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Molecular characterization of partial fusion gene and C-terminus extension length of haemagglutinin-neuraminidase gene of recently isolated Newcastle disease virus isolates in Malaysia | Berhanu et al. Virology Journal 2010 7 183 http www.virologyj.eom content 7 1 183 VIROLOGY JOURNAL RESEARCH Open Access Molecular characterization of partial fusion gene and C-terminus extension length of haemagglutinin-neuraminidase gene of recently isolated Newcastle disease virus isolates in Malaysia Ayalew Berhanu1 2 Aini Ideris1 3 Abdul R Omar1 3 Mohd Hair Bejo1 Abstract Background Newcastle disease ND caused by Newcastle disease virus NDV is a highly contagious disease of birds and has been one of the major causes of economic losses in the poultry industry. Despite routine vaccination programs sporadic cases have occasionally occurred in the country and remain a constant threat to commercial poultry. Hence the present study was aimed to characterize NDV isolates obtained from clinical cases in various locations of Malaysia between 2004 and 2007 based on sequence and phylogenetic analysis of partial F gene and C-terminus extension length of HN gene. Results The coding region of eleven NDV isolates fusion F gene and carboxyl terminal region of haemagglutininneuraminidase HN gene including extensions were amplified by reverse transcriptase PCR and directly sequenced. All the isolates have shown to have non-synonymous to synonymous base substitution rate ranging between 0.081 - 0.264 demonstrating presence of negative selection. Analysis based on F gene showed the characterized isolates possess three different types of protease cleavage site motifs namely 112RRQKRF117 112RRRKRF117 and 112GRQGRL117 and appear to show maximum identities with isolates in the region such as cockatoo 14698 90 Indonesia Ch 2000 China local isolate AF2240 indicating the high similarity of isolates circulating in the South East Asian countries. Meanwhile one of the isolates resembles commonly used lentogenic vaccine strains. On further characterization of the HN gene Malaysian isolates had C-terminus extensions of 0 6 and 11 amino acids. Analysis of the phylogenetic tree revealed that .
