Computational protocol: Emergence of Epidemic Dengue-1 Virus in the Southern Province of Sri Lanka

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Protocol publication

[…] Full genome sequencing of dengue virus isolates was done in accordance with the protocols described in Christenbury et al. []. Sanger sequencing reads were processed and assembled into full genomes with the Geneious 8.1.7 program. The full genome sequences for these samples have been deposited into GenBank (KT445955, KT445956, KT445957, KT445958, KT445959, KT445960, KT445961, KT445962, and KT445963). The nine full genomes from the present study were then aligned with 1604 unique, full genome DENV1 sequences present in GenBank using MAFFT. FastTree 2.1.5 was then used to infer an approximately-maximum-likelihood phylogenetic tree. The clade consisting of the 9 Galle sequences and 15 other sequences (KP 398852, KJ468234, KJ726664, KJ726662, KJ726663, JN054255, HQ891313, HQ891314, JN054256, HQ891316, HQ891315, EU280167, FJ196844, FJ176779, and AB608787) was selected. 25 other sequences representative of the tree’s diversity were selected by taking sequences (GU131678, JQ922548, FV537256, HI553375, KF921911, GU131973, AB074760, JQ287661, JQ287664, JQ287663, GU131778, JF459993, JQ287662, KF955446, KJ649286, KJ189363, AB204803, GU131833, JQ915076, AB519681, HG316481, AY835999, KF921935, KF921933, and EU863650) from different clades of the tree. These sequences were then aligned using MAFFT and a maximum likelihood tree constructed using raxmlGUI 1.5 beta with a general-time reversible GAMMA nucleotide model and ML+Rapid Bootstrapping algorithm with 1000 bootstrap replicates. […]

Pipeline specifications

Software tools Geneious, MAFFT, FastTree, raxmlGUI
Application Phylogenetics
Organisms Dengue virus 2, Homo sapiens, Viruses
Diseases Dengue, HIV Infections