A Planet of Viruses - Carl Zimmer [22]
HIV, scientists found, belongs to a large group of slow-growing retroviruses, known as lentiviruses. Lentiviruses infect many mammals, including cats, horses, cows, and monkeys. In 1991, Preston Marx of New York University and his colleagues discovered that HIV-2 was closely related to lentiviruses that infect an African species of monkey called sooty mangabeys. They concluded that HIV-2 descended from a mangabey lentivirus. In West Africa, where HIV-2 is most common, some people keep the monkeys as pets; others eat them. Infected mangabeys may have introduced their lentivirus into humans with a bite.
It took scientists longer to pin down the origins of HIV-1, the strain that causes the vast majority of AIDS cases. That’s because the closest relatives of HIV-1 lived in primates that are much harder to study: chimpanzees. Relatively few chimpanzees live in captivity, and trying to get blood samples from chimpanzees in the wild can be a staggeringly hard job. They’re elusive, strong, and not fond of people with needles. Scientists had to develop new ways to test them for HIV, such as searching for the viruses in their feces. Slowly, scientists amassed a collection of HIV-1–like lentiviruses from chimpanzees. Comparing the viruses to each other, they discovered that some strains of HIV-1 are more closely related to certain chimpanzee viruses that they are to other HIV-1 strains. The branchings of the viral tree suggest that HIV-1 actually evolved from chimpanzee viruses several times.
But when did this transition happen? Some scientists tried to get an answer to that question by looking back at patients who had died mysteriously before the discovery of HIV. In 1988, for example, researchers discovered that a Norwegian sailor named Arvid Noe, who died in 1976, had HIV in his tissues. Reaching back further into HIV’s history was nearly impossible, because many of its earliest victims lived in poor countries and died without any careful medical tests that would identify unusual diseases like pneumocystis pneumonia.
It turned out that the viruses replicating in living people offered some powerful clues to the origins of HIV. Through the 1990s, scientists at Los Alamos National Laboratory amassed a database of genetic sequences of HIV taken from thousands of patients. They could then use supercomputers to compare these viruses and figure out which mutations the viruses had acquired since they diverged from a common ancestor. By adding up these mutations, the researchers found that HIV gradually acquires mutations at a roughly regular rate. In other words, the mutations piled up like sand in an hourglass. By measuring how high the sand had piled up, they could estimate how much time had passed. They estimated that the common ancestor of HIV-1 existed in 1933.
That estimate has been confirmed by the remarkable discovery of HIV preserved in tissues stored away in hospitals in Kinshasa, the capital of the Democratic Republic of the Congo in central Africa. In 1998, David Ho and his colleagues at Rockefeller University reported that they had isolated HIV from a blood sample taken from a patient in Kinshasa in 1959. In 2008, Michael Worobey and his colleagues at the University of Arizona discovered HIV in a second tissue sample from another pathology collection in Kinshasa, dating back to 1960. These two samples allowed researchers to confirm that HIV emerged in the early 1900s.
The molecular clock created by the Los Alamos researchers was accurate enough to predict the age of the Kinshasa viruses based on their genetic sequence alone. But the two viruses also provide a surprising glimpse at the diversity of HIV in Kinshasa around 1960. Worobey and his colleagues found that the old viruses