achieved 95-95-95 targets.
    Conclusions: The 95-95-95 targets provide a useful benchmark for monitoring progress towards HIV epidemic control, but do not contextualize underlying population structures and so may direct interventions towards groups that represent a marginal fraction of the population with viraemia.
    Sprache Englisch
    Erscheinungsdatum 2024-04-22
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2024.04.21.24306145
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Artikel ; Online: Estimating the potential to prevent locally acquired HIV infections in a UNAIDS Fast-Track City, Amsterdam.

    Blenkinsop, Alexandra / Monod, Mélodie / van Sighem, Ard / Pantazis, Nikos / Bezemer, Daniela / Op de Coul, Eline / van de Laar, Thijs / Fraser, Christophe / Prins, Maria / Reiss, Peter / de Bree, Godelieve J / Ratmann, Oliver

    eLife

    2022  Band 11

    Abstract: Background: More than 300 cities including the city of Amsterdam in the Netherlands have joined the UNAIDS Fast-Track Cities initiative, committing to accelerate their HIV response and end the AIDS epidemic in cities by 2030. To support this commitment, ...

    Abstract Background: More than 300 cities including the city of Amsterdam in the Netherlands have joined the UNAIDS Fast-Track Cities initiative, committing to accelerate their HIV response and end the AIDS epidemic in cities by 2030. To support this commitment, we aimed to estimate the number and proportion of Amsterdam HIV infections that originated within the city, from Amsterdam residents. We also aimed to estimate the proportion of recent HIV infections during the 5-year period 2014-2018 in Amsterdam that remained undiagnosed.
    Methods: We located diagnosed HIV infections in Amsterdam using postcode data (PC4) at time of registration in the ATHENA observational HIV cohort, and used HIV sequence data to reconstruct phylogeographically distinct, partially observed Amsterdam transmission chains. Individual-level infection times were estimated from biomarker data, and used to date the phylogenetically observed transmission chains as well as to estimate undiagnosed proportions among recent infections. A Bayesian Negative Binomial branching process model was used to estimate the number, size, and growth of the unobserved Amsterdam transmission chains from the partially observed phylogenetic data.
    Results: Between 1 January 2014 and 1 May 2019, there were 846 HIV diagnoses in Amsterdam residents, of whom 516 (61%) were estimated to have been infected in 2014-2018. The rate of new Amsterdam diagnoses since 2014 (104 per 100,000) remained higher than the national rates excluding Amsterdam (24 per 100,000), and in this sense Amsterdam remained a HIV hotspot in the Netherlands. An estimated 14% [12-16%] of infections in Amsterdan MSM in 2014-2018 remained undiagnosed by 1 May 2019, and 41% [35-48%] in Amsterdam heterosexuals, with variation by region of birth. An estimated 67% [60-74%] of Amsterdam MSM infections in 2014-2018 had an Amsterdam resident as source, and 56% [41-70%] in Amsterdam heterosexuals, with heterogeneity by region of birth. Of the locally acquired infections, an estimated 43% [37-49%] were in foreign-born MSM, 41% [35-47%] in Dutch-born MSM, 10% [6-18%] in foreign-born heterosexuals, and 5% [2-9%] in Dutch-born heterosexuals. We estimate the majority of Amsterdam MSM infections in 2014-2018 originated in transmission chains that pre-existed by 2014.
    Conclusions: This combined phylogenetic, epidemiologic, and modelling analysis in the UNAIDS Fast-Track City Amsterdam indicates that there remains considerable potential to prevent HIV infections among Amsterdam residents through city-level interventions. The burden of locally acquired infection remains concentrated in MSM, and both Dutch-born and foreign-born MSM would likely benefit most from intensified city-level interventions.
    Funding: This study received funding as part of the H-TEAM initiative from Aidsfonds (project number P29701). The H-TEAM initiative is being supported by Aidsfonds (grant number: 2013169, P29701, P60803), Stichting Amsterdam Dinner Foundation, Bristol-Myers Squibb International Corp. (study number: AI424-541), Gilead Sciences Europe Ltd (grant number: PA-HIV-PREP-16-0024), Gilead Sciences (protocol numbers: CO-NL-276-4222, CO-US-276-1712, CO-NL-985-6195), and M.A.C AIDS Fund.
    Mesh-Begriff(e) Acquired Immunodeficiency Syndrome/epidemiology ; Bayes Theorem ; Cities/epidemiology ; HIV Infections/diagnosis ; HIV Infections/epidemiology ; HIV Infections/prevention & control ; Homosexuality, Male ; Humans ; Male ; Phylogeny
    Sprache Englisch
    Erscheinungsdatum 2022-08-03
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.76487
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Buch ; Online: Bayesian mixture models for phylogenetic source attribution from consensus sequences and time since infection estimates

    Blenkinsop, Alexandra / Sofocleous, Lysandros / di Lauro, Francesco / Kostaki, Evangelia Georgia / van Sighem, Ard / Bezemer, Daniela / van de Laar, Thijs / Reiss, Peter / de Bree, Godelieve / Pantazis, Nikos / Ratmann, Oliver

    2023  

    Abstract: In stopping the spread of infectious diseases, pathogen genomic data can be used to reconstruct transmission events and characterize population-level sources of infection. Most approaches for identifying transmission pairs do not account for the time ... ...

    Abstract In stopping the spread of infectious diseases, pathogen genomic data can be used to reconstruct transmission events and characterize population-level sources of infection. Most approaches for identifying transmission pairs do not account for the time that passed since divergence of pathogen variants in individuals, which is problematic in viruses with high within-host evolutionary rates. This is prompting us to consider possible transmission pairs in terms of phylogenetic data and additional estimates of time since infection derived from clinical biomarkers. We develop Bayesian mixture models with an evolutionary clock as signal component and additional mixed effects or covariate random functions describing the mixing weights to classify potential pairs into likely and unlikely transmission pairs. We demonstrate that although sources cannot be identified at the individual level with certainty, even with the additional data on time elapsed, inferences into the population-level sources of transmission are possible, and more accurate than using only phylogenetic data without time since infection estimates. We apply the approach to estimate age-specific sources of HIV infection in Amsterdam MSM transmission networks between 2010-2021. This study demonstrates that infection time estimates provide informative data to characterize transmission sources, and shows how phylogenetic source attribution can then be done with multi-dimensional mixture models.
    Schlagwörter Quantitative Biology - Populations and Evolution ; Statistics - Methodology
    Thema/Rubrik (Code) 310
    Erscheinungsdatum 2023-04-13
    Erscheinungsland us
    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  10. Artikel ; Online: Many but small HIV-1 non-B transmission chains in the Netherlands.

    Bezemer, Daniela / Blenkinsop, Alexandra / Hall, Matthew / van Sighem, Ard / Cornelissen, Marion / Wessels, Els / van Kampen, Jeroen / van de Laar, Thijs / Reiss, Peter / Fraser, Christophe / Ratmann, Oliver

    AIDS (London, England)

    2021  Band 36, Heft 1, Seite(n) 83–94

    Abstract: Objective: The aim of this study was to investigate introductions and spread of different HIV-1 subtypes in the Netherlands.: Design: We identified distinct HIV-1 transmission chains in the Netherlands within the global epidemic context through viral ...

    Abstract Objective: The aim of this study was to investigate introductions and spread of different HIV-1 subtypes in the Netherlands.
    Design: We identified distinct HIV-1 transmission chains in the Netherlands within the global epidemic context through viral phylogenetic analysis of partial HIV-1 polymerase sequences from individuals enrolled in the ATHENA national HIV cohort of all persons in care since 1996, and publicly available international background sequences.
    Methods: Viral lineages circulating in the Netherlands were identified through maximum parsimony phylogeographic analysis. The proportion of HIV-1 infections acquired in-country among heterosexuals and MSM was estimated from phylogenetically observed, national transmission chains using a branching process model that accounts for incomplete sampling.
    Results: As of 1 January 2019, 2589 (24%) of 10 971 (41%) HIV-1 sequenced individuals in ATHENA had non-B subtypes (A1, C, D, F, G) or circulating recombinant forms (CRF01AE, CRF02AG, CRF06-cpx). The 1588 heterosexuals were in 1224, and 536 MSM in 270 phylogenetically observed transmission chains. After adjustments for incomplete sampling, most heterosexual (75%) and MSM (76%) transmission chains were estimated to include only the individual introducing the virus (size = 1). Onward transmission occurred mostly in chains size 2-5 amongst heterosexuals (62%) and in chains size at least 10 amongst MSM (64%). Considering some chains originated in-country from other risk-groups, 40% (95% confidence interval: 36-44) of non-B-infected heterosexuals and 62% (95% confidence interval: 49-73) of MSM-acquired infection in-country.
    Conclusion: Although most HIV-1 non-B introductions showed no or very little onward transmission, a considerable proportion of non-B infections amongst both heterosexuals and MSM in the Netherlands have been acquired in-country.
    Mesh-Begriff(e) HIV Infections ; HIV-1/genetics ; Heterosexuality ; Homosexuality, Male ; Humans ; Male ; Netherlands/epidemiology ; Phylogeny
    Sprache Englisch
    Erscheinungsdatum 2021-09-29
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 639076-6
    ISSN 1473-5571 ; 0269-9370 ; 1350-2840
    ISSN (online) 1473-5571
    ISSN 0269-9370 ; 1350-2840
    DOI 10.1097/QAD.0000000000003074
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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