Table 2 Secondary outcomes of UZ-CHS Birth cohort study

1. Comparison of morbidity of HEU vs. HUU infants, defined as impaired growth, immune- and neuro-development and/ or frequent of clinically relevant infections.

2. To determine any association of ART exposure in utero and during breast feeding with pregnancy outcome, infant (HUU, HEU, HEI) growth and immune- and neuro-development.

3. To determine vertical transmission rates for HIV at birth and within the first 2 years of life and assess risk factors for transmission.

4. To determine the association between maternal baseline and delivery ART levels in different compartments and infant HIV infection, mortality and morbidity.

5. To determine HIV drug resistance profiles in mother and infants unresponsive to ART.

6. To assess abnormalities including lipid profiles, bone, haematological and hepatic toxicities associated with exposure to ART among mothers and infants.

7. To determine antenatal co-infections including HBV, HCV, CMV, syphilis, intestinal helminths and parasites as single infection or combined infections in HIV-infected and HIV -uninfected - women and determine the impact on pregnancy outcome, infant mortality and morbidity.

8. To determine the prevalence of infant infectious comorbidities; HBV, HCV, CMV, syphilis, including time points of infections and impact on mortality and morbidity.

9. To determine the prevalence of maternal NCDs (malnutrition/ obesity, anaemia, diabetes, hypertensive disorders) and determine their impact on pregnancy outcomes, infant mortality and morbidity.

10. To determine infant non-infectious comorbidities (e.g. anaemia, atopic dermatitis, congenital infections and other conditions) and their impact on mortality and morbidity.

11. To determine maternal household non-biological factors (socioeconomic state, hygiene) and determine their impact on pregnancy outcome, infant mortality and morbidity.

12. To determine antenatal reference ranges for MUAC, haemoglobin from FBC analyses, and biochemistry (kidney function, liver function tests, bone, lipid profiles) in pregnant women with a favourable outcome of pregnancy.

13. To assess delayed neurological development using the Denver II tool in HUU, HEU and HEI infants from 6 weeks to 2 years of age.

14. To determine humoural immune responses to EPI vaccines (e.g. antibody levels against measles, tetanus, diphtheria, pertussis, polio and rotavirus) in HUU, HEU and HEI infants.

15. To determine maternal intestinal parasites load using 18S sequencing in pregnancy and relate it to infant immune development and atopy (anti-inflammatory (IL-4, − 5, − 13) and regulatory cytokines (IL-10, TGF-β) at delivery, 6 weeks 48 and 96 weeks of age.

16. To determine immune activation and systemic inflammatory biomarkers in HUU, HEU and HEI infants at delivery, 6, 48 and 96 weeks of age.

17. To determine biomarkers for endothelial dysfunction including microbial translocation in HUU, HEU and HEI infants at delivery, 6, 48 and 96 weeks of age.

18. To determine host genetic markers for infectious disease susceptibility including HLA and KIR gene variants and their association with infection rates of HIV and co-infections in mothers and their infants.

19. To characterize pathogen genetic diversity including HIV, HBV, HCV, CMV subtypes, prevalent in our study population at time of infection/ earliest available samples and/or at 2 years.