Computational protocol: Possible involvement of distinct phylogenetic clusters of HIV-1 variants in the discrepancies between coreceptor tropism predictions based on viral RNA and proviral DNA

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Protocol publication

[…] Viral tropism of each sequence or read obtained using population-based sequencing and deep sequencing, respectively, was interpreted using G2P 2.5 [] with a false-positive rate (FPR) cut-off of 10 % according the European guidelines []. Phylogenetic trees were constructed from the C2V3C3 sequences using the neighbor-joining method and the Maximum Composite Likelihood model and were assessed using the Bootstrap test (1,000 replicates) performed using MEGA version 6 software []. Putative dual infection was suggested according to previously proposed criteria: in the env C2V3 region, when the two clusters in the phylogenetic tree were separated by a branch with a bootstrap value >90 % obtained from more than 500 randomly selected reads, and when the net mean distance between the two groups was >5 % [, ]. Statistics was conducted using IBM SPSS Statistics version 21 software (IBM, Tokyo, Japan). The level of significance was set at 0.05.Nucleotide sequences reported are available in the DDBJ databases with the accession numbers AB981480–AB981579 for population-based sequencing data and DRX021920–DRX021929 for deep sequencing data. […]

Pipeline specifications

Software tools MEGA, SPSS
Databases DDBJ G2P
Applications Miscellaneous, Phylogenetics
Organisms Human immunodeficiency virus 1, Homo sapiens
Diseases HIV Infections
Chemicals Nucleotides