Background: Indonesia is one of the countries most severely affected by H5N1 highly pathogenic avian influenza (HPAI) virus in terms of poultry and human health. However, there is little information on the diversity of H5N1 viruses circulating in backyard farms, where chickens and ducks often intermingle. In this 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

AC Hurt

Akhmad Junaidi

B Olsen

D Stallknecht

D Vijaykrishna

DA Senne

DA Steinhauer

DC Wiley

DE Swayne

DJ Alexander

DJ Hulse-Post

E Basuno

EC Claas

Frank Wong

GJ Smith

H Heine

Hendra Wibawa

IT Schulze

J Henning

J Stevens

J Wang

JD Brown

JL McKimm-Breschkin

Joanne Meers

Joerg Henning

John Bingham

K Sekikawa

KM Sturm-Ramirez

LV Gubareva

M Matrosovich

MA Rameix-Welti

Paul Selleck

Peter Daniels

PM Colman

R Takano

RA Fouchier

RJ Connor

S Krauss

S Kumar

SL Kosakovsky Pond

T Hall

TT Lam

WHO/OIE/FAO H5N1 Evolution Working Group

Y Ha

Y Uchida

English

PubMed

Abstract Background Indonesia is one of the countries most severely affected by H5N1 highly pathogenic avian influenza (HPAI) virus in terms of poultry and human health. However, there is little information on the diversity of H5N1 viruses circulating in backyard farms, where chickens and ducks often intermingle. In this 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. Results 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 hemagglutinin (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. Conclusions The 2.1.3 clade was the most common lineage found in this study. All the viruses had sequence characteristic of HPAI, but negligible variations in other recognized amino acids at the HA and NA proteins which determine virus phenotypes. Multiple genetic variants appeared to be circulating simultaneously within poultry communities. 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.</p

Junaidi Akhmad

Selleck Paul

Wong Frank

Henning Joerg

Wibawa Hendra

Bingham John

Daniels Peter

Meers Joanne

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A molecular and antigenic survey of H5N1 highly pathogenic avian influenza virus isolates from smallholder duck farms in Central Java, Indonesia during 2007-2008

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Henning, Joerg

Wong, Frank

Selleck, Paul

Junaidi, Akhmad

Bingham, John

Daniels, Peter

Meers, Joanne

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A molecular and antigenic survey of H5N1 highly pathogenic avian influenza virus isolates from smallholder duck farms in Central Java, Indonesia during 2007-2008

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