Meningitis itself is not a disease, just a description that means that the tissues around the brain and spinal cord have become inflamed. In the United States, bacterial infections can cause meningitis, as can enteroviruses, mumps, and herpes simplex. But a high percentage of cases, as doctors say, have no known etiology: Nobody knows why the patient’s brain and spinal cord swell.
This was the case with the Dhaka eruption. CHRF is one of the leading microbiology laboratories in Southeast Asia and is responsible for tracking meningitis in the country for the World Health Organization. “Every case of meningitis that comes in, we cultivate,” Saha told me. “We do antigen tests for pneumococci, Neisseria meningitidis, Hemophilus influenzae and GBS” or group B streptococci – the four infections most likely to cause meningitis. “Then we do a much more sensitive and specific test for Streptococcus pneumoniae bacteria as this causes the highest percentage of cases. And then we also do real-time PCR to look for DNA fragments from one of these pathogens. ”
When the outbreak began, the cause was thought to be bacterial again, but none of the tests could locate a pathogen. Over the next year, Saha worked to solve the puzzle, sometimes in collaboration with other laboratories. A partnership with an organization in China broke up when the group was unwilling to share their techniques. Another group of researchers in Canada did their own tests on the meningitis samples, but couldn’t figure out the cause either. Not long after that, Saha was attending a conference at the British Museum where she gave a presentation entitled “The Dark Side of Meningitis”. “It was a negative conversation,” recalls Saha. “How: Why does everyone only talk about the successful cases? We have to talk about thousands of cases each year where we have no idea what is causing the disease. ”
Before meeting DeRisi, Saha was skeptical about further collaboration. But the two hit it off right away. Although DeRisi could be impatient, Saha liked that he was direct and appreciated that his “ethics are very strong. In his head he says: That’s right; that is wrong; I’ll do that. ”Still, she proceeded cautiously. “Because IDseq was new and I’m very meticulous, I built in a lot of controls,” she told me. Of the 97 CSF samples, only 25 came from actual mystery meningitis cases. The remainder were either from cases for which Saha’s lab had already identified the cause or were not meningitis at all. Several were just water. “The idea was that all of this be tested and the process dazzled,” says Saha. “Because I had to see whether the platform worked or not.”
However, when Saha and her team ran the mysterious meningitis samples through IDseq, the result was surprising. Rather than uncovering a bacterial cause as expected, a third of the samples showed signs of the Chikungunya virus – particularly a neuroinvasive strain that was thought to be extremely rare. “At first we thought: That can’t be true!” Saha remembers. “But the moment Joe and I realized it was Chikungunya, I went back and looked at the other 200 samples that we had collected around the same time. And we also found the virus in some of these samples. ”
Until recently, chikungunya was a comparatively rare disease that occurs mainly in parts of central and east Africa. “Then it just exploded across the Caribbean and Africa and across Southeast Asia to India and Bangladesh,” DeRisi told me. No cases of chikungunya were reported in Latin America in 2011. In 2014 it was a million.
Common chikungunya can cause permanent neurological damage and lifelong joint pain. DeRisi called the disease “enormously devastating” and noted that chikungunya means “distorted” in the Kimakonde language spoken in Tanzania. But one neuroinvasive version that caused brain damage and particularly affected children and infants was particularly alarming.