Computational protocol: Characterization of H7N2 Avian Influenza Virus in Wild Birds and Pikas in Qinghai-Tibet Plateau Area

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Protocol publication

[…] Viruses were sequenced as previously described. Briefly, total RNA was extracted from allantoic fluid with Trizol® LS (Invitrogen, Carlsbad, CA), followed by RT-PCR using a One-Step RT-PCR kit (Qiagen, Hilden, Germany) with universal influenza primers. PCR products were cloned into the pMD18-T vector, and sequenced. Viral sequences were aligned using Clustal W within the BioEdit software package (version 5.0.9). Maximum likelihood phylogenetic trees were inferred with 1000 bootstraps using MEGA (Version 6). […]

Pipeline specifications

Software tools Clustal W, BioEdit, MEGA
Application Phylogenetics
Organisms Hemisus marmoratus, Viruses, Gallus gallus, Mus musculus
Diseases Infection, HIV Infections