After losing his interferon research grant he worked at Kings County Hospital Center and as Director of Continuing Medical Education at the Bureau of VD Control for the New York City Department of Health.

[3] Sonnabend died on 24 January 2021 at Wellington Hospital in London, as a result of complications arising from a heart attack he had suffered three weeks earlier.

[11] Sonnabend's "multifactorial model" led him to argue from very early in the emerging pandemic that frequent unprotected anal sex increased the risk of what would come to be known as AIDS.

[1][2][3][5] One of CRI's early achievements was a trial that contributed to the approval of inhaled pentamidine for preventing Pneumocystis pneumonia, a common AIDS-related infection.

In 2000, PWA Health Group merged with Direct Aids Alternative Information Resources (DAAIR),[5] but the combined organisation closed in 2003 and was superseded in July of the following year by the New York Buyers' Club.

[1][3] In the late 1980s, Sonnabend became a prominent critic of the use of AZT monotherapy to treat asymptomatic, HIV-positive people, which he thought was based on insufficient clinical evidence.

Nevertheless, he did prescribe the drug in short courses for people with indications of elevated interferon, which he believed might play an important role in pathogenesis and could be controlled by AZT.

[16][24] The effects of modern medication helped to change Sonnabend's views on AIDS causation, leading him to assert that, "the evidence now strongly supports a role for HIV.

He suggested that in many people HIV lies dormant without provoking a sufficient immune response to generate a positive antibody test result (seroconversion).

[3][21] In the 1980s, Sonnabend criticised activists who he believed were overplaying the threat of a heterosexual AIDS epidemic in America, causing a rift that led to his resignation from AMF.

[26]Despite his unconventional and often controversial opinions, mainstream AIDS researchers have in recent years become less critical of Sonnabend, recognising his devotion as a physician and patients' champion.

[1] In 2000, he was recognised as an inaugural Award of Courage Honoree by amfAR:[1] Joseph Sonnabend, M.D., made Olympian contributions to the fight against AIDS during years when this was a lonely and thankless endeavor.

He designed community-based clinical trials when there were few precedents for such research, and he displayed ethical and professional leadership in virtually every other AIDS-related field of action.