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Vukuzazi

Vukuzazi HIV polymerase sequences:2018-2020.

South Africa, 2018 - 2020
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Reference ID
AHRI.Vukuzazi.PANGEASequence.2023.v1
Producer(s)
Prof. Willem Hanekom, Prof. Thumbi Ndung’u, Dr. Kobus Herbst
Collections
Vukuzazi Data
Metadata
Documentation in PDF DDI/XML JSON
Created on
Jul 17, 2023
Last modified
Jul 17, 2023
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4302
  • Identification
  • Version
  • Scope
  • Coverage
  • Producers and sponsors
  • Sampling
  • Data collection
  • Data processing
  • Access policy
  • Metadata production

    • Identification

    Survey ID number
    AHRI.Vukuzazi.PANGEASequence.2023.v1
    Title
    Vukuzazi HIV polymerase sequences:2018-2020.
    Country
    Name Country code
    South Africa ZA
    Abstract
    Vukuzazi ("Wake up and know yourself " in isiZulu) was established in 2018 to offer a community-based health phenotyping and comprehensive bio-sampling to all resident adult (=15 years) members of the Africa Health Research Institute demographic health surveillance population, while building upon the existing wealth of demographic and HIV information collected over the previous 20 years. The objective of the platform was to determine the prevalence and overlap of infectious diseases and NCDs in the population 20 years into the HIV epidemic. Additionally, the platform aimed to create a data, image and biorepository that could be used to understand the host, pathogen, social and environmental determinants of specific states of health and disease in the population.

    The purpose of the genomic HIV data was to understand HIV transmission patterns among HIV infected individuals in rural KwaZulu Natal. To address this question, consensus polymerase sequences were derived from HIV positive samples with viral load greater than 200 copies/ml.
    Kind of Data
    HIV Genomic Data, Viral Load
    Unit of Analysis
    Each sequence derived from a single specimen

    Version

    Version Description
    v1.0.0

    Scope

    Topics
    Topic Vocabulary URI
    HIV-1;phylogeny;population surveillance; Epidemics; HIV infections; Africa Africa Health Research Institute
    Keywords
    HIV polymerase sequence; phylodynamics; phylogeny; HIV-1

    Coverage

    Geographic Coverage
    uMkhanyakude district in northern KwaZulu-Natal
    Universe
    HIV positive individuals enrolled in Vukuzazi study with a VL >200 copies/ml

    Producers and sponsors

    Primary investigators
    Name Affiliation
    Prof. Willem Hanekom Africa Health Research Institute
    Prof. Thumbi Ndung’u Africa Health Research Institute
    Dr. Kobus Herbst Africa Health Research Institute
    Producers
    Name
    Africa Health Research Institute
    Funding Agency/Sponsor
    Name Role
    Wellcome Trust Core funding
    Other Identifications/Acknowledgments
    Name Affiliation Role
    Sweetness Dube AHRI Data Documentation
    Dickman Gareta AHRI Head of Research Data Management
    Dr. Anne Derache AHRI Clinical Research Coordinator
    Dr. Resign Gunda AHRI Vukuzazi Programme Manager
    PANGEA consortium Big Data Institute Oxford Sequencing platform

    Sampling

    Sampling Procedure
    HIV positive individuals enrolled in Vukuzazi study between 2018 and 2020. Individuals blood were attempted for sequencing if they:
    1. Had a viral load done.

    Viral load was above 200 copies/ml

    Data collection

    Dates of Data Collection
    Start End
    2018-01-01 2020-03-30

    Data processing

    Data Editing
    Consensus sequences were derived from full-length HIV Next Generation Sequencing data generated by the PANGEA-HIV 2 (phylogenetics and Networks for Generalised Epidemics in Africa). Consensus sequences are presented in the standard fasta file format.

    Access policy

    Access conditions
    Access to the data requires accurate completion of the online data access application form accessible on the AHRI Data repository(<https://data.ahri.org/>). Data users are required to abide by the data use conditions stipulated on the application for access to the data. Failure to do so may result in their data access privileges being revoked by the Data Custodian. In order to recognise the effort and intellectual contributions of AHRI investigators in producing and curating the data, users of AHRI data must acknowledge the source of the data and abide by the terms and conditions under which the data is accessed and must cite the dataset in publication using the citation provided as part of this documentation. All analytical datasets published on the AHRI Data Repository are assigned digital object identifier (DOIs) and the DOIs can be found on the Data Repository under Study Description tab - Access policy. AHRI data users are required to always cite the dataset using the relevant DOI.
    Citation requirements
    Hanekom, W., Ndung'u, T., & Herbst, K. (2023). Vukuzazi HIV polymerase sequences:2018-2020. [Data set]. Africa Health Research Institute.
    DOI:https://doi.org/10.23664/AHRI.Vukuzazi.PANGEASequence.2023

    Metadata production

    DDI Document ID
    DDI.AHRI.Vukuzazi.PANGEASequence.2023.v1
    Producers
    Name
    Africa Health Research Institute
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