Oldest Near Full Length HIV-1 Genome Found From 1966

A near-complete HIV genome sequence has been found in one of 1,600 tissue samples collected in Kinshasa, Democratic Republic of Congo, in the 1960s. Dating from 1966, the genome is 10 years older than any comparable discovery. Although older HIV sequences have been found, these were all short fragments with much less information to offer about HIV’s origins. The discovery has allowed scientists to test theories on the timing of HIV’s appearance and the speed with which it mutates.

Although the world did not become aware of AIDS until the 1980s, and the oldest confirmed cases date from a decade before, there is plenty of evidence the virus is much older. Judging by the accumulation of mutations in different viral strains, virologists have estimated the transformation from simian immunodeficiency virus (SIV) to HIV occurred between 1881 and 1920. Inconsistencies in estimates of the rate SIV evolves have led some to question these dates, however. Finding old HIV sequences and comparing them with modern ones is the most likely way to resolve these debates.

The question of HIV’s origins has taken on new significance now the world faces a new virus that also crossed from non-human animals. The more we know about how deadly diseases jump the species barrier, the better our chances of preventing them in future. KU Leuven University’s Dr Sophie Gryseels is part of a team that has produced a new method, known as the jackhammer RT-PCR, particularly suited to detecting viral genome sequences in old samples. They claim to have found eight of the oldest nine HIV-1 sequences located so far.

The earliest of these was from 1976, but Gryseels and co-authors describe in Proceedings of the National Academy of Sciences finding the virus in a sample taken in 1966 from a man who was 38 at the time. Nothing is known about his subsequent life. A comparison of the sequence with versions collected today “provides direct evidence that HIV-1 molecular clock estimates spanning the last half-century are remarkably reliable,” the paper concludes.

The virus is from HIV-1 group M, which accounts for more than 98 percent of cases.

Finding older sequences is important, the authors argue, because “rates of molecular evolution appear to vary depending on the time frame considered, so rates estimated over a recent time frame can not necessarily be extrapolated [further back].”

Inevitably, conspiracy theories about the origins of HIV are popular, including that it came from an infected batch of polio vaccines or was deliberately created as a bioweapon. All these rely, however, on HIV having first appeared relatively recently. Evidence dating it to at least the 1920s, like this discovery, refutes such claims.

That doesn’t mean HIV’s appearance was random, however. There are good reasons to believe displacement caused by colonization expanded the bushmeat trade, exposing hunters to SIV, just as SARS-CoV-2 may result from human encroachment on animal habitats.