Measuring mortality due to HIV-associated tuberculosis among adults in South Africa: comparing verbal autopsy, minimally-invasive autopsy, and research data. Data from the Lesedi Kamoso study

Persistent identifier

10.17037/DATA.169

Description

This dataset outlines causes of death (CoD) for 259 HIV-positive adults enrolled in the TB Fast Track and XPHACTOR studies, two large studies investigating HIV-associated tuberculosis (TB) in South Africa. It contains basic decedent demographics; CoD assigned by physicians with access to clinical data, including, in some, data from minimally-invasive autopsy (MIA); and CoD assigned by interpretation of (VA) data, by physicians, InterVA-4 software, and SmartVA-Analyze software.

Data access conditions

Anonymised data may be requested for the purpose of research verification only. Applicants may be required to sign a Data Transfer Agreement prior to being provided with data. All data requests are handled by the study team.

Data codebook

The VAvsMIA_data contains variables listed in the following table. Information on the data collection, processing and analysis method may be found in associated publications. Please consult study authors with any questions.

Variable Name Variable Label Answer Label Answer Code Variable Type
id Participant ID Open ended   Numeric
Dem_prevtb Ever treated for TB?     Numeric
    No 0  
    Yes 1  
    NA 7  
    Dont Know 9  
Dem_study Parent study     Numeric
    TB Fast Track 1  
    XPHACTOR 2  
Dem_sex Participant gender     Numeric
    Male 1  
    Female 2  
Dem_agedeath Participant age at death Numeric   Numeric
Dem_enrtod Time from enrolment to death Numeric   Numeric
Dem_dtova Time from death to VA Numeric   Numeric
Dem_sacitizen Is participant a South African citizen?     Numeric
    No 0  
    Yes 1  
    NA 7  
    Don’t Know 9  
Dem_black Participant ethnicity     Numeric
    Other 0  
    Black African 1  
    Not applicable 7  
    Don’t Know 9  
Dem_urban Is participant enrolled in urban area?     Numeric
    No 0  
    Yes 1  
    Not applicable (NA) 7  
    Dont Know 9  
Dem_educ Participant highest education completed     Numeric
    None/Pre-school 1  
    Grd 1-3 2  
    Grd 4-7 3  
    Grd 8-11 4  
    Grd 12 5  
    Matric/Dip 6  
    BA 7  
    MS/PhD 8  
    Other 9  
Dem_cd4 Most recent CD4 count Open ended   Numeric
Dem_mia Minimally-invasive autopsy (MIA) conducted     Numeric
    No 0  
    Yes 1  
    NA 7  
    Dont Know 9  
Dem_married Marital status     Numeric
    Single 1  
    Married 2  
    Married-separated 3  
    Cohabitating 4  
    Divorced 5  
    Widowed 6  
Dem_hincom Household monthly income     Numeric
    <R600 1  
    R601-1000 2  
    R1001-2000 3  
    R2001-4000 4  
    >R4000 5  
    Dont Know 7  
Dem_artenrol Taking ART at enrolment?     Numeric
    No 0  
    Yes 1  
    NA 7  
    Dont Know 9  
va_resp VA respondent     Numeric
    Grandparent 10  
    Parent 11  
    Child 12  
    Sibling 13  
    Other relative (older gen) 14  
    Other relative (same gen) 15  
    Other relative (younger gen) 16  
    Other relative (unspecified) 17  
    Partner 18  
    Friend 19  
    Caregiver 20  
    Other 21  
L3_icd L3 CoD - ICD-10 category     Numeric
    HIV/AIDS 1  
    PTB 2  
    Other infectious 3  
    Malignancy 4  
    Other NCD 5  
    External/traumatic or pregnancy-related 6  
    Indeterminate 7  
L3_sd L3 CoD - study-defined     Numeric
    TB in an HIV-positive adult 1  
    HIV-associated cause, other than TB 2  
    Non-AIDS, non-HIV-associated cause in an HIV-positive adult 3  
    TB in an HIV-negative adult 4  
    Non-TB cause in an HIV-negative adult 5  
    Indeterminate cause 6  
L2_sd L2 coD - study-defined     Numeric
    TB in an HIV-positive adult 1  
    HIV-associated cause, other than TB 2  
    Non-AIDS, non-HIV-associated cause in an HIV-positive adult 3  
    TB in an HIV-negative adult 4  
    Non-TB cause in an HIV-negative adult 5  
    Indeterminate cause 6  
L2_icd L2 CoD - ICD-10 category     Numeric
    HIV/AIDS 1  
    PTB 2  
    Other infectious 3  
    Malignancy 4  
    Other NCD 5  
    External/traumatic or pregnancy-related 6  
    Indeterminate 7  
PCVA_sd PCVA CoD - study-defined     Numeric
    TB in an HIV-positive adult 1  
    HIV-associated cause, other than TB 2  
    Non-AIDS, non-HIV-associated cause in an HIV-positive adult 3  
    TB in an HIV-negative adult 4  
    Non-TB cause in an HIV-negative adult 5  
    Indeterminate cause 6  
PCVA_icd PCVA CoD - ICD-10 category     Numeric
    HIV/AIDS 1  
    PTB 2  
    Other infectious 3  
    Malignancy 4  
    Other NCD 5  
    External/traumatic or pregnancy-related 6  
    Indeterminate 7  
IVA_icd InterVA-4 CoD - ICD-10 category     Numeric
    HIV/AIDS 1  
    PTB 2  
    Other infectious 3  
    Malignancy 4  
    Other NCD 5  
    External/traumatic or pregnancy-related 6  
    Indeterminate 7  
IVA_causen InterVA-4 CoD 1     Numeric
    01.01 Sepsis (non-obstetric) 10  
    01.02 Acute resp infect, incl pneumonia 11  
    01.03 HIV/AIDS related death 12  
    01.04 Diarrhoeal diseases 13  
    01.05 Malaria 14  
    01.06 Measles 15  
    01.07 Meningitis and encephalitis 16  
    01.08, 10.05 Tetanus 17  
    01.09 Pulmonary tuberculosis 18  
    01.10 Pertussis 19  
    01.11 Haemorrhagic fever 20  
    01.99 Other and unspecified infect dx 21  
    02.01 Oral neoplasms 22  
    02.02 Digestive neoplasms 23  
    02.03 Respiratory neoplasms 24  
    02.04 Breast neoplasms 25  
    02.05, 02.06 Reproductive neoplasms M,F 26  
    02.99 Other and unspecified neoplasms 27  
    03.01 Severe anaemia 28  
    03.02 Severe malnutrition 29  
    03.03 Diabetes mellitus 30  
    04.01 Acute cardiac dx 31  
    04.02 Stroke 32  
    04.03 Sickle cell with crisis 33  
    04.99 Other and unspecified cardiac dx 34  
    05.01 Chronic obstructive pulmonary dx 35  
    05.02 Asthma 36  
    06.01 Acute abdomen 37  
    06.02 Liver cirrhosis 38  
    07.01 Renal failure 39  
    08.01 Epilepsy 40  
    98 Other and unspecified NCD 41  
    10.06 Congenital malformation 42  
    10.01 Prematurity 43  
    10.02 Birth asphyxia 44  
    10.03 Neonatal pneumonia 45  
    10.04 Neonatal sepsis 46  
    10.99 Other and unspecified neonatal CoD 47  
    11.01 Fresh stillbirth 48  
    11.02 Macerated stillbirth 49  
    12.01 Road traffic accident 50  
    12.02 Other transport accident 51  
    12.03 Accid fall 52  
    12.04 Accid drowning and submersion 53  
    12.05 Accid expos to smoke, fire & flame 54  
    12.06 Contact with venomous plant/animal 55  
    12.10 Exposure to force of nature 56  
    12.07 Accid poisoning and noxious substances 57  
    12.08 Intentional self-harm 58  
    12.09 Assault 59  
    12.99 Other and unspecified external CoD 60  
    09.01 Ectopic pregnancy 61  
    09.02 Abortion-related death 62  
    09.03 Pregnancy-induced hypertension 63  
    09.04 Obstetric haemorrhage 64  
    09.05 Obstructed labour 65  
    09.06 Pregnancy-related sepsis 66  
    09.07 Anaemia of pregnancy 67  
    09.08 Ruptured uterus 68  
    09.99 Other and unspecified maternal CoD 69  
    99 Indeterminate 70  
IVA_lik1 InterVA-4 - likelihood 1 Open ended   Numeric
IVA_causen2 InterVA-4 CoD 2     Numeric
    01.01 Sepsis (non-obstetric) 10  
    01.02 Acute resp infect, incl pneumonia 11  
    01.03 HIV/AIDS related death 12  
    01.04 Diarrhoeal diseases 13  
    01.05 Malaria 14  
    01.06 Measles 15  
    01.07 Meningitis and encephalitis 16  
    01.08, 10.05 Tetanus 17  
    01.09 Pulmonary tuberculosis 18  
    01.10 Pertussis 19  
    01.11 Haemorrhagic fever 20  
    01.99 Other and unspecified infect dx 21  
    02.01 Oral neoplasms 22  
    02.02 Digestive neoplasms 23  
    02.03 Respiratory neoplasms 24  
    02.04 Breast neoplasms 25  
    02.05, 02.06 Reproductive neoplasms M,F 26  
    02.99 Other and unspecified neoplasms 27  
    03.01 Severe anaemia 28  
    03.02 Severe malnutrition 29  
    03.03 Diabetes mellitus 30  
    04.01 Acute cardiac dx 31  
    04.02 Stroke 32  
    04.03 Sickle cell with crisis 33  
    04.99 Other and unspecified cardiac dx 34  
    05.01 Chronic obstructive pulmonary dx 35  
    05.02 Asthma 36  
    06.01 Acute abdomen 37  
    06.02 Liver cirrhosis 38  
    07.01 Renal failure 39  
    08.01 Epilepsy 40  
    98 Other and unspecified NCD 41  
    10.06 Congenital malformation 42  
    10.01 Prematurity 43  
    10.02 Birth asphyxia 44  
    10.03 Neonatal pneumonia 45  
    10.04 Neonatal sepsis 46  
    10.99 Other and unspecified neonatal CoD 47  
    11.01 Fresh stillbirth 48  
    11.02 Macerated stillbirth 49  
    12.01 Road traffic accident 50  
    12.02 Other transport accident 51  
    12.03 Accid fall 52  
    12.04 Accid drowning and submersion 53  
    12.05 Accid expos to smoke, fire & flame 54  
    12.06 Contact with venomous plant/animal 55  
    12.10 Exposure to force of nature 56  
    12.07 Accid poisoning and noxious substances 57  
    12.08 Intentional self-harm 58  
    12.09 Assault 59  
    12.99 Other and unspecified external CoD 60  
    09.01 Ectopic pregnancy 61  
    09.02 Abortion-related death 62  
    09.03 Pregnancy-induced hypertension 63  
    09.04 Obstetric haemorrhage 64  
    09.05 Obstructed labour 65  
    09.06 Pregnancy-related sepsis 66  
    09.07 Anaemia of pregnancy 67  
    09.08 Ruptured uterus 68  
    09.99 Other and unspecified maternal CoD 69  
    99 Indeterminate 70  
IVA_lik2 InterVA-4 - likelihood 2 Open ended   Numeric
IVA_causen3 InterVA-4 CoD 3     Numeric
    01.01 Sepsis (non-obstetric) 10  
    01.02 Acute resp infect, incl pneumonia 11  
    01.03 HIV/AIDS related death 12  
    01.04 Diarrhoeal diseases 13  
    01.05 Malaria 14  
    01.06 Measles 15  
    01.07 Meningitis and encephalitis 16  
    01.08, 10.05 Tetanus 17  
    01.09 Pulmonary tuberculosis 18  
    01.10 Pertussis 19  
    01.11 Haemorrhagic fever 20  
    01.99 Other and unspecified infect dx 21  
    02.01 Oral neoplasms 22  
    02.02 Digestive neoplasms 23  
    02.03 Respiratory neoplasms 24  
    02.04 Breast neoplasms 25  
    02.05, 02.06 Reproductive neoplasms M,F 26  
    02.99 Other and unspecified neoplasms 27  
    03.01 Severe anaemia 28  
    03.02 Severe malnutrition 29  
    03.03 Diabetes mellitus 30  
    04.01 Acute cardiac dx 31  
    04.02 Stroke 32  
    04.03 Sickle cell with crisis 33  
    04.99 Other and unspecified cardiac dx 34  
    05.01 Chronic obstructive pulmonary dx 35  
    05.02 Asthma 36  
    06.01 Acute abdomen 37  
    06.02 Liver cirrhosis 38  
    07.01 Renal failure 39  
    08.01 Epilepsy 40  
    98 Other and unspecified NCD 41  
    10.06 Congenital malformation 42  
    10.01 Prematurity 43  
    10.02 Birth asphyxia 44  
    10.03 Neonatal pneumonia 45  
    10.04 Neonatal sepsis 46  
    10.99 Other and unspecified neonatal CoD 47  
    11.01 Fresh stillbirth 48  
    11.02 Macerated stillbirth 49  
    12.01 Road traffic accident 50  
    12.02 Other transport accident 51  
    12.03 Accid fall 52  
    12.04 Accid drowning and submersion 53  
    12.05 Accid expos to smoke, fire & flame 54  
    12.06 Contact with venomous plant/animal 55  
    12.10 Exposure to force of nature 56  
    12.07 Accid poisoning and noxious substances 57  
    12.08 Intentional self-harm 58  
    12.09 Assault 59  
    12.99 Other and unspecified external CoD 60  
    09.01 Ectopic pregnancy 61  
    09.02 Abortion-related death 62  
    09.03 Pregnancy-induced hypertension 63  
    09.04 Obstetric haemorrhage 64  
    09.05 Obstructed labour 65  
    09.06 Pregnancy-related sepsis 66  
    09.07 Anaemia of pregnancy 67  
    09.08 Ruptured uterus 68  
    09.99 Other and unspecified maternal CoD 69  
    99 Indeterminate 70  
IVA_lik3 InterVA-4 - likelihood 3 Open ended   Numeric
SmartVA_icd SmartVA-Analyze CoD - ICD-10 category     Numeric
    HIV/AIDS 1  
    PTB 2  
    Other infectious 3  
    Malignancy 4  
    Other NCD 5  
    External/traumatic or pregnancy-related 6  
    Indeterminate 7