Rhabdo paper out in PNTD

Our new paper on the discovery of two novel rhabdoviruses in Nigeria is out in PLoS Neglected. In this study we used NextGeneration Illumina sequencing to look for viruses in the blood of sick and healthy individuals. Surprisingly, we discovered the presence of two completely rhabdoviruses in healthy individuals. Rhabdoviruses include e.g. rabies virus and the new viruses we discovered were only 35% identical to already known viruses and to each other. In the individuals with fevers of unknown origin we mostly found already known pathogenic viruses including Lassa virus, HIV, and hepatitis.

You can access the paper here:

http://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003631

These viruses clustered together with Bas-Congo virus, which had been described to be responsible for causing a viral hemorrhagic fever in a cluster of patients a couple of years back:

http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1002924

I always found that study problematic as it was an N=1 study and causality could never be determined. Furthermore, several other pathogenic organisms were found in the blood from the individual where Bas-Congo was sequenced, including e.g. Rotavirus, which is known to be endemic in the area and can cause severe disease. Despite this that paper got a lot of press and it was suggested that Bas-Congo might be a new human pathogen:

http://www.ncbi.nlm.nih.gov/pubmed/23374120

Based on our new study, and together with several recent studies discovering rhabdoviruses, I find it to be highly unlikely that Bas-Congo is a viral hemorrhagic fever-causing virus. The most likely explanation is that it’s just another rhabdovirus infecting humans, and that infection with these viruses might be quite common (in Africa?). This serves as a warning sign for future studies – causality cannot and should not be established based on individual samples without any additional evidence.

GenomeWeb also made a commentary, which can be accessed here:

https://www.genomeweb.com/sequencing-technology/blood-rna-sequencing-healthy-west-africans-ids-new-rhabdoviruses

Our summary:

Next-generation sequencing, a high-throughput method for sequencing DNA and RNA, has the potential to transform virus discovery because it does not depend on culturing the pathogen or a priori knowledge of the pathogen’s nucleic acid sequence. We used next-generation sequencing to identify RNA viruses present in the blood of patients with unexplained fever, as well as apparently healthy individuals in a peri-urban community in Nigeria. We found several well-characterized viruses in the blood of the febrile patients, including HIV-1, hepatitis B and C, as well as Lassa virus. We also discovered two novel rhabdoviruses in the blood of two apparently healthy (afebrile) females, which we named Ekpoma virus-1 and Ekpoma virus-2. Rhabdoviruses are distributed globally and include several human pathogens from the genera lyssavirus and vesiculovirus (e.g., rabies, Chandipura and vesicular stomatitis virus). The novel rhabdoviruses identified in this study are most similar to Bas-Congo virus, which was recently identified in an individual with an acute febrile illness. Furthermore, we demonstrate evidence of high levels of previous exposure to the two rhabdoviruses among our larger study population. Our results suggest that such rhabdovirus infections could be common, and may not necessarily cause overt disease. 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.