Full genomic sequence of an African avian paramyxovirus type 4 strain isolated from a wild duck.
A random amplification/deep sequencing approach was applied to determine the complete genomic sequence of an Avian Paramyxovirus Type 4 (APMV-4) strain isolated from a wild duck in South Africa in 2010. This sequence represents the fourth full genome of APMV-4 in public sequence databases and the first for the African continent. A total of 87,402,081 Illumina paired-end reads were obtained of which 47,338,867 (54.16 %) mapped to the reference genome EU877976. The entire genomic sequence of 15,054 nt, including the intact termini, was recovered at a high redundancy (coverage per base: average = 198,861.06, minimum = 52 and maximum = 1,790,889). Pairwise comparison of full genomic nucleotide sequences indicated that APMV-4/Egyptian goose/South Africa/N1468/10 shared 97.3 % sequence identity with APMV-4/KR/YJ/06, 96.4 % sequence identity with APMV-4/mallard/Belgium/15129/07 and 90.8 % nucleotide sequence identity with APMV-4/duck/HK/D3/75. Genomic features were consistent with previously sequenced viruses including predicted open reading frames for the NP, P, F and L genes, but variations in coding regions for the M and HN genes were identified. The sequencing approach adopted in this study could successfully indicate quasispecies in the viral stock.
ARC-Onderstepoort Veterinary Institute, Onderstepoort 0110, South Africa. celia.abolnik@up.ac.za
Celia
C
Abolnik
Minique
M
de Castro
Jasper
J
Rees
D000483:Alleles; D000818:Animals; D018109:Avulavirus / Q000235:genetics / Q000302:isolation & purification* / Q000472:pathogenicity; D045463:Avulavirus Infections / Q000662:veterinary* / Q000821:virology; D001483:Base Sequence; D002874:Chromosome Mapping; D030541:Databases, Genetic; D004372:Ducks / Q000821:virology*; D005787:Gene Frequency; D015723:Gene Library; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D016366:Open Reading Frames; D010750:Phosphoproteins / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D013019:South Africa; D014764:Viral Proteins / Q000235:genetics
C431770:L protein, paramyxoviridae; C055859:P protein, Sendai virus; D010750:Phosphoproteins; D014764:Viral Proteins