{"doc_desc":{"title":"Documentation:Vukuzazi HIV polymerase sequences:2018-2020.","idno":"DDI.AHRI.Vukuzazi.PANGEASequence.2023.v1","producers":[{"name":"Africa Health Research Institute","abbreviation":"AHRI","affiliation":"","role":""}]},"study_desc":{"title_statement":{"idno":"AHRI.Vukuzazi.PANGEASequence.2023.v1","title":"Vukuzazi HIV polymerase sequences:2018-2020."},"authoring_entity":[{"name":"Prof. Willem Hanekom","affiliation":"Africa Health Research Institute"},{"name":"Prof. Thumbi Ndung\u2019u","affiliation":"Africa Health Research Institute"},{"name":"Dr. Kobus Herbst","affiliation":"Africa Health Research Institute"}],"oth_id":[{"name":"Sweetness Dube","affiliation":"AHRI","email":"","role":"Data Documentation"},{"name":"Dickman Gareta","affiliation":"AHRI","email":"","role":"Head of Research Data Management"},{"name":"Dr. Anne Derache","affiliation":"AHRI","email":"","role":"Clinical Research Coordinator"},{"name":"Dr. Resign Gunda","affiliation":"AHRI","email":"","role":"Vukuzazi Programme Manager"},{"name":"PANGEA consortium","affiliation":"Big Data Institute Oxford","email":"","role":"Sequencing platform"}],"production_statement":{"producers":[{"name":"Africa Health Research Institute","affiliation":"","role":""}],"funding_agencies":[{"name":"Wellcome Trust","abbreviation":"WT","role":"Core funding"}],"grant_no":"097410\/Z\/11\/Z"},"version_statement":{"version":"v1.0.0"},"study_info":{"keywords":[{"keyword":"HIV polymerase sequence; phylodynamics; phylogeny; HIV-1","vocab":"Africa Health Research Institute","uri":"www.ahri.org"}],"topics":[{"topic":"HIV-1;phylogeny;population surveillance; Epidemics; HIV infections; Africa","vocab":"Africa Health Research Institute","uri":"www.ahri.org"}],"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.\n\nThe 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.","coll_dates":[{"start":"2018-01-01","end":"2020-03-30","cycle":""}],"nation":[{"name":"South Africa","abbreviation":"ZA"}],"geog_coverage":"uMkhanyakude district in northern KwaZulu-Natal","analysis_unit":"Each sequence derived from a single specimen","universe":"HIV positive individuals enrolled in Vukuzazi study with a VL >200 copies\/ml","data_kind":"HIV Genomic Data, Viral Load"},"method":{"data_collection":{"sampling_procedure":"HIV positive individuals enrolled in Vukuzazi study between 2018 and 2020. Individuals blood were attempted for sequencing if they:\n1. Had a viral load done.\n\nViral load was above 200 copies\/ml","cleaning_operations":"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."}},"data_access":{"dataset_use":{"cit_req":"Hanekom, W., Ndung'u, T., & Herbst, K. (2023). Vukuzazi HIV polymerase sequences:2018-2020. [Data set]. Africa Health Research Institute.\nDOI:https:\/\/doi.org\/10.23664\/AHRI.Vukuzazi.PANGEASequence.2023","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."}}},"schematype":"survey","tags":[{"tag":"PANGEA"},{"tag":"Vukuzazi"}]}