Visualisation of sequence and demographic data to assist HIV surveillance in Northern KwaZulu-Natal: extending the TasP/iSense dashboard to include markers of HIV drug resistance mutations.
South Africa, 2012 - 2016
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AHRI.TasP.DataEveryWhere.Dashboard.2016.v1
Visualisation of sequence and demographic data to assist HIV surveillance in Northern KwaZulu-Natal: extending the TasP/iSense dashboard to include markers of HIV drug resistance mutations.
| Name | Country code |
|---|---|
| South Africa | ZA |
This proposal aims to extend an existing collaboration between AHRI and UCL. As part of the iSense project, teams from AHRI and UCL have successfully developed a dashboard that integrates information from mobile computers used for TasP field visits with data from the clinics to display spatial coverage of homestead visits, highlighting those that require follow-up visits to ensure linkage to care. The dashboard provides a broad snapshot of the state of the study, spatially aggregating geographical zones in order to preserve the privacy of trial participants.
The aim of this proposal is to extend this framework to visualise presence and prevalence of drug resistance mutations (DRMs) within the study area. A higher prevalence of DRMs than expected may be linked to several factors, e.g. poor drug adherence, and thus of value to clinicians and healthcare workers in terms of focusing efforts and resource allocation.
The existing dashboard is built on pseudonymised demographic data grouped into geographic hexagons. Within the PANGEA project, we have independently assembled HIV genomes from patient clinical samples and identified DRMs for each sample. To map the DRMs to each geographical hexagon, we require a lookup table to link the TasP/PANGEA IDs to hexagons.
Each sample ID should be linked to a single hexagon where possible.
Version
V1.0.0
Scope
| Topic | Vocabulary | URI |
|---|---|---|
| HIV-1; Incidence; Phylogeny; Epidemics; Population Surveillance; Rural Population; HIV Infections; Africa | Africa Health Research Institute | www.ahri.org |
Coverage
South Africa
Clusters: the trial area consists of 150 local areas (neighbourhoods). These were aggregated into 34 clusters of between one
and six contiguous neighbourhoods, each cluster comprising an average of 1 000 individuals >15 years of age. Clusters
were designed to encompass social networks based on earlier studies. TasP phase 1 has been implemented in 10 geographic
clusters (5 control and 5 intervention). Twelve additional clusters have been opened in June 2014.
Locations: corresponds to physical locations. There are two types of locations: homesteads and TasP clinics.
Homesteads: the population lives in scattered homesteads that are not concentrated into villages or compounds. All usable
and occupied homesteads were eligible for trial participation.
Households: each homestead coul be composed of one or several households. An household remains always attached to the
same homestead.
Eligible individuals : all 16 years or older and resident household members. Each individuals is attached to an household. In
case of internal migration, an individual could move to another household.
TasP clinics: dedicated trial clinics implemented in each survey cluster.
Producers and sponsors
| Name | Affiliation |
|---|---|
| Frampton, Dan | Division of Infection and Immunity, UCL, London Division of Infection and Immunity, UCL, London UCL, London |
| McKendry, Rachel | London Center for Nanotechnology, UCL, London |
| Pillay, Deenan | Africa Health Research Institute |
| Name |
|---|
| Africa Health Research Institute |
| Name | Role |
|---|---|
| South African Medical Research Council | Genotyping funding source |
| Engineering and Physical Sciences Research Council | Design and implementation of dashboard within the iSense project |
| Name | Affiliation | Role |
|---|---|---|
| Jaco Dreyer | Africa Health Research Institute | Linking sample and demographic data design |
| Ed Manley | UCL Centre for Advanced Spatial Analysis (CASA), London | Implementation of iSense dashboard design |
| Dave Concannon | UCL Centre for Advanced Spatial Analysis (CASA), London | Implementation of iSense dashboard |
Sampling
HIV positive individuals within the TasP surveillance area of the Africa Health Research Insititute from 2012 to 2016.
Data collection
| Start | End |
|---|---|
| 2012-01-01 | 2016-12-04 |
Data processing
Samples were sequenced at the Durban based laboratory of AHRI; genome assembly and downstream sequence analysis was performed at UCL.
Data Access
Data is available to researchers upon application and approval by AHRI data governance committee. Application for the data can be done online through the following link: https://data.africacentre.ac.za/index.php/auth/login
Metadata production
DDI.AHRI.TasP.DataEveryWhere.Dashboard.2016.v1
| Name |
|---|
| Africa Health Research Institute |