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PANGEA1 HIV Clinical Data

South Africa, 2010 - 2013
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Reference ID
AHRI.PANGEA1.HIV.Clinical.Data.2019.v1
Producer(s)
De Oliveira, Tulio, Pillay, Deenan,
Metadata
Documentation in PDF DDI/XML JSON
Created on
Jun 15, 2016
Last modified
Feb 21, 2019
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  • Identification
  • Version
  • Scope
  • Coverage
  • Producers and sponsors
  • Sampling
  • Data collection
  • Data processing
  • Data Access
  • Metadata production

    • Identification

    Survey ID number

    AHRI.PANGEA1.HIV.Clinical.Data.2019.v1
    Title

    PANGEA1 HIV Clinical Data
    Country
    Name Country code
    South Africa ZA
    Abstract

    The purpose of this study was address one key question: What is the contribution of external sources of HIV in driving the epidemic within a community. High rates of cross-community transmission calls into question the efficacy of increasing local coverage of antiretroviral therapy to prevent new infections. To address this question, 1068 polymerase sequences were derived from sampling conducted within the Africa Health Research Insitute's demographic surveillance area between 2010 and 2013. AHRI genotypes were analysed against a large national dataset of homologous sequences in a novel phylodynamic framework to infer the overall transmission dynamics within the community. This allowed us to enumerate the relative contribution of local transmission versus external introductions to the overall HIV incidence in the community. Major variables within the dataset to answer this question are: (1) the genotype; (2) the community's location from which the genotype was derived; and (3) the date of sampling.
    Kind of Data

    HIV Genomic Data
    Unit of Analysis

    Each sequences derived from a single specimen.

    Version

    Version Description

    V1.0.0

    Scope

    Topics
    Topic Vocabulary URI
    HIV-1; Incidence; Phylogeny; Epidemics; Population Surveillance; Rural Population; HIV Infections; Africa Africa Health Research Institute AHRI
    Keywords
    HIV polymerase sequence; date of sampling; phylodynamics, phylogeny, HIV-1

    Coverage

    Geographic Coverage

    Treatment as Prevention trial area of the Africa Health Research Institute.
    Universe

    HIV positive participants enrolled in the Treatment as Prevention 12449 ANRS trial, who linked to care

    Producers and sponsors

    Primary investigators
    Name Affiliation
    De Oliveira, Tulio KwaZulu-Natal Research Innovation Sequencing Platform
    Pillay, Deenan Africa Health Research Institute
    Producers
    Name
    Africa Health Research Institute
    Funding Agency/Sponsor
    Name Role
    South African Medical Research Council Genotyping funding source
    Other Identifications/Acknowledgments
    Name Affiliation Role
    Wilkinson, Eduan KwaZulu-Natal Research Innovation Sequencing Platform Cleaned, aligned and help analyse the sequence data.

    Sampling

    Sampling Procedure

    HIV positive individuals within the demographic surveillance area of the Africa Health Research Insititue from 2010 to 2013. Individuals blood spots were only attempted sequencing if they:
    A) Had a viral load done
    B) Viral load was above 1,550 copies/ml
    C) The laboratory got approximately 60% success rate on sequencing them, they should have the list that they attempt to sequence and the ones that were successful.

    Data collection

    Dates of Data Collection
    Start End
    2010-01-01 2013-12-04

    Data processing

    Data Editing

    Sequences were generated by the Durban based laboratory of AHRI. Sequences were aligned with one another in ClustalW and are presented in the standard fasta file format.

    Data Access

    Access conditions
    1. The representative of the Receiving Organization agrees to comply with the following conditions:
    2. Access to the restricted data will be limited to the Lead Researcher and other members of the research team listed in this request.
    3. Copies of the restricted data or any data created on the basis of the original data will not be copied or made available to anyone other than those mentioned in this Data Access Agreement, unless formally authorized by the Data Archive.
    4. The data will only be processed for the stated statistical and research purpose. They will be used for solely for reporting of aggregated information, and not for investigation of specific individuals or organizations. Data will not in any way be used for any administrative, proprietary or law enforcement purposes.
    5. The Lead Researcher must state if it is their intention to match the restricted microdata with any other micro-dataset. If any matching is to take place, details must be provided of the datasets to be matched and of the reasons for the matching. Any datasets created as a result of matching will be considered to be restricted and must comply with the terms of this Data Access Agreement.
    6. The Lead Researcher undertakes that no attempt will be made to identify any individual person, family, business, enterprise or organization. If such a unique disclosure is made inadvertently, no use will be made of the identity of any person or establishment discovered and full details will be reported to the Data Archive. The identification will not be revealed to any other person not included in the Data Access Agreement.
    7. The Lead Researcher will implement security measures to prevent unauthorized access to licensed microdata acquired from the Data Archive. The microdata must be destroyed upon the completion of this research, unless the Data Archive obtains satisfactory guarantee that the data can be secured and provides written authorization to the Receiving Organization to retain them. Destruction of the microdata will be confirmed in writing by the Lead Researcher to the Data Archive.
    8. Any books, articles, conference papers, theses, dissertations, reports, or other publications that employ data obtained from the Data Archive will cite the source of data in accordance with the citation requirement provided with the dataset.
    9. An electronic copy of all reports and publications based on the requested data will be sent to the Data Archive.
    10. The original collector of the data, the Data Archive, and the relevant funding agencies bear no responsibility for use of the data or for interpretations or inferences based upon such uses.
    11. This agreement will come into force on the date that approval is given for access to the restricted dataset and remain in force until the completion date of the project or an earlier date if the project is completed ahead of time.
      If there are any changes to the project specification, security arrangements, personnel or organization detailed in this application form, it is the responsibility of the Lead Researcher to seek the agreement of the Data Archive to these changes. Where there is a change to the employer organization of the Lead Researcher this will involve a new application being made and termination of the original project.
    12. Breaches of the agreement will be taken seriously and the Data Archive will take action against those responsible for the lapse if willful or accidental. Failure to comply with the directions of the Data Archive will be deemed to be a major breach of the agreement and may involve recourse to legal proceedings. The Data Archive will maintain and share with partner data archives a register of those individuals and organizations which are responsible for breaching the terms of the Data Access Agreement and will impose sanctions on release of future data to these parties.

    Metadata production

    DDI Document ID

    DDI.AHRI.PANGEA1.HIV.Clinical.Data.2019.v1
    Producers
    Name
    Africa Health Research Institute
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