University of Cape Town
04 Infectious Diseases Toolkit (1.36 MB)

H3Africa PHWG Data Collection Toolkit - Infectious Diseases v2.0

Download (1.36 MB)
posted on 2022-11-14, 14:20 authored by Nicki Tiffin, Tsaone Tamuhla, Liberata Mwita, Taryn Allie, Milaine Tchanga, Samah Ahmed, Upendo Masamu, Lyndon ZassLyndon Zass, Katherine JohnstonKatherine Johnston, Nihad Alsayed


The Infectious Disease toolkit can be used to collect essential phenotypes associated with Infectious Disease related research, including information related to Malaria, Trypanosomiasis / Sleeping Sickness, Tuberculosis (TB) and HIV.


The phenotype protocols contained in the toolkit range from Interviewer/Self-administered questionnaires to clinically-administered and bioassay/lab-based assessments. The toolkit is applicable to human participants of all life stages, though some phenotype protocols are age-specific. For more information on administration of the toolkit, see the toolkit guideline.


The toolkit consists of both existing and novel data collection standards, and was based on several existing resources. These resources are listed below:

  1. H3Africa Case Report Form Instruments
  2. Sickle In Africa Core Data Elements (
  3. Allie, T., Jackson, A., Ambler, J., Johnston, K., Du Bruyn, E., Schultz, C., Boloko, L., Wasserman, S., Davis, A., Meintjes, G., Wilkinson, R. J., & Tiffin, N. (2021). TBDBT: A TB DataBase Template for collection of harmonized TB clinical research data in REDCap, facilitating data standardisation for inter-study comparison and meta-analyses. PloS one, 16(3), e0249165.
  4. Protocol - Sexual Risk Behavior - Male (
  5. Protocol - Sexual Risk Behavior - Female (
  6. Enhanced COVID-19 Notifiable Medical Conditions (NMC) Notification Form (SA)
  7. WHO Global COVID-19 Clinical Platform: Rapid core case report form
  8. Protocol - Complete Blood Count (CBC) (
  9. Protocol - Liver Function - Assay (
  10. Protocol - Sexual Risk Behavior - Male (
  11. Protocol - Sexual Risk Behavior - Female (
  12. HIV Cohorts Data Exchange Protocol (


H3ABioNet: a sustainable African Bioinformatics Network for H3Africa

National Human Genome Research Institute

Find out more...



Computational Biology, University of Cape Town