ABSTRACT
The complete genome sequence of an African Newcastle disease virus (NDV) strain isolated from a chicken in Togo in 2009 was determined. The genome is 15,198 nucleotides (nt) in length and is classified in genotype VII in the class II cluster. Compared to common vaccine strains, the African strain contains a previously described 6-nt insert in the downstream untranslated region of the N gene and a novel 6-nt insert in the HN-L intergenic region. Genome length differences are a marker of the natural history of NDV. This is the first description of a class II NDV strain with a genome of 15,198 nt and a 6-nt insert in the HN-L intergenic region. Sequence divergence relative to vaccine strains was substantial, likely contributes to outbreaks, and illustrates the continued evolution of new NDV strains in West Africa.
GENOME ANNOUNCEMENT
Newcastle disease virus (NDV) causes a devastating disease in chickens worldwide (2). NDV is a member of the family Paramyxoviridae and has a nonsegmented, negative-sense RNA genome consisting of six transcriptional units (3′-NP-P-M-F-HN-L-5′) (8). NDV strains have been classified into classes I (9 genotypes) and II (11 genotypes) (4). Class I strains are usually avirulent and have genome lengths of 15,198 nucleotides (nt). Class II contains both virulent and avirulent strains. Class II strains isolated prior to 1960 (genotypes I to IV and IX) have genomes of 15,186 nt, while more recent strains (genotypes V to VIII and XI) have genomes of 15,192 nt. Relative to the 15,186-nt genome, the 15,192-nt genome has an insertion of 6 nt in the 5′ (downstream) noncoding region of the N gene and the 15,198-nt genome has an insertion of 12 nt in the P open reading frame (ORF) that increases the length of P by four amino acids. Thus, NDV is a diverse and continually evolving virus (1, 5, 6). Predominantly circulating strains associated with disease outbreaks are genotypes V to VIII of class II (9).
In West Africa, the increasing reports of NDV outbreaks in vaccinated flocks suggest the emergence of new NDV strains that may be somewhat mismatched with common vaccine strains (10). However, little sequence information is available for NDV strains circulating in this region, and molecular characterization of NDV strains has involved partial sequences of the F gene (3). To date, no complete genome sequence of African NDV strains has been available. In this study, the complete consensus genome sequence of an African NDV strain (chicken/Togo/AKO18/2009) isolated from a live bird market in Togo was determined by reverse transcription-PCR using overlapping consensus primers and direct sequencing. The 3′ and 5′ termini were determined by rapid amplification of cDNA ends (11). The genome was found to be 15,198 nt in length and contains the above-mentioned insert in the N gene as well as a novel 6-nt insert in the intergenic sequence between the HN and L genes (8338-UUUUUU-8343), compared to the 15,186-nt genomes of vaccine strains B1 and LaSota (class II, genotype II). Phylogenetic analysis classified this African strain into class II, genotype VII. The amino acid sequence identities of the N, P, M, F, HN, and L proteins between the African strain and the strains LaSota and B1 (which share 99% identity) are 91%, 82%, 89%, 89%, 87%, and 93%, respectively. This indicates that the African strain is substantially distinct from the vaccine strains in use, suggesting that antigenic differences might affect the efficacy of current vaccines and vaccination practice.
The sequence of the F protein cleavage site is a major determinant of NDV pathogenicity (7). The cleavage sites of virulent NDV strains contain multiple basic residues, whereas avirulent strains have fewer basic residues. The African strain has a virulent F protein cleavage-site sequence (RRRKR↓F). The data presented here provide evidence of a novel strain with a novel genome length variation circulating in West Africa.
Nucleotide sequence accession number.The genome sequence of the NDV strain has been deposited in GenBank (accession number JX390609).
ACKNOWLEDGMENTS
This work was supported by NIAID contract N01A060009 (85% support) and the NIAID, NIH, Intramural Research Program (15% support). R. J. Webby and M. F. Ducatez were supported by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under contract no. HHSN266200700005C and by the American Lebanese Syrian Associated Charities (ALSAC).
The views expressed herein do not necessarily reflect the official policies of the Department of Health and Human Services, nor does mention of trade names, commercial practices, or organizations imply endorsement by the U.S. government.
FOOTNOTES
- Received 23 July 2012.
- Accepted 23 July 2012.
- Copyright © 2012, American Society for Microbiology. All Rights Reserved.
