Computational protocol: Distribution of human immunodeficiency virus type 1 subtypes in the State of Amazonas, Brazil, and subtype C identification

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Protocol publication

[…] Amplified products (gag, pol, and env) were purified using the Wizard PCR Preps DNA Purification System Kit (Promega). Sequencing reactions were performed using the inner PCR primers and the DYEnamic™ ET Dye Terminator Kit according to manufacturer instructions, and products were sequenced using the MegaBace 1000 DNA Sequencing System. Electropherograms were analyzed with ChromasPro Version 1.41 (Technelysium Pty Ltda., Australia).The HIV-1 sequences of Brazilian isolates (gag, pol, and env) were aligned and edited using the BioEdit 7.0.5.3 program. The sequences were compared to those in the Los Alamos database, which includes 40 prototypes for the genotypes A-D, F-H, J, and K, 14 CRFs and the out group sequence (O group). Neighbor joining (NJ) trees were constructed using the Phylip package (version 3.6) and PAUP* 4.0b10 program (Sinauer Associates, USA). The NJ trees were constructed using the (GTR+I+G) and (TMV+I+G) nucleotide substitution models, as selected by the Modeltest 3.06 program. The reliability of the NJ trees was assessed by analyzing 1000 bootstrap replicates. The likelihood ratio test was used to calculate statistical support (reported as P values) for the branches. Trees were drawn with the TreeView X 0.5.0 program. Sequences obtained in this study are available in GenBank under accession numbers FJ011469-FJ011532.Recombination analysis was performed using SimPlot 3.5.1, which evaluates the differences between phylogenetic trees at each fragment (window) along with the alignment. Bootscanning was performed with alignment (available at http://lasp.cpqgm.fiocruz.br/retrovirusHIV.html). The gag, pol, and env regions were concatenated to get the query sequence, gaps were deleted to obtain a continuous sequence, and the sequences were then analyzed by multiple alignment. […]

Pipeline specifications

Software tools ChromasPro, BioEdit, PHYLIP, ModelTest-NG, TreeViewX
Application Phylogenetics
Organisms Human immunodeficiency virus 1
Diseases Immunologic Deficiency Syndromes, HIV Infections