title: Analysis of the crow lung transcriptome in response to infection with highly pathogenic H5N1 avian influenza virus.
abstract: The highly pathogenic avian influenza (HPAI) H5N1 virus, currently circulating in Asia, causes severe disease in domestic poultry as well as wild birds like crow. However, the molecular pathogenesis of HPAIV infection in crows and other wild birds is not well known. Thus, as a step to explore it, a comprehensive global gene expression analysis was performed on crow lungs, infected with HPAI H5N1 crow isolate (A/Crow/India/11TI11/2011) using high throughput next generation sequencing (NGS) (GS FLX Titanium XLR70). The reference genome of crow is not available, so RNA seq analysis was performed on the basis of a de novo assembled transcriptome. The RNA seq result shows, 4052 genes were expressed uniquely in noninfected, 6277 genes were expressed uniquely in HPAIV infected sample and of the 6814 genes expressed in both samples, 2279 genes were significantly differentially expressed. Our transcriptome profile data allows for the ability to understand the molecular mechanism behind the recent lethal HPAIV outbreak in crows which was, until recently, thought to cause lethal infections only in gallinaceous birds such as chickens, but not in wild birds. The pattern of differentially expressed genes suggest that this isolate of H5N1 virus evades the host innate immune response by attenuating interferon (IFN)-inducible signalling possibly by down regulating the signalling from type I IFN (IFNAR1 and IFNAR2) and type II IFN receptors, upregulation of the signalling inhibitors suppressor of cytokine signalling 1 (SOCS1) and SOCS3 and altering the expression of toll-like receptors (TLRs). This may be the reason for disease and mortality in crows.
authors.affiliation: High Security Animal Disease Laboratory, Indian Veterinary Research Institute, Anand Nagar, Bhopal 462021, Madhya Pradesh, India.
authors.forename: Periyasamy
authors.initials: P
authors.lastname: Vijayakumar
authors.affiliation: High Security Animal Disease Laboratory, Indian Veterinary Research Institute, Anand Nagar, Bhopal 462021, Madhya Pradesh, India. Electronic address: reach2anamika@yahoo.com.
authors.forename: Anamika
authors.initials: A
authors.lastname: Mishra
authors.affiliation: High Security Animal Disease Laboratory, Indian Veterinary Research Institute, Anand Nagar, Bhopal 462021, Madhya Pradesh, India.
authors.forename: Pradip B
authors.initials: PB
authors.lastname: Ranaware
authors.affiliation: National Institute of Animal Nutrition and Physiology, Adugodi, Bangalore 560030, Karnataka, India.
authors.forename: Atul P
authors.initials: AP
authors.lastname: Kolte
authors.affiliation: High Security Animal Disease Laboratory, Indian Veterinary Research Institute, Anand Nagar, Bhopal 462021, Madhya Pradesh, India.
authors.forename: Diwakar D
authors.initials: DD
authors.lastname: Kulkarni
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, Scotland, UK.
authors.forename: David W
authors.initials: DW
authors.lastname: Burt
authors.affiliation: High Security Animal Disease Laboratory, Indian Veterinary Research Institute, Anand Nagar, Bhopal 462021, Madhya Pradesh, India.
authors.forename: Ashwin Ashok
authors.initials: AA
authors.lastname: Raut
mesh_terms: D000818:Animals; D030161:Avian Proteins / Q000096:biosynthesis*; D046368:Crows; D005786:Gene Expression Regulation; D007113:Immunity, Innate; D053124:Influenza A Virus, H5N1 Subtype; D005585:Influenza in Birds / Q000378:metabolism* / Q000473:pathology; D008168:Lung / Q000378:metabolism* / Q000473:pathology; D053633:Receptor, Interferon alpha-beta / Q000096:biosynthesis; D050826:Suppressor of Cytokine Signaling Proteins / Q000096:biosynthesis; D051193:Toll-Like Receptors / Q000096:biosynthesis; D059467:Transcriptome
chemical_list: D030161:Avian Proteins; D050826:Suppressor of Cytokine Signaling Proteins; D051193:Toll-Like Receptors; D053633:Receptor, Interferon alpha-beta
keywords: Avian influenza virus infection; De novo transcriptomics; High-throughput RNA sequencing; Host immune response; Jungle crows