Possible new dicistrovirus: Ervivirus

Abstract from Victoria et al., 2008.

Background: In 1988 the Global Polio Eradication Initiative was founded, facing over 350,000 worldwide infections of poliovirus in children. Despite large strides in poliovirus eradication, four countries, India, Afghanistan, Nigeria and Pakistan are still endemic for polio. As part of the initiative stool samples are routinely collected from children with acute flaccid paralysis (AFP) and screened by serology and PCR for picornaviruses, including poliovirus. Methods: Poliovirus and enterovirus negative stool or stool-inoculated tissue culture supernatants from children presenting with AFP collected in Pakistan were used in these studies. We employed a shotgun metagenomics approach using sequence independent amplification of viral nucleic acids to detect new and divergent viruses. PCR products were cloned and sequenced by traditional Sanger sequencing or used directly for large scale 454 pyrosequencing. Sequences were assembled based on 95% identity over at least 35bp and characterized by nucleotide and protein BLAST similarities. A group of dicistroviridae-like viruses were identified, tentatively named Ervivirus. Conserved Ervivirus domains were used for consensus PCR primer design in prevalence and diversity studies. Results: Ervivirus exhibited only 22% amino acid identity to the closest dicis[c]trovirus family member, Israel acute paralysis virus of bees. Genomic arrangement of Ervivirus mirrored that of the dicistroviruses in which non-structural genes are 5’ of structural genes, separated by a non-coding spacer region which was slightly larger in Ervivirus (250bp) when compared to dicistroviruses (170-200bp). Three genetic variants were identified in 14 samples tested exhibiting 80-85% amino acid identity to Ervivirus. Neighbor-joining and maximum likelihood phylogenetic reconstruction of conserved coding sequences indicate Ervivirus is a deeply rooted new genus within the Dicistroviridae family whose only reported host to date are invertebrates. Conclusions: We have identified novel dicistro-like virus isolated from children with AFP provisionally named Ervivirus. This is the first evidence of picornalike viruses with a dicistronic genomic arrangement from mammalian samples. Ervivirus cellular tropism and prevalence are currently underway to determine linkage to AFP.

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References

Victoria, J.G., Kapoor, A., Wang, C., Shafer, R.W., Naeem, A., Sharif, S., Shaukat, S., Masroor, M., Angez, M., Zaidi, S.Z. and Delwart, E.L. (2008). Identification of novel di[s]cistro-like virus from stool samples of children with acute flaccid paralysis.  [abstract]. International Conference on Emerging Infectious Diseases 2008: slide sessions and poster abstracts. Emerg Infect Dis [serial on the Internet]. 14 Mar 2008. Available from http://www.cdc.gov/eid/content/14/3/ICEID2008.pdf.