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Full genomic sequence of an African Avian Paramyxovirus Type 4 strain isolated from a wild duck.
MedLine Citation:
PMID:  22918714     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
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.
Authors:
Celia Abolnik; Minique de Castro; Jasper Rees
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-8-24
Journal Detail:
Title:  Virus genes     Volume:  -     ISSN:  1572-994X     ISO Abbreviation:  Virus Genes     Publication Date:  2012 Aug 
Date Detail:
Created Date:  2012-8-24     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  8803967     Medline TA:  Virus Genes     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Affiliation:
ARC-Onderstepoort Veterinary Institute, Private Bag X05, Onderstepoort, 0110, South Africa, celia.abolnik@up.ac.za.
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