MOESM1 of Characterization update of HIV-1 M subtypes diversity and proposal for subtypes A and D sub-subtypes reclassification
Creators: name: Désiré, Nathalie
name: Cerutti, Lorenzo
name: Hingrat, Quentin Le
name: Perrier, Marine
name: Emler, Stefan
name: Calvez, Vincent
name: Descamps, Diane
name: Anne-Geneviève Marcelin
name: Hué, Stéphane
name: Benoit Visseaux
Publisher: name: figshare
Year: 2018
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Genetics
subject: Pharmacology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology

description: Additional file 1: Fig. S1. Full genome genetic distance comparisons between HIV-1 subtype A sub-subtypes according to our classification proposal. X-axis scale lines indicate genetic distance thresholds allowing, in our alignment and model conditions, for group, subtype and sub-subtype identification. Fig. S2. Phylogenetic tree of sub-type A obtained with pol gene. Sequences from A1, A2, A3, A4 and A6 clades have been collapsed for readability. One pol sequence was identified in the A7 clade in addition to the two full genome sequences and is highlighted by an arrow. The tree has been obtained with PhyML 3.0, using GTR-G nucleotide substitution model and branch support obtained by bootstrap method is given for each node. Several sequences, depicted in black, clustered outside the defined clades but cannot be retained in the classification proposal because of poor branch support values or absence of available full genome sequences. Fig. S3. Phylogenetic tree of sub-type A obtained with gag gene. Sequences from A1, A2, A3, A4 and A6 clades have been collapsed for readability. One pol sequence was identified in the A7 clade in addition to the two full genome sequences and is highlighted by an arrow. The tree has been obtained with PhyML 3.0, using GTR-G nucleotide substitution model and branch support obtained by bootstrap method is given for each node. Several sequences, depicted in black, clustered outside the previously defined clades but cannot be retained in the classification proposal because of poor branch support values or absence of available full genome sequences. Fig. S4. Genetic distance comparisons between HIV-1 subtype D sub-subtypes according to our new classification proposal. X-axis scale lines indicate genetic distance thresholds allowing, in our alignment and model conditions, for group, subtype and sub-subtype identification. Fig. S5. Genetic distance comparisons between HIV-1 groups, subtypes and sub-subtypes using pol sequences. X-axis scale lines indicate genetic distance thresholds allowing, in our alignment and model conditions, for group, subtype and sub-subtype identification. Genetic distance ranges compatible with intra-sub-subtype, inter-sub-subtype, inter-subtype and inter-group comparisons are indicated by the numbers 1, 2, 3 and 4, respectively. Fig. S6. Subtypes A (A) and D (B) pol sequences maximum likelihood phylogenetic trees. Names of all sub-subtypes are indicated according to the new classification proposal. Fig. S7. Pol gene genetic distance comparisons between HIV-1 subtype A sub-subtypes according to our classification proposal. X-axis scale lines indicate genetic distance thresholds allowing, in our alignment and model conditions, for group, subtype and sub-subtype identification. Fig. S8. Pol gene genetic distance comparisons between HIV-1 subtype D sub-subtypes according to our classification proposal. X-axis scale lines indicate genetic distance thresholds allowing, in our alignment and model conditions, for group, subtype and sub-subtype identification. Table S1. Full genome sequence used for our analysis and the corresponding clade in our classification proposal. Table S2. Full genome genetic distance distributions observed within each corresponding clade. Table S3. Net genetic divergence between each identified sub-subtypes. The “net genetic divergence” between each identified sub-subtypes within corresponding subtypes, which also takes into account the within-sub-subtype diversity, was calculated as follow: if dx,y is the average genetic divergence between two sub-subtypes, x and y, and dx and dy are the genetic diversities within populations x and y, respectively, net divergence, Dx,y, is given by the expression Dx,y = dx,y − (dx + dy)/2.