Molecular and Antigenic Survey of H5N1 Bird Flu Virus in Indonesian Ducks

4 December 2011, at 12:00am

A molecular and antigenic survey by CSIRO researchers of H5N1 highly pathogenic avian influenza (HPAI) virus isolates from smallholder duck farms in Central Java, Indonesia during 2007-2008 reveals that multiple genetic variants were present simultaneously within poultry populations and that ducks are more likely than chickens to survive infection and represent a long-term host for H5N1.

Indonesia is one of the countries most severely affected by H5N1 highly pathogenic avian influenza (HPAI) virus in terms of poultry and human health, according to Hendra Wibawa of CSIRO-Australian Animal Health Laboratory in Geelong and co-authors there and at the University of Queensland and the Disease Investigation Centre Regional IV at Yogyakarta in Indonesia. In their paper published in Virology Journal recently, they continue that there is little information on the diversity of H5N1 viruses circulating in backyard farms, where chickens and ducks often intermingle.

In their study, H5N1 virus infection occurring in 96 smallholder duck farms in central Java, Indonesia from 2007-2008 was investigated and the molecular and antigenic characteristics of H5N1 viruses isolated from these farms were analysed.

The researchers found that all 84 characterised viruses belonged to H5N1 clade 2.1 with three virus sublineages being identified: clade 2.1.1 (1), clade 2.1.3 (80), and IDN/6/05-like viruses (3) that did not belong to any of the present clades. All three clades were found in ducks, while only clade 2.1.3 was isolated from chickens.

There were no significant amino acid mutations of the haemagglutinin (HA) and neuraminidase (NA) sites of the viruses, including the receptor binding, glycosylation, antigenic and catalytic sites and NA inhibitor targets.

All the viruses had polybasic amino acids at the HA cleavage site. No evidence of major antigenic variants was detected. Based on the HA gene, identical virus variants could be found on different farms across the study sites and multiple genetic variants could be isolated from HPAI outbreaks simultaneously or at different time points from single farms. HPAI virus was isolated from both ducks and chickens; however, the proportion of surviving duck cases was considerably higher than in chickens.

The 2.1.3 clade was the most common lineage found in this study, concluded Wibawa and co-authors. All the viruses had sequence characteristic of HPAI but negligible variations in other recognised amino acids at the HA and NA proteins which determine virus phenotypes. Multiple genetic variants appeared to be circulating simultaneously within poultry communities.

They also noted that the high proportion of live duck cases compared to chickens over the study period suggests that ducks are more likely to survive infection and they may better suit the role of long-term maintenance host for H5N1. As some viruses were isolated from dead birds, there was no clear correlation between genetic variations and pathogenicity of these viruses.


Wibawa H., J. Henning, F. Wong, P. Selleck, A. Junaidi, J. Bingham, P. Daniels and J. Meers. 2011. A molecular and antigenic survey of H5N1 highly pathogenic avian influenza virus isolates from smallholder duck farms in Central Java, Indonesia during 2007-2008. Virology Journal, 8:425. doi:10.1186/1743-422X-8-425

Further Reading

- You can view the full report by clicking here.

Further Reading

- You can visit the Avian Flu page by clicking here.

December 2011