Computational protocol: A Single HIV 1 Cluster and a Skewed Immune Homeostasis Drive the Early Spread of HIV among Resting CD4+ Cell Subsets within One Month Post Infection

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Protocol publication

[…] HIV envelope genes were cloned in plasma after extraction of RNA and reverse transcription and in cells after extraction of DNA from PBMCs and rectal biopsies. Amplification of the ENV C2V5 region of the gp120 gene by nested PCR followed, as previously described . Clonal analysis was performed with a limiting dilution approach. Samples were purified with the QIAquick PCR purification HIV kit (Qiagen), and PCR products were sequenced with the fluorescent dideoxy-terminator method (Big Dye Terminator kit, Perkin Elmer) on an ABI 330 Genetic Analyzer Sequencer (Applied Biosystem). Sequences were verified with Sequence Navigator software. All sequences of the ENV C2V5 gene region were aligned with Clustal X 2.011 software. Pairwise evolutionary distances were estimated with DNAdist, with Kimura’s two-parameter method , and the phylogenetic trees were built by a neighbor-joining method (DNAdist module – Phylip Package v3.67). The reliability of each tree topology was estimated from 1000 bootstrap replicates. […]

Pipeline specifications

Software tools Clustal W, PHYLIP
Application Phylogenetics
Organisms Human immunodeficiency virus 1
Diseases Infection, Leukemia, Lymphoid, HIV Infections