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Picornavirus
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 Abstract from Kapoor et al. (2008a):

Background: RNA viruses implicated in acute flaccid paralysis (AFP) include enteroviruses, echoviruses, coxsackieviruses and flaviviruses. Existing molecular reagents frequently fail to identify highly divergent variants or novel viruses. Methods: Stool samples from children presenting with AFP were used for virus isolation in cell culture. Some virus isolates could not be identified using serological and PCR assays. We used a metagenomic shotgun sequencing approach and found several sequences in one sample showing distant protein similarities to Picornaviruses. Large scale sequencing (454 pyrosequencing) and RACE were used to acquire the complete genome of a new virus, tentatively named Dekavirus type-1. PCR primers targeting conserved nonstructural genes were used to determine the prevalence of Dekavirus in stool samples from children with AFP. Results: The Dekavirus genome codes for a single polyprotein flanked by 5- and 3- non-translated regions, similar to all Picornaviruses. Phylogenetic analysis of Dekavirus establishes it as an outlier showing mean protein identity of only 16-32% to other genera of Picornaviridae. Six genetic variants of Dekavirus were found in 14 stool samples from AFP children suggesting a high prevalence among this disease group. The complete genome sequence also was acquired from another divergent Dekavirus virus variant showing 82% amino acid identity to Dekavirus type-1. Conclusions: We characterized two new Picornaviruses from AFP cases and provisionally named them Dekavirus type 1 and type 2. Dekavirus type-1 is divergent enough to be assigned as the prototype member of a new genus in Picornaviridae. A large study based on PCR detection and serology is underway to determine if Dekaviruses are linked to AFP.

Abstract from Kapoor et al. (2008b):

Despite the near eradication of poliovirus, acute flaccid paralysis (AFP) of viral etiology still inflicts frequent, severe, and at time permanent damages to children, particularly in developing countries with poor sanitation. No viruses have been identified for over half of the remaining cases of non-polio AFP. This study describes identification and molecular characterization of novel picornaviruses from stool samples of children with non-polio AFP. Partial genome of 29 and complete genome of 5 new picornaviruses were acquired and phylogenetic analysis indicated them to be sufficiently divergent from all currently known picornaviruses to qualify as members of a new proposed genus Dekavirus (DKV) in the Picornaviridae family. All DKV variants sequenced lacked leader peptide coding region that is characteristic feature of other closely related genera. Our results indicate that DKVs can be classified in four virus species showing <60% amino acid identity in P3 gene comparable to that reported between species of human enteroviruses (HEV). The wide range of genetic diversity exhibited both within and between the Dekaviruses species also supports the possibility that, like HEVs, they may be involved in a variety of clinical manifestations.

References

Kapoor, A., Victoria, J.G., Naeem, A., Sharif, S., Shaukat, S., Masroor, M., Angez, M., Wang, C., Shafer, R.W., Zaidi, S.Z. and Delwart, E.L. (2008a). Characterization of a highly divergent picornavirus prevalent in stool samples of children with acute flaccid paralysis. [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.

Kapoor, A., Victoria, J.G., Simmonds, P., Naeem, A., Sharif, S., Shaukat, S., Masroor, M., Angez, M., Wang, C., Shafer, R.W., Zaidi, S.Z. and Delwart, E.L. (2008b). Characterization of a highly divergent picornavirus prevalent in stool samples of children with acute flaccid paralysis. Poster presented at EUROPIC 2008: XVth Meeting in Sitges, Barcelona, Spain, 26-30th May 2008