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Deep Sequencing Study Implicates New Rabies-related Virus in Hemorrhagic Fever Outbreak

NEW YORK (GenomeWeb News) – An international research team has used deep genome sequencing to link a new rabies-related virus to a 2009 outbreak of hemorrhagic fever in the Democratic Republic of the Congo.

As researchers based in US, DRC, Gabon, and France reported online last night in PLoS Pathogens, they identified and began characterizing the novel virus using a combination of Roche 454 and Illumina deep sequencing on samples from one of the individuals infected during an acute hemorrhagic fever outbreak in the central African country. Two individuals died during the outbreak and a third was hospitalized with hemorrhagic symptoms.

"These are the only three cases known to have occurred, although there could be additional outbreaks from this virus in the future," co-senior author Charles Chiu, an infectious disease researcher affiliated with the University of California at San Francisco and the UCSF-Abbott Viral Diagnostics and Discovery Center, said in a statement.

The new virus is a member of the rhabdovirus family, which includes rabies virus and other viruses that can infect plants, insects, and mammals. It was dubbed Bas-Congo virus, or BASV, as a nod to the southwestern DRC province where the 2009 outbreak occurred.

Now, investigators hope that by more fully characterizing the virus and its mode of transmission they might gain an edge in dealing with future flare-ups of the disease.

"Although the source of the virus remains unclear, our study findings suggest that BASV may be spread by human-to-human contact and is an emerging pathogen associated with acute hemorrhagic fever in Africa," Chiu and his co-authors wrote.

The outbreak began in a village called Magala in the spring of 2009 when a 15-year-old boy was admitted to a local health center with bloody vomiting and diarrhea, accompanied by bleeding from his nose, mouth, and eyes. A second child, a 13-year-old girl who attended the same school, became sick just over a week later. And a week after that a 32-year-old nurse who had cared for both patients started showing signs of the same disease.

Both children died within three days of their first symptoms. The third patient was transferred to a hospital in the nearby city of Boma and survived the infection. His blood samples were used to develop antibodies to detect the disease.

These samples also served as a source of viral DNA for sequencing experiments, which the research team conducted after PCR-based analyses failed to uncover any known hemorrhagic fever-causing viruses.

Researchers first identified a suspicious virus using Roche 454 pyrosequencing. With ultra-deep Illumina HiSeq 2000 sequencing they then sequenced and assembled some 98 percent of its single-stranded RNA genome.

No other viral candidates could be identified, the team reported, though there were no samples available to test for the first two patients.

Nonetheless, the surviving man's blood contained antibodies targeting the virus, as did samples from a health care worker who had treated him in the Boma hospital but did not develop hemorrhagic symptoms.

Investigators didn't find evidence of BASV infection when they screened samples collected from individuals with hemorrhagic fevers of unknown origin in DRC between 2008 and 2010. Nor did it turn up when they tested 50 randomly selected blood donor samples from that country.

A phylogenetic analysis of the virus indicated that it is more closely related to rabies virus and other members of the rhabdovirus family than it is to previously identified hemorrhagic fever-causing viruses such as Ebola virus, Lassa virus, or Crimean-Congo Hemorrhagic Fever virus.

Even so, the team's comparison of the BASV genome with other rhabdovirus sequences indicated that the new virus is divergent and distinct, sharing just 34 percent sequence identity with other members of that viral family.

"Active epidemiological investigation and disease surveillance will be needed to fully ascertain the clinical and public health of BASV infection in humans," study authors noted, "as well as to prepare for potentially larger human outbreaks from this newly discovered pathogen."

Based on the transmission events in the 2009 outbreak, for instance, they suspect BASV can be passed from one person to another. But it is unclear whether a rodent, bat, insect, or other organism served as the origin source of infection. And more research is needed to narrow in on the animal reservoir used by BASV, if any.

That aspect of BASV biology is being explored by researchers participating in the US Agency for International Development's emerging pandemic threats program, known as PREDICT, and by investigators from the San Francisco-based disease and pathogen detection company Metabiota (formerly called Global Viral Forecasting Inc.).

Metabiota Vice President Joseph Fair was a co-first author on the current study. Nathan Wolfe, founder and chairman of the company's not-for-profit sister organization Global Viral, was a co-author.

"The fact that it belongs to a family of viruses known to infect a wide variety of mammals, insects, and other animals means that it may perpetually exist in insect or other 'host' species and was accidentally passed to humans through insect bites or some other means," Global Viral's Wolfe said in a statement.

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