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CDC Helps Identify Virus Behind Hemorrhagic Fever Outbreak In Bolivia

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A Bolivian rice farmer arrived at a local rural clinic with a fever, muscle and joint pain, vomiting, rash, abdominal pain, and an ache behind the eyes. Those caring for him suspected dengue fever, caused by mosquito-borne dengue virus.

But a dengue test came back negative.

Before the 2019 outbreak was over, five people were infected and three died, including the farmer. When researchers in Bolivia and the U.S. retraced the chain of transmission and infectious agent behind the mysterious disease, they found that the culprit, was a hemorrhagic fever-causing arenavirus called Chapare virus, not seen for nearly two decades.

Viral sequences in samples from several infected individuals helped the team place Chapare within the "New World" arenavirus collection — evolutionary cousins to hemorrhagic fever-related arenaviruses such as Lassa virus in Sierra Leone, Liberia, and other parts of West Africa — and highlighted rodents as possible carriers responsible for passing the virus to humans in Bolivia.

As importantly, the new molecular clues made it possible to come up with a reliable diagnostic test for finding and curbing Chapare virus outbreaks in the future.

"They now have the ability to test in-country. That marked huge gains for Bolivia to improve its surveillance and diagnostic capacity for this virus and also other infectious diseases in general," explained Caitlin Cossaboom, an epidemiologist and Epidemic Intelligence Service officer at the U.S. Centers for Disease Control and Prevention, who shared details from the outbreak investigation at the American Society of Tropical Medicine and Hygiene virtual annual meeting last week.

When the rice farmer first arrived at the clinical, local health officials were not expecting a virus that could be transmitted from person-to-person through infected bodily fluids. So when a young medical resident suctioned saliva from the infected man's mouth, she did not take extra precautions such as putting on goggles or other additional protective gear.

The doctor's symptoms, identical to those of the farmer, began nine days later. She was transported by ambulance to Bolivia's capital city, La Paz, unwittingly infecting an ambulance worker who gave her CPR on the way. It took 16 days for his symptoms to develop, though he eventually recovered. The farm worker and medical resident did not.

The transmission chain continued from there.

A fourth person was infected at the hospital in La Paz: a gastroenterologist who did an endoscopy procedure on the young medical resident. His fatal disease developed two weeks later. A fifth infection turned up in the farm worker's son-in-law. He farmed the same area as his father-in-law, but had also helped the ailing man to the bathroom in hospital. The younger man survived.

The outbreak and mystery around the disease grew. The hospital ruled out severe dengue. Tests for yellow fever and Machupo, the viral culprit behind Bolivian hemorrhagic fever, likewise came back negative.

Concerned Bolivian officials called in collaborators at the CDC, and together the US and Bolivian team began to better understand the outbreak.

All of the patients who had samples available for testing were infected with a hemorrhagic fever-causing virus called Chapare, an arenavirus in the Mammarenavirus genus. The virus was first found in Bolivia in late 2003 and early 2004, and characterized for a study published in the journal PLOS Pathogens in 2008. Only one confirmed case was linked to that outbreak.

"There were several cases during that time where people were presenting with symptoms of a viral hemorrhagic fever," Cossaboom explained, noting that members of the CDC Viral Special Pathogens Branch analyzed clinical samples from one individual to find the new Chapare virus at the time.

They did not rule out the possibility that human-to-human transmission occurred in that outbreak, she added, but there was not enough epidemiological information available to know if that was the case.

When a similar series of unexplained infections occurred in 2019, Cossaboom and her colleagues worked with investigators in Bolivia to do a far more detailed epidemiological sleuthing, uncovering at least three instances of human-to-human Chapare virus spread.

The researchers also turned to viral isolation and genetic sequencing approaches to characterize Chapare virus in the patient samples, and to spell out its RNA-based genome.

"There was a cluster of people with these vague clinical signs, and they were initially presumed to have dengue, but again tested negative for all of the testing in-country," Cossaboom said. "So again clinical specimens were sent to the Viral Special Pathogens branch at CDC, and that time we were able to identify it as a novel strain of Chapare virus and then develop a diagnostic test."

Chapare sequences found in 2019 were closely related to the Chapare virus found in 2003, they noted, and resembled other New World, or Tacaribe complex, arenaviruses such as the Sabia, Junin, Guanarito, and Machupo viruses — implicated in Brazilian, Argentine, Venezuelan, and Bolivian hemorrhagic fevers, respectively.

The team drew on such sequence clues to design a RT-PCR-based Chapare virus test, which is now available for testing viral hemorrhagic fever samples at high biosecurity labs at the National Center for Tropical Diseases in Bolivia. The center has found three apparent Chapare virus cases since the 2019 outbreak, though confirmatory testing at the CDC has not yet been done.

Using the same diagnostic test, the investigators also picked up Chapare virus RNA in the pigmy rice rat and the small-eared pigmy rice rat—suspected rodent carrier species found across Bolivia and other parts of South America.

"That was the first suggestion that these rodent species may be the reservoir of Chapare, but certainly more work does need to be done before that's proven definitively, and that does include surveillance of rodents in the area. That is a next step that is needed,” said Cossaboom.

By testing samples from the survivors of the 2019 outbreak, meanwhile, the CDC-led team has flagged bodily fluids the might pose an infection risk to healthcare workers treating individuals with Chapare.

But to take appropriate precautions, those caregivers in the region need to remember that the virus is out there and have it on their differential list when diagnosing fever conditions, Cossaboom said.

Just how widespread the virus is, and when it might show up again, is anyone's guess. The goal now is to make sure we're ready if it does.

"The key to controlling Chapare virus and other similar viruses, is for there to be community awareness but also healthcare provider awareness," Cossaboom said. "As a product of this investigation, we worked very closely with the Pan-American Health Organization, as well as the Bolivian Ministry of Health to develop a communications package. The theme is, 'Look Beyond Dengue.'"

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