Abstract
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.
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