AHRI.PANGEA1.Data.2019.v1
PANGEA1 Demographic and Clinical Data.2019.v1
Name | Country code |
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South Africa | ZA |
PANGEA is an international consortium of researchers based in Africa, the US and the UK studying transmission dynamics in HIV epidemics in sub-Saharan Africa. The goal of the consortium is to analyse HIV phylogenetic and demographic data to identify individual and population-level factors that drive the epidemic, analyse the dynamics of the epidemic and translate these findings into information that can be used to more effectively target interventions. PANGEA encompasses four analysis themes: (1) molecular epidemiology and mathematical modelling, (2) phylodynamics, (3) mobility and migration, and (4) clinical science, drug resistance and ethics. Major variables within the dataset to answer this question are: (1) the genotype; (2) the participant's geolocation from which the genotype was derived; and (3) the date of sampling, (4) all relevant clinical data and (5) all relevant demographic data.
Clinical and Demographic data
Each sequences derived from a single specimen, but some sequences may have been repeated on the same specimen, or on another time point, depending on the quality of the sequence.
V1.0.0
Topic | Vocabulary | URI |
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HIV-1; Incidence; Phylogeny; Epidemics; Population Surveillance; Rural Population; HIV Infections; Africa | Africa Health Research Institute | AHRI |
South Africa
HIV genome extracted and sequenced from participants infected with HIV
Name | Affiliation |
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Pillay, Deenan | Africa Health Research Institute |
Name |
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Africa Health Research Institute |
Name | Role |
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PANGEA consortium, funded by the Bill & Melinda Gates Foundation | Genotyping funding source |
Name | Affiliation | Role |
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Derache, Anne | Africa Health Research Insitute | Cleaned, aligned and help analyse the sequence data. |
HIV positive individuals within the demographic surveillance area of the Africa Health Research Insititue from 2010 to 2016. Full-length HIV deep sequencing was attempted on samples that:
A) Had a blood sample taken (not DBS)
B) Had a viral load >1000 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.
Start | End |
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2010-01-01 | 2016-12-04 |
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.
DDI.AHRI.PANGEA1.Data.2019.v1
Name |
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Africa Health Research Institute |