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Molecular characterization of Nipah virus, a newly emerging, highly pathogenic paramyxovirus

Brian H. Harcourt¹, Azaibi Tamin¹, William J. Bellini¹,
Thomas G. Ksiazek², Pierre Rollin², and Paul A. Rota^1
1Respiratory and Enterovirus Branch and ²Special Pathogens Branch,
National Center for Infectious Diseases, Centers for Disease Control and Prevention,
Atlanta, Georgia, USA

Recently a new paramyxovirus, now known as Nipah (NV), emerged in Malaysia and Singapore causing fatal encephalitis in humans and a respiratory syndrome in pigs. NV is related antigenically to Hendra virus (HV) and the goal of this project was to begin to characterize the genome of this emerging pathogen. The sequence of RT-PCR products derived using primers that recognized conserved regions at or near the RNA editing site of the phosphoprotein gene demonstrated 89 % homology to HV. Using a combination of RT-PCR primers specific for HV that cross-hybridized with NV and primers designed from regions of homology shared among paramyxoviruses, the nucleotide sequence of the nucleocapsid (N), phosphoprotein (P) and matrix (M) genes have been obtained. In addition, a cDNA library derived from RNA from NV-infected Vero cells was screened using the HV F and G genes as hybridization probes. Plasmid clones that contained the entire F or G open reading frames (ORFs) were identified and sequenced. With the exception of the polyadenylation signal of the M gene, intergenic regions, the gene start and stop signals and the RNA editing site of NV and HV were identical. The ORFs for the V and C proteins within the P gene were found in NV, but the ORF encoding a potential short basic protein found in the P gene of HV was not conserved in NV. The N, P/V/C, M, F and G ORFs in NV have nucleotide homologies ranging from 92% to 67% compared to HV. The predicted F protein of NV had a single amino acid substitution (K to R) in the fusion cleavage sequence. Phylogenetic analysis demonstrated that while HV and NV are closely related, they are clearly distinct from any of the established genera within the family Paramyxoviridae and should be considered as a new genus.

Abstract - Presented at the Virus Evolution Workshop
Ardmore, OK
October 21 - 24th, 1999

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e-mail: mroossinck@noble.org

Dr. Marilyn Roossinck
Plant Biology Division
The Noble Foundation
P.O. Box 2180
Ardmore, OK 73402

phone: 580 224-6630