Computational protocol: Epidemiology and Molecular Virus Characterization of Reemerging Rabies, South Africa

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Protocol publication

[…] After viral RNA underwent extraction and RT-PCR (,), the amplicons obtained were purified with a commercial kit (Wizard SV Gel and PCR Clean-Up System, Promega, Madison, WI, USA) and sequenced bidirectionally on an ABI377 automated DNA sequencer (Applied Biosystems, Foster City, CA, USA) with the G/L primer set. A 592-bp nucleotide portion of the cytoplasmic domain of the glycoprotein and the G-L intergenic region of the virus isolates included in the study sample were aligned in ClustalW (). A phylogenetic tree was constructed with the neighbor-joining method () in MEGA (Molecular Evolutionary Genetics Analysis) software version 2.1 (), and 1,000 replications. The phylogenetic tree was visualized with TreeView ().All available isolates from humans and a panel of dog rabies virus isolates from Vhembe were selected (Appendix Table). Virus isolates from other provinces in South Africa and neighboring countries were also included in phylogenetic reconstruction of the molecular epidemiology. […]

Pipeline specifications

Software tools Clustal W, MEGA, TreeViewX
Application Phylogenetics
Organisms Canis lupus familiaris, Homo sapiens