Computational protocol: A Newly Emerging HIV-1 Recombinant Lineage (CRF58_01B) Disseminating among People Who Inject Drugs in Malaysia

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Protocol publication

[…] Near full length genomes were aligned with the HIV-1 reference subtypes and CRFs of epidemiological significance in Southeast Asia downloaded from the Los Alamos HIV database (http://www.hiv.lanl.gov/) using ClustalX 2.0. Nucleotide sequences were then manually adjusted using BioEdit 7.0 with reference to the HIV Sequence Compendium 2011 (http://www.hiv.lanl.gov/) to ensure accurate codon alignment. In addition, newly published CRFs of regional significance such as CRF48_01B and CRF51_01B to CRF55_01B were included in the alignment. Phylogenetic trees were constructed by the neighbour-joining method based on the Kimura two-parameter model with a transition-transversion ratio of 2.0 using MEGA 5.05 . The reliability of the branching orders were analysed by bootstrap analysis of 1000 replicates. Bootscanning analysis was performed using SimPlot version 3.5.1 and followed by informative site analysis to identify the specific recombination breakpoints shared by the novel CRF candidates. All possible parental reference strains were included in the similarity plot to identify the closely related parental strains prior to subsequent analyses. Sub-region trees were constructed to confirm the parental origin of each segment in the near full length genome. Such methods have been established and widely used in various studies to characterize recombinant genomes, including HIV-1. All sequences reported in this study have been deposited in GenBank with accession numbers reported in . […]

Pipeline specifications

Software tools Clustal W, BioEdit, MEGA, SimPlot
Application Phylogenetics
Organisms Human immunodeficiency virus 1
Diseases HIV Infections, Substance-Related Disorders