I do not know of any tool now. I would however suggest a mixed method approach using client records in facilities with PMTCT programs and FGD / IDI in the women's support groups. It is pertinent to consider the psycho-social environment and the rights of the participants. All the best!
Could you not use CD4 counts and viral load to compare the two groups and relate to out come? They are readily available in our environment. You could also consider using the HIV subtypes eg HIV-! and HIV-II as we know the former is more aggressive. Full blood counts if regular could also be used.