VRDL-1: A possible new sapelovirus of human or simian origin

Abstract from Victoria et al., 2008.

Background: Public surveillance of bacterial and viral infections is critical in detecting and preventing new outbreaks of known viruses. Occasionally, identification of a specific causative agent using all available serological, histology and genetic tests fails. Six such untypable samples collected between 1963 and 1980, three from homogenized insect tissues inoculated by intracerebral injection of fetal mouse brain and three derived from human tissues in cell culture inoculations, were targeted for viral discovery. Methods: Viral particles were purified from cells and cellular debris by 0.45μm filtration. Following digestion of all non-encapsidated nucleic acid with DNase and RNase, protected viral RNA and DNA was amplified using sequence independent reverse transcription and random amplification. Products were cloned, sequenced and analyzed using BLAST. Results: In all 6 cases a single viral agent was rapidly identified by limited sequencing (between 42-108 clones) and labeled as VRDL-1 through VRDL-6. Initial sequencing provided between 16% - 75% of viral genomes. All viruses derived from human samples (VRDL1, VRDL2 and VRDL-4) belonged to the picornaviridae family and ranged from 77% to 99% amino acid identity to known viruses. Insect derived viruses (VRDL-3, VRDL-5, VRDL-6) exhibited amino acid identities between 25% to 98% to the segmented reoviridae family. VRDL-4 and VRDL-5 represent viruses which at the time of collection and initial typing were unknown but have since been well characterized. VRDL-3 and VRDL-6 are highly divergent viruses, potentially members of a new viral genus within the reoviridae family. VRDL-1 shared a high percentage of sequence identity to several simian picornaviruses sequences within the provisional “Sapelovirus” genus. VRDL-1 likely originated from the primary primate cell lines used during tissue culture as many simian enteroviruses were identified as contaminants between 1950 and 1980. The entire VRDL-1 genome was obtained, representing a new member of the “Sapelovirus” genus. Conclusions: Nonspecific shotgun sequencing of virus particles is both simple and effective for rapidly detecting highly divergent viruses, including reoviridae and picornaviridae family members, where traditional techniques, such as consensus PCR, have failed.

References

Victoria, J.G.,  Kapoor, A.,  Dupuis, K.,  Schnurr, D.P. and  Delwart, E.L. (2008). Rapid identification of divergent and novel viruses from previously untypable California State Department of Public Health Pathogen Surveillance Program samples [abstract]. International Conference on Emerging Infectious Diseases 2008: slide sessions and poster abstracts. Emerging Infectious Diseases [serial on the Internet]. 2008 Mar 14. Available from http://www.cdc.gov/eid/content/14/3/ICEID2008.pdf.