Computational protocol: Phyloepidemiological Analysis Reveals that Viral Divergence Led to the Paucity of Simian Immunodeficiency Virus SIVmus/gsn/mon Infections in Wild Populations

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Protocol publication

[…] The SIV status of all specimens was evaluated with two nested primer sets amplifying highly conserved regions of the polymerase gene as previously described (, ).The first round was performed with primers polis4 and PolOR or NDR1 to PolOR followed by Polis2 to Uni2 or Polis4 to Uni2, respectively. PCR amplifications were performed using a Long Expand PCR kit (Roche Applied Science) according to the manufacturer's instructions. Amplified fragments were agarose gel purified and externally Sanger sequenced. Phylogenetic analyses were carried out on viral nucleotide sequence alignments by using MUSCLE in the MEGA v7 software package. Ignoring all gaps, an alignment of 319 bp was investigated, corresponding to base pairs 3727 to 4047 of SIVmusOI81 (accession number KF304707.1), a highly conserved region. The best-fitting distance model of nucleotide substitution for each alignment was inferred using the maximum likelihood (ML) method, with goodness of fit measured by the Bayesian information criterion (BIC) in TOPALI v2.5. The model with the lowest BIC score was a general time-reversible (GTR) model with discrete gamma and invariant among-site rate variation. In the ML method (implemented in PhyML), the reliability of branching orders was tested using the bootstrap approach (100 replicates).Serum samples collected from fresh bushmeat (from 39 mustached guenons and 22 greater spot-nosed guenons) and dried blood spots (from 244 mona guenons) were also screened for the presence of SIV antibodies by use of an in-house SIVmus/mon/gsn lineage-specific enzyme-linked immunosorbent assay (ELISA), using a synthetic SIVgsn-derived V3 loop peptide (GNKTIRNLQIGAGMTFYSQVIVGGNTRKAYC) as antigen () and performing the ELISA as previously described (). […]

Pipeline specifications

Software tools MEGA-V, TOPALi, PhyML
Applications Phylogenetics, GWAS
Organisms Simian immunodeficiency virus, Pan troglodytes, Viruses, Cercocebus torquatus, Human poliovirus 1 Mahoney, Homo sapiens
Diseases Acquired Immunodeficiency Syndrome, Cytomegalovirus Infections, Immunologic Deficiency Syndromes, Infection, Virus Diseases, HIV Infections, Epstein-Barr Virus Infections