Computational protocol: The Epidemiological and Molecular Aspects of Influenza H5N1 Viruses at the Human Animal Interface in Egypt

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Protocol publication

[…] Avian samples were collected for diagnostic purposes by veterinarians from farms they provide care for through the period of 2006 to 2010. As those specimens were collected as part of the routine animal care, no animal care and use committee approval was sought. Five isolated viruses were included in this analysis (). All samples were tested for the presence of influenza A viruses by detection of M gene using one-step RT-PCR kit (Qiagen, Valencia, CA). Samples were subtyped using specific primers (). Comparative analysis of HA genes for all H5N1 viruses was carried out and compared with the available sequences using the NCBI influenza virus resource for both avian and human H5N1 viruses. Sequences were analyzed using the BioEdit program . Sequences were aligned with ClustalW . Phylogenetic analyses were carried out using MEGA version 4.0.2, with the neighbor-joining method, Poisson correction . Bootstrap values (1000 replications) are indicated on the tree. […]

Pipeline specifications

Software tools BioEdit, Clustal W, MEGA
Databases NCBI Influenza Virus Resource
Application Phylogenetics
Organisms Homo sapiens