Computational protocol: Natural Rabies Infection in a Domestic Fowl (Gallus domesticus): A Report from India

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Protocol publication

[…] Touch impressions of the brain were stained by Seller’s stain and examined for the presence of Negri bodies. Impressions, fixed in high grade chilled acetone at -20°C, were subjected to the fluorescent antibody test (FAT) for detection of rabies virus nucleoprotein antigens []. A one step TaqMan real time PCR targeting the nucleoprotein gene was carried out as described earlier [] on the brain tissue for confirmation of rabies virus infection. Partial gene sequencing was carried out by amplifying a 446 bp region in the nucleoprotein gene using nested PCR []. PCR products were purified using a commercial kit (QIAquick Gel purification kit, Qiagen, UK) and custom sequenced from Amnion Biosciences Pvt. Ltd, Bangalore, India using gene specific primers. The sequence was deposited in the GenBank database under accession number KP316199. Partial nucleoprotein gene sequences of rabies virus isolates from GenBank representing various geographical regions in India and two other countries from the Indian subcontinent i.e Sri Lanka and Nepal were used to investigate the phylogenetic relationship with the present rabies virus strain. The sequences were aligned using ClustalW, and a maximum likelihood phylogeny tree was constructed using MEGA5 software [] with bootstrap replication values of 1000. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Gallus gallus, Rabies lyssavirus, Canis lupus familiaris
Diseases Encephalitis, Infection, Virus Diseases, HIV Infections