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Reassortant Avian Influenza A(h5n1) Viruses with H9n2-pb1gene in Poultry, Bangladesh

Isabella Monne
Istituto Zooprofilattico Sperimentale delle Venezie,Padova, Italy

Francesco Bonfante
Istituto Zooprofilattico Sperimentale delle Venezie,Padova, Italy

Silvia Ormelli
Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy

Annalisa Salviato
Istituto Zooprofilattico Sperimentale delle Venezie,Padova, Italy

Mohammed Giasuddin
Bangladesh Livestock Research Institute National Reference Laboratory for Avian Influenza, Dhaka

Filip Claes
Food and Agriculture Organization of the United Nations Animal Health Service, Rome, Italy

Gwenaëlle Dauphin
Food and Agriculture Organization of the United Nations Animal Health Service, Rome, Italy

Mat Yamage
Food and Agriculture Organization of the United Nations Emergency Center for Transboundary Animal Diseases, Dhaka, Bangladesh

Abstract/ Executive Summary:

Bangladesh has reported a high number of outbreaks of highly pathogenic avian influenza (HPAI) (H5N1) in poultry. We identified a natural reassortant HPAI (H5N1) virus containing a H9N2-PB1 gene in poultry in Bangladesh. Our findings highlight the risks for prolonged co-circulation of avian influenza viruses and the need to monitor their evolution.

Keywords: Avian influenza virus; Bangladesh; HPAI

Location: Bangladesh

Start Date: 31-12-2011

End Date: 31-04-2012

Program Area: Animal Health and Management

Commodity: Poultry

Objectives:

1. Identification of a natural reassortant HPAI (H5N1) virus containing a H9N2-PB1 gene in poultry in Bangladesh

Methodology:

The Study - A total of 18 tracheal and 1 cloacal samples were collected from chickens in 14 layer farms (15 samples) and 2 live-bird markets (4 samples) in 13 districts of Bangladesh during December 2011–April 2012. The samples were submitted by the Department of Livestock Services Dhaka to the World Organisation for Animal Health/United Nations Food and Agriculture Organization Reference laboratory for Avian Influenza in Italy for confirmatory diagnosis and genetic analysis. All samples tested positive for the H5N1 subtype by real-time reverse transcription PCR (rRT-PCR) and virus isolation (www.oie.int/fileadmin/Home/eng/ Health_standards/tahm/2.03.04_AI.pdf). Because the H7 subtype is also notifiable and the H9N2 subtype circulates in the poultry population in Bangladesh, samples were tested for these subtypes as well; results were negative. The complete genome of 18 HPAI (H5N1) isolates and the hemagglutinin (HA) gene of 1 virus (A/chicken/ Bangladesh/12VIR-7140-9/2012) were successfully sequenced, as described. The nucleotide sequences obtained in this study have been submitted to GenBank (accession nos. KC616462–KC616606). Maximumlikelihood (ML) trees were estimated for all 8 gene segments (HA, neuraminidase [NA], nucleoprotein [NP], basic polymerase protein [PB] 1 and 2, polymerase [PA], matrix [M], and nonstructural [NS]) by using the best-fit general time reversible + I + Γ4 model of nucleotide substitution in PhyML. A bootstrap resampling process (1,000 replications) using the neighbor-joining method was used to assess the robustness of individual nodes of the phylogeny, incorporating the ML substitution model defined above. Analysis of the topologic differences between the 8 ML phylogenetic trees revealed that an intersubtype reassortment event took place and caused replacement of the PB1 gene of 2 of the HPAI (H5N1) viruses from Bangladesh (A/chicken/Bangladesh/12VIR-7140-7/2012 and A/ chicken/Bangladesh/12VIR-7140-16/2012) with the PB1 gene of an H9N2 subtype virus. In the HA gene, all the viruses from Bangladesh analyzed fell within clade 2.3.2.1 and had high similarity (98.2%–99.7%) to viruses from Bangladesh and India identified in 2011.

Source of Information: Emerging Infectious Diseases • Vol. 19, No. 10, October 2013

Article Link (Online Journal): www.cdc.gov/eid

Funding Source:

Total Budget (Tk.) :

Achievement/Findings:

Although reassortment represents a major mechanism behind the emergence and evolution of the HPAI (H5N1) in Asia, data suggest that, in the past decade, these viruses have only sporadically provided the backbone for generation of novel intersubtype reassortants. This is surprising considering the prolonged and extensive co-circulation of subtype H5N1 and H9N2 viruses in poultry in Asia; it is unclear whether the limited evidence is because of insufficient surveillance or the low capacity of subtype H5N1 viruses to undergo intersubtype reassortment. We have documented the emergence and circulation of a novel natural H5N1/H9N2 7:1 reassortant strain in Bangladesh in 2012. This finding shows that the HPAI (H5N1) viruses circulating in this area are continuously evolving. Although it is difficult to ascertain where and when the reassortment event occurred, the identification of genetic clustering of the strains analyzed here with subtype H5N1 and H9N2 viruses identified in India confirms intense cross-border transmission between these regions, which has resulted in a favorable epidemiologic system for influenza viruses evolution.

Knowledge Management: Journal