“It’s a lot of years of work in there,” Michael Worobey, the scientist whose group carried out the work, said of the research, which was recently posted to the preprint site bioRxiv. “Just on that sequence we’ve been plugging away for more than five years.”
Worobey, whose lab has repeatedly performed virologic archeology on old tissue and blood samples, said the paper has not yet been submitted to a scientific journal for publication. As such, it has not been through the peer review process where independent scientists kick its tires, so to speak.
But Oliver Pybus, a professor of evolution and infectious diseases at the University of Oxford, praised the work.
“Generating a complete genome … from an archived tissue specimen is technically impressive,” Pybus told STAT. “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.”
Dr. Jacques Pepin, an infectious diseases professor at the University of Sherbrooke, in Quebec, who has written about the history of the AIDS epidemic, called Worobey’s latest work a “technological feat.” Pepin is is working on a second edition “The Origin of AIDS,” due out in late 2020, and said this work will factor in to the updates.
The sample that was examined dates from 1966. The sequence extracted from it is older by a decade than the previous oldest full-length sequence. It provides a snapshot of what the virus looked like when it was circulating undetected in central Africa 15 years before a cluster of strange infections among gay men in the United States led to recognition of a new disease that was eventually called AIDS.
Genetic codes of viruses that infected people in earlier days of the AIDS epidemic can be used by scientists to try to date when the HIV virus moved from primates into people. By studying differences in the viral sequences, scientists estimate how long it has been since the known sequences could have diverged from a common source. It doesn’t tell them when the event happened, but it can suggest that it had to have been prior to a particular time, Worobey said, adding that the new data suggest the jump likely did not happen in the 1920s.
Although there have been a number of estimates of when HIV started transmitting among people, most now focus on the early 1900s. Pepin said it might even have occurred in the final years of the 1800s.
Worobey, who has developed a method for extracting DNA from samples that he calls “jackhammering,” spent time in DRC about 20 years ago while working on his Ph.D. at the University of Oxford.
He learned about a repository of old tissue samples at the University of Kinshasa, and with the help of co-author Dr. Jean-Jacques Muyembe — a renowned Ebola expert and director of DRC’s National Institute of Biomedical Research — he received permission to study them, looking to see if any contained HIV DNA. The tissue specimens were extracted from patients in Kinshasa — then Leopoldville — for diagnostic purposes between 1959 and 1967.
“It was kind of moldering in cardboard boxes in a big heap in the back room,” Worobey said of the collection.