Computational protocol: High Prevalence of West Nile Virus in Domestic Birds and Detection in 2 New Mosquito Species in Madagascar

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Protocol publication

[…] Positive amplicons were purified on a 1% (w/v) agarose gel by electrophoresis with the QIAquick gel extraction kit (Qiagen), and sequenced commercially (Macrogen, Korea).For the determination of WNV genotype of the Malagasy strains, a total of 42 WNV GenBank partial sequences of 228 bp of the envelope gene and 1 partial sequence of JEV were selected according to their origin (Asia, Europe, Africa and America), their host (human, birds, mosquitoes) and their lineage. Basic Local Alignment Search Tool (BLAST) alignments were generated using MUSCLE [] through the Mega 5 software []. A phylogenetic tree was generated by neighbour-joining distance analysis with node values generated by 1000 bootstraps replications, using the Mega 5 software []. […]

Pipeline specifications

Software tools BLASTN, MUSCLE, MEGA
Applications Phylogenetics, Nucleotide sequence alignment
Organisms West Nile virus, Homo sapiens, Anas platyrhynchos, Gallus gallus, Meleagris gallopavo, Human poliovirus 1 Mahoney, Viruses
Diseases Infection, West Nile Fever, HIV Infections