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Full genomic sequence of an African Avian Paramyxovirus Type 4 strain isolated from a wild duck

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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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Acknowledgments

Hope Kekana is thanked for propagating the APMV-4 strain in eggs and Dion du Plessis is thanked for valuable discussions and revision of the manuscript. This work was funded by the South African National Department of Agriculture, Forestry and Fisheries.

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Correspondence to Celia Abolnik.

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Abolnik, C., de Castro, M. & Rees, J. Full genomic sequence of an African Avian Paramyxovirus Type 4 strain isolated from a wild duck. Virus Genes 45, 537–541 (2012). https://doi.org/10.1007/s11262-012-0805-y

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Keywords

  • Avian Paramyxovirus Type 4
  • Genome
  • Egyptian goose
  • Illumina