Treatment as Prevention ANRS 12249 - datasets for Lancet HIV pain paper

HIV drug treatment for TasP patients in care in TasP clinics. One row per regimen and per patient.
Each time a patient switched from one regimen to another regimen, a new record was stored in that dataset.

This dataset contains one row per registered households.

This dataset corresponds to Clinical History and Examination forms (CHE) completed by nurses in tasP clinics. The following sections of the questionnaire are provided in separate datasets:
- 11. Concomitant medication not recorded in ART or TB regimen -> HIV Drug Treatments dataset
- 12. Adverse Events -> Adverse Events dataset
- 24. Drug Prescriptions -> HIV Drug Treatments dataset
- 25. Action Plan -> Action Plans dataset

This dataset contains the resuts of the clinical tests done for patients in care in TasP clinics. It contains one row per test date and per individual.

This dataset contains all ARTemis Lab test results (in particular CD4 counts and viral loads) for TasP registered individuals linked to ARTemis.

This file contains data from ARTemis database for each registered TasP individual linked to ARTemis. One row per individual.

The data collated here is obtained from patients' records completed during routine HIV clinical care within the Hlabisa Treatment and Care Programme. The HIV treatment and Care programme was implemented as a joint initiative by the Department of Health (DoH) and the Africa Centre for Health and Population Studies (http://www.africacentre.ac.za) in response to the Comprehensive HIV and AIDS Care Management and Treatment Plan in 2004. HIV treatment and care is offered in 17 nurse-led primary health-care (PHC) clinics and 1 district hospital. The data comprises HIV positive patients pre- and post- ART initiation. However for patients pre-ART only the personal identifiers (name, sex and South African ID number) and the CD4 counts measured for assessment of ART eligibility are recorded. All patients within ARTemis are HIV positive and all patients are aware of their HIV status. This database was initially set up for monitoring and evaluating (M&E) patients and programme performance and outcomes. Over time in addition to M&E, these data are used to answer research questions to better understand issues related to HIV and ART in HIV positive patients.

Routine data collection schedule is summarized below:

Basic details

Age, sex, address, ID number, contact details, treatment clinic (collected at ART initiation only or when need arises during follow-up)

Socio-demographic details

Grants received, employment, school attendance, number of dependents (collected at ART initiation only)

Tuberculosis (TB) record

Tuberculosis (TB) record

Previous history of TB, TB treatment at initiation, new episodes of TB (collected only in those receiving ART)

ART record

WHO clinical stage, Previous ART and/or PMTCT, ART regimen at initiation, changes in ART regimen during treatment

Laboratory data

For patients on ART

Baseline and 6-monthly CD4 and HIV viral load, baseline haematology and biochemistry

For patients pre-ART

All pre-ART CD4 cell counts routinely done in accordance with the South African ART guidelines are recorded

This dataset corresponds to the Adverse Events section of the CHE (clinical history examination) forms. It contains one row per recorded adverse event.

This dataset contains SCBs and SCCs forms (clinic-based survey, ART consellor administered), one row per form.

This dataset corresponds to the Action Plans section of the CHE (clinical history examination) forms. It contains one row per recordedaction plan.

Trial clusters

This table contains one row per visit. There are two sorts of visits: homestead visits and TasP clinic visits, that can be identified through the variable LocationType.

LocationId refers to a homestead or to a TasP visit, according to the sort of visit.

Several individuals could be surveyed for a same homestead visit while a TasP clinic visit always concerns only one individual.

This dataset contains Household Information / Assets forms. One row per form.

This file contains one row per Clinic Follow-Up form (CFU) completed by Trial Counsellor. Data from question 3.5 (Adherence Pill Identification Test) are provided in a seperate dataset (CFU Pill tests).

This file contains data from question 3.5 (Adherence Pill Identification Test), one row per pill. You can link data with CFUs dataset using CVIntId.

This dataset contains one row per Local Area. Local Areas are used in sexual behaviours questionnaires.

This dataset contains one row per Census Round, i.e. one row per survey round and per cluster. That dataset provides the corresponding Calendar Rounds and Data Collection Cycles, please refer to TasP Definition document for details.

This dataset contains SCI forms (clinic-based survey, independent interwiever administered), one row per form.

This dataset contains individual consents. One row per individual.

Serious Adverse Events - Initial Notifications. This dataset contains one row per SAE notification.

One row per event.

One row per drug

One row per complementary form

One row per drug

This dataset corresponds to Clinic Baseline Visit (CBC) forms completed by ART counsellors in TasP clinics.

This dataset indicates specimens collected within TasP (at home or in TasP clinics), one row per specimen.

This dataset contains Individual Questionnaires (IQ1, IQ2, IQ3 and IQP) completed at home by fieldworkers.

The database doesn't allow the completion of more than one IQ1, one IQ2 and one IQ3 per individual.

The database does however allow the completion of more than one IQP per individual.

According to the protocol, an IQ3 should be completed only if an IQ2 has been previously completed. However, there are few cases of individuals having completed an IQ3 without having completed an IQ2.
Also, an individual should normally complete a maximum of one IQ per calendar round, but some individuals have completed two IQs during the same calendar round (at different dates).
Finally, although definition of logical rounds is based on IQ completion, there are some inconsistencies between logical rounds as recorded in the individuals file and completion of IQs.

IQ1 and IQ3 are identical (they have the same questionnaire), while IQ2 is a shorter questionnaire with specific questions.

Dataset contains multiple rows per individual sequence analysed with the Next Generation Sequencing method and include information about drug resistance minority variants

This dataset corresponds to Beliefs about medicines questionnaire (BMQ) forms completed by ART counsellors in TasP clinics.

Dataset contains 1 row per individual sequence analysed. All sequences contained in this dataset has been analysed with the Next Generation Sequencing method.

This dataset corresponds to reasons why a household refused participantion in the study. Colleced by fieldworkers

Dataset contains 1 row per individual Next Generation Sequencing (NGS) sequence analysed. Dataset provided details of the Sequence assembly quality for each sample analysed.

Dataset contains 1 row per individual sequence analysed. All sequences contained in this dataset has been analysed with the Sanger method.

Locations, i.e Homesteads and TasP clinics

This dataset corresponds to the Linkage to Care Tracking forms completed by the TasP Linkage to Care Team.

This dataset contains one row per exit form completed, including both population and clinic exits.
In Phase 1 (before 31st of May 2014), there were no formal distinction between population and clinic exits, only one form being used in the field (EXI). Since June 2014 two exit forms are used (EXIH and EXIC). Phase 1 forms have been manually recoded (using all available information, including field notes) to identify properly population and clinic exits. Please refer to variables PopulationExitComputed, ClinicExitComputed and PopulationExitTypeComputed.
Variables: DTHDateComputed, ExitDateComputed, NMCDateComputed, OUTDateComputed, TRODateComputed, LFUDateComputed have been populating by taking into account the following corrections: (i) if exit date was missing or (ii) the year of the exit date was unknown or (iii) exit date was after VisitDate, then VisitDate (the date the exit from has been completed) was used instead of the exit date.

Dataset contains one record per Individual visit (encounter) in the Africa Centre Clinical Database (ACCDB)

Dataset contains multiple records per Individual for each Therapy received in the Africa Centre Clinical Database (ACCDB)

Registered individuals.

An individual is registered during the first calendar round he/she is eligible, i.e. all individuals who have been eligible at least once are registered and all registered individuals have been eligible at least once. Individuals could be registered only in a fully contacted household where the household head or another key informant accepted to participate.

These file contains individual trial statuses, one row per trial status.

Duplicated Trial Statuses (same visit date / same trial status) have been removed. Exit Trial Statuses have been re-created from the Exits datasets importing only Population Exits.

This file contains the results of HIV tests performed on Dried Blood Spots (DBS) collected during the home-based survey. This file contains one row per test.