Researchers have extracted a near-complete HIV-1 genome from the lymph node tissue of a man in the Democratic Republic of Congo who has been embedded in wax since 1966.
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The nub of tissue, which is around the size of the nail on the pinky finger, was sliced from the 38-year old man who had been fixed with formalin in a protective block of paraffin, with the viral RNA hidden in his lymph node for more than 50 years.
Once freed from its wax casing, the near-complete HIV-1 genome that the team extracted supports the theory that the virus was transmitted to humans from monkeys within the first decade or two of the 20th century.
The genome, which provides a more accurate “molecular clock” for assessing the evolution of HIV, is the oldest example of an almost complete HIV-1 genome to date.
Analysis of the genome has shown that it does not demonstrate an evolutionary timeline that is any different from those generated from more recent samples and dispels the “patient zero” myth – the theory that HIV was introduced to the United States after it was transmitted to a flight attendant.
HIV-1, which is one of the main viruses that causes AIDS, was first discovered in 1983. Older samples containing the genetic sequence of the virus are scarce and their genetic material has usually degraded.
The researchers write:
With very little direct biological data of HIV-1 from before the 1980s, far-reaching evolutionary and epidemiological inferences regarding the long pre-discovery phase of this pandemic are based on extrapolations by phylodynamic models of HIV-1 genomic sequences gathered mostly over recent decades.”
Understanding the origins of the HIV epidemic
The near-complete sequence extracted from this 1966 sample is ten years older than the previous oldest full-length sequence generated.
It provides a glimpse of how the virus looked when it was circulating undetected in central Africa, 15 years prior to a when a string of infections among gay men in the U.S., led to the acknowledgment that a new disease had emerged that researchers eventually called AIDS.
According to lead researcher Michael Worobey and team, calculating exactly when the HIV/AIDS pandemic originated is of great significance because it enables researchers to understand which factors did or did not contribute to the emergence of the causal virus.
Researchers have used the genetic sequences of viruses that infected people in earlier days of the AIDS epidemic to try to estimate when exactly the HIV virus jumped from primates to humans. By comparing differences in the viral sequences, researchers can estimate how long ago the sequences could have diverged from the same source.
This cannot determine when the jump to humans happened, but it can be used to deduce that it had to have been before a particular time.
Previous efforts to pinpoint the precise time of origin have suggested that the virus was introduced to humans during the early 20th century in Central Africa, where once-isolated populations had mixed and merged.
Now, Worobey says the new data suggest HIV probably did not move from primates to humans during the 1920s and Pepin thinks it may even have done so in the late 1800s
Worobey and team say their recovery of the first HIV-1 genome from the 1960s provides direct evidence that the estimates that have been made over the last 50 years are remarkably reliable.
The researchers write:
Analyses did not significantly alter root and internal node age estimates based on post-1978 HIV-1 sequences… And, because this genome itself was sampled only about a half-century after the estimated origin of the pandemic, it empirically anchors this crucial inference with high confidence.”
Worobey, whose team performs virologic archaeology studies on old tissues and blood samples, says the research has involved many years of work: “Just on that sequence, we’ve been plugging away for more than five years.”
Confirming the theory
It should be noted that the work has so far only been posted on the preprint website bioRxiv and has not yet been submitted to a scientific journal or undergone peer review.
However, Oliver Pybus, a professor of evolution and infectious diseases at the University of Oxford, has praised the work, saying that the generation of a genetic sequence from an archived tissue specimen is technically impressive.
“Although its discovery doesn’t substantially alter our current model of the early genetic history of the AIDS pandemic, it does improve our confidence in conclusions previously drawn from modern and partial HIV gene sequences,” says Pybus.
Infectious Disease expert Jacques Pepin (University of Sherbrooke, Quebec) is an author of literature on the history of the AIDS epidemic and is currently working on the second edition of his book “The Origin of AIDS,” which is due to be published late next year. Pepin has called Worobey’s work a “technological feat” and says he plans to factor in the updates in his latest publication.
In conclusion, Worobey and team write: “This unique archival HIV-1 sequence provides direct genomic insight into HIV-1 in 1960s DRC [Democratic Republic of Congo], and, as an ancient-DNA calibrator, it validates our understanding of HIV-1 evolutionary history.”
Gryseels, S., et al. (2019). A near-full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue. bioRxiv. https://doi.org/10.1101/687863.