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Blood RNA Sequencing on Healthy West Africans IDs New Rhabdoviruses

NEW YORK (GenomeWeb) – A team from Nigeria, the US, and Australia unwittingly uncovered two new rhabdoviruses in blood samples from healthy West African individuals as part of a sequencing-based study of another condition.

As they reported in PLOS Neglected Tropical Diseases yesterday, the researchers did RNA sequencing on genetic material isolated from the blood of hundreds of individuals in southeastern Nigeria in search of viruses that can cause unexplained acute febrile illness.

Comparisons between viral particles in the blood of cases and controls did bring them to viral sequences that were more common in individuals with unexplained acute febrile illness — including stretches of sequence that corresponded with viruses such as hepatitis B, hepatitis C, HIV-1, and Lassa virus.

But the team saw striking nucleic acid patterns in the samples from two of the healthy controls, as well. The healthy women each carried sequences from previously unknown rhabdoviruses — dubbed Ekpoma virus-1 (EKV-1) and Ekpoma virus-2 (EKV-2). The viruses most closely resembled the Bas-Congo virus, which was previously implicated in an illness with hemorrhagic fever-like features.

Still, the researchers' subsequent assays suggest that a significant proportion of individuals in the region carry antibodies to EKV-1 and/or EKV-2, suggesting exposure to the viruses may be relatively common.

"Our results suggest that such rhabdovirus infections could be common, and may not necessarily cause overt disease," wrote the study's authors, who were led by Pardis Sabeti from Harvard University and the Broad Institute, and Christian Happi at Redeemer's University and the Irrua Specialist Teaching Hospital in Nigeria.

"The identification of viral nucleic acid sequences in apparently healthy individuals highlights the need for a broader understanding of all viruses infecting humans as we increase efforts to identify viruses causing human disease," they added.

High-throughput sequencing has been making its way into virome research, both as a means of diagnosing viral disease and discerning the collections of viruses that may be carried in and on the human body, the team noted.

As an offshoot of a research collaboration focused on Lassa fever, the researchers decided to use next-generation sequencing to search for other viral culprits in individuals from southern Nigeria with unexplained acute febrile illness and symptoms overlapping with hemorrhagic fever who had tested negative for Lassa virus by reverse transcription PCR.

Using the Illumina HiSeq 2500, they sequenced RNA from pooled or individual blood samples for 195 individuals with unexplained acute febrile illness. A similar approach was used to characterize potential RNA virus sequences in the blood of 328 unaffected controls from the same population.

The team's analysis of singleton and pooled samples from the fever cases and controls revealed a similar proportion of viral reads in the RNA sequence data in both groups. Individuals with and without febrile illness tended to carry mainly non-pathogenic viruses such as the so-called GB virus C.

In the fever cases, meanwhile, the researchers detected sequences coinciding with Lassa virus and HIV-1, as well as DNA viruses such as herpesviruses and hepatitis viruses.

From pooled control samples, though, they also saw signs of the new rhabdoviruses, which they linked back to samples from a 45-year-old woman and a 19-year-old woman from Ekpoma, a town in Nigeria, using a PCR assay on the sample pool.

After generating Sanger sequences to flesh out the EKV-1 and EKV-2 genomes, the group compared them with previously described viral sequences, demonstrating that they fell within the Tibrovirus genus with the Bas-Congo virus.

When they used enzyme-linked immunosorbent assays on blood samples from hundreds of Nigerian and American individuals, the researchers found that an estimated 10 percent of Nigerians carried antibodies against EKV-1, while about half had EKV-2-specific antibodies.