Phylogeography of H5N1 avian influenza virus in Indonesia

Abstract

Highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype are a major concern to human and animal health in Indonesia. This study aimed to characterize transmission dynamics of H5N1 over time using novel Bayesian phylogeography methods to identify factors which have influenced the spread of H5N1 in Indonesia. We used publicly available hemagglutinin sequence data sampled between 2003 and 2016 to model ancestral state reconstruction of HPAI H5N1 evolution. We found strong support for H5N1 transmission routes between provinces in Java Island and inter-island transmissions, such as between Nusa Tenggara and Kalimantan Islands, not previously described. The spread is consistent with wild bird flyways and poultry trading routes. H5N1 migration was associated with the regions of high chicken densities and low human development indices. These results can be used to inform more targeted planning of H5N1 control and prevention activities in Indonesia.

In vitro expression of the recombinant fusion protein of Newcastle disease virus from local Indonesian isolates by using a cell-free protein expression system

“…Office International des Epizooties (OIE) categorizes ND in the A list of animal diseases, which includes infectious diseases with rapid and serious spreading and affecting public health and socio economic communities ( [OIE] Office Internationalof Epi zootics 2015). As other infectious viral disease outbreak which had been reported in Indonesia poultry industry, such as avian influenza (Njoto et al 2018), infectious bur sal disease (Parede et al 2003), and avian encephalomyeli tis (Haryanto et al 2016). An outbreak of ND can cause a devastating effect as it causes almost 100% mortality in susceptible poultry (Alexander et al 2012).…”

Isolation and molecular characterization of the hemagglutinin gene of H9N2 avian influenza viruses from poultry in Java, Indonesia

“…The first group is an highly pathogenic AIV, for example, the H5N1 subtype which can cause mortality up to 100%. This subtype has become a major concern for human and animal health in Indonesia, especially the entire province of Java, since 2003 [ 5 ], and vaccinations have been routinely administered against this subtype. The second group was infected with various types of domestic and wild birds with mild to moderate infection called low pathogenic avian influenza virus (LPAIV) [ 6 ].…”

Innate Immune Responses to Avian Influenza Viruses in Ducks and Chickens

“…Mallards are more resistant to disease caused by influenza than most other species, including those caused by highly pathogenic avian influenza viruses [20,21,22]. However, even mallard ducks sometimes succumb to fatal infection by certain strains of H5 HPAI viruses, particularly certain strains belonging to the Eurasian lineage of HPAI H5 viruses tracing back to the Chinese strain A/goose/Guangdong/1/1996 [12,23,24,25]. Poultry outbreaks and human infections with HPAI H5N1 strains of this lineage began occurring in large numbers in Southeast Asia between 2003 and 2004.…”