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 Berhanu 1,2 , Aini Ideris 1,3* , Abdul R Omar 1,3 , Mohd Hair Bejo 1 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 haemagglutinin- neuraminidase (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 112 RRQKRF 117 , 112 RRRKRF 117 and 112 GRQGRL 117 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 the existence of three genetic groups; namely, genotype II, VII and VIII. Conclusions: The study concluded that the occurrence of three types of NDV genotypes and presence of varied carboxyl terminus extension lengths among Malaysian isolates incriminated for sporadic cases. Background Newcastle disease (ND) is a highly contagious disease of birds and has been regarded throughout the world as one of the most important diseases of poultry and other birds [1], in which infection with the extremely virulent viruses may result in sudden, high mortality with comparatively few clinical signs. The causative agent, NDV, is avian Paramyxovirus under the Avulavirus and has a negative- sense, single-stranded RNA genome [2]. So far, NDV strains with genomic sizes of 15,186, 15192 and 15198 nucleotides which codes for at least six proteins including nucleoprotein (N), phosphoprotein (P), matrix (M) pro- tein, fusion (F) protein, haemagglutinin-neuraminidase (HN) protein and RNA polymerase (L) [2-4] have been identified. Among the six major proteins, the two interac- tive surface glycoproteins, the F and the HN proteins, are involved in cell surface attachment and cell membrane fusion [3,5]. * Correspondence: aiini@admin.upm.edu.my 1 Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Darul Ehsan, Malaysia Full list of author information is available at the end of the article Berhanu et al. Virology Journal 2010, 7:183 http://www.virologyj.com/content/7/1/183 © 2010 Berhanu et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.