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This was said at the President's Emergency Plan for AIDS Annual Meeting on Monday at the Durban International Convention Centre.
The conference heard that heroin is the drug most frequently used intravenously.
Okey Nwanyanwu, from the Medical Research Council, said there had been an increase of injection and non-injection drug use in sub-Saharan Africa, but limited attention had been paid to intravenous drug use in South Africa.
Studies conducted in Durban, Pretoria and Cape Town found that 33 percent of prostitutes and homosexuals in Durban were HIV-positive, the most out of the three cities.
The study, which was conducted last year between October and November, found that condom use among prostitutes and homosexuals was erratic or non-existent.
Drug users reported sharing needles and needle disposal practices, which put them and others at risk of contracting HIV. In both groups, there was a lack of awareness about where to access HIV treatment and preventative services.
Nwanyanwu said: There is a rise in injection use among these groups. Sex workers use drugs to cope with the sex work. Condom use is also erratic because they are less informed about HIV prevention.
Men who have sex with men use condoms erratically and the majority of them are most likely to have sex without condoms. Many of them use injections.