Computational protocol: Superinfection with drug-resistant HIV is rare and does not contribute substantially to therapy failure in a large European cohort

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Protocol publication

[…] We used RAxML v7.2 [] and MrBayes v3.1.8 [] to reconstruct phylogenetic trees. A GTR substitution model was assumed in both cases (based on the advised protocol for RAxML, and also for MrBayes to obtain consistent results). In the RAxML analyses, branch support values were computed based on bootstrap replicates (-autoMR method of RAxML), while posterior probabilities were used with MrBayes. In the case of MrBayes 10,000,000 generations were simulated on 4 chains of 3 simultaneous runs, with 10,000 steps discarded as burnins. We used PAUP [] to calculate maximum likelihood sequence distances under the GTR model without building a phylogenetic tree. [...] We downloaded 44244 partial HIV-1 B sequences from the Los Alamos HIV Database ( that spanned HXB2 coordinates 2253-3290, and merged them with 26130 sequences spanning the same region in the Virolab/ EUResist database. Note that the latter count included also sequences from patients who were part of the Virolab/EUResist database but were not eligible for the detection of superinfection, because only one sequence was available from them. Sequence alignment was done by Muscle v3.8.31 []. Pol sequences were aligned by Muscle in batches of 1000 sequences, then these partial alignments were merged using the HXB2 reference sequence as a guide. Codons associated with drug resistance were removed based on the Stanford HIV Drug Resistance Database (as of 2009) []; gap-stripping (with a threshold of 50%) removed all insertions relative to the reference sequence. A local BLAST database was compiled from the alignment. Another BLAST database was built from publicly available env sequences (13725 sequences downloaded from the Los Alamos HIV Database) for the validation procedure that involved also env. env sequence alignment was constructed with translated amino acid sequences using Muscle v3.8.31 []. Sequence translation was done by transeq []; frame-shifts were corrected manually. […]

Pipeline specifications

Software tools RAxML, MrBayes, PAUP*, MUSCLE
Databases HIV Drug Resistance Database
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Human immunodeficiency virus 2, Homo sapiens
Diseases HIV Infections