10.17037/DATA.169
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.
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.
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 |