10.6084/m9.figshare.7502972.v1
Nathalie Désiré
Nathalie
Désiré
Lorenzo Cerutti
Lorenzo
Cerutti
Quentin Le Hingrat
Quentin
Le Hingrat
Marine Perrier
Marine
Perrier
Stefan Emler
Stefan
Emler
Vincent Calvez
Vincent
Calvez
Diane Descamps
Diane
Descamps
Anne-Geneviève Marcelin
Anne-Geneviève
Marcelin
Stéphane Hué
Stéphane
Hué
Benoit Visseaux
Benoit
Visseaux
MOESM1 of Characterization update of HIV-1 M subtypes diversity and proposal for subtypes A and D sub-subtypes reclassification
Springer Nature
2018
HIV
Nomenclature
Viral diversity
Phylogenetic
Evolution
2018-12-22 05:00:00
Journal contribution
https://springernature.figshare.com/articles/journal_contribution/MOESM1_of_Characterization_update_of_HIV-1_M_subtypes_diversity_and_proposal_for_subtypes_A_and_D_sub-subtypes_reclassification/7502972
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.