Most South Africans would not make this distinction and would believe Mbeki to have denied the link and would have acted accordingly. Also, there is evidence to suggest that Mbeki did question the link between HIV and AIDS specifically. Moneyweb has published an interesting article relating the whole saga and concludes:
It was on July 9 that Mbeki first publicly questioned the causal link between HIV and AIDS. In his address to the International AIDS conference in Durban he stated that it seemed to him that the phenomenon of immune collapse among black Africans could not be blamed on a single virus.
In an interview with Time Magazine, September 4 2000, Mbeki stated that, "the notion that immune deficiency [AIDS] is only acquired from a single virus [HIV] cannot be sustained." When asked whether he was prepared to "acknowledge that there is a link between HIV and AIDS?" he replied, "This is precisely where the problem starts. No, I am saying that you cannot attribute immune deficiency solely and exclusively to a virus."
Over the following days various ministers were asked whether they believed HIV caused AIDS. Most refused to answer in the affirmative - clearly out of fear of being seen to contradict Mbeki. Tshabalala-Msimang, Kader Asmal, Trevor Manuel and Essop Pahad himself, were all reported to have evaded answering the question directly. It was only on September 13 that Labour Minister Membathisi Mdadlana broke ranks to publicly state, "Yes, of course HIV causes AIDS."
In his written reply to a question posed to him in parliament on the September 20 Mbeki reiterated his position: "There is no doubt that there are many factors that result in the breakdown of the body's immune system. Repeated infections, malnutrition, lack of access to clean water, impact negatively on the immune system." For Mbeki the contention that HIV contributed to this immune deficiency was an unproven one, although he was keeping an open mind on the matter. "There may well be a virus that also results in a breakdown of the immune system", he added.
In his spoken reply he answered derisively to the question of whether HIV caused AIDS: "When one asks a question: does HIV cause AIDS, the question is: does a virus cause a syndrome? How does a virus cause a syndrome? It cannot, really, truly....I think it is incorrect from everything that I read to say immune deficiency is acquired exclusively from a single virus."
On September 28 Mbeki addressed the ANC caucus in parliament behind closed doors. Howard Barrell reported in the Mail & Guardian the following week that, in the meeting, Mbeki had spoken approvingly "of a conference of about 60 dissident scientists held in Uganda in September; quoted from a document from that conference challenging the view that HIV causes AIDS; said (again) that the HI virus had never been isolated." (The declaration of the conference can be accessed here.)
He also "told ANC MPs that it was their duty to inform themselves so that they could counter the huge propaganda offensive that was being mounted to say that HIV caused AIDS."
He also, "repeated his view that if one agrees that HIV causes AIDS, then it must be treated with drugs, and those drugs are produced by the big Western drug companies; these drug companies therefore need HIV to cause AIDS, so they promote the thesis that HIV causes AIDS."
He also, "said the CIA had become involved in covertly promoting the view that HIV causes AIDS; as part of the same effort, the US government was ignoring what the dissidents' conference in Uganda had demonstrated...."
He also said it was not "clear that members of his Cabinet supported him on the HIV/AIDS issue; he wanted to know where they stood". At this point, apparently, "there was some muttering in the caucus from some MPs who pointed accusingly at, among others, Membathisi Mdadlana."
The report was so accurate a number of ANC MPs canvassed by Angela Quintal for Sapa "discounted that the information was acquired by way of routine leaks by ANC MPs, and insisted their caucus had somehow been bugged." The week after it was published the police swept parliament for bugs.
On October 4 in Business Day the head of the ANC presidency, Smuts Ngonyama, took issue with an article in which the newspaper's parliamentary correspondent, Wyndham Hartley, had called for the pressure to be kept on cabinet ministers to acknowledge the causal link between HIV and AIDS. Ngonyama (or Mbeki) stated that:
"Hartley should read President Mbeki's speech at the Durban international AIDS conference and his comments in the recent issue of Time magazine. He will see that, among other things, what the president is challenging is the assertion that AID AIDS without S is the exclusive fault of a single virus. To substantiate his opinion, Hartley must produce evidence that HIV is the sole cause of AIDS."