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. 2020 Sep 22;15(9):e0238995. doi: 10.1371/journal.pone.0238995

Table 2. Amino acid signatures of BCAR and BPANDEMIC datasets.

Location Gene gag pol vif vpu tat rev
Protein P24 P24 P24 P7 PR RT RT Vif Vpu Tat Rev
Position 27 120 148 12 41 207 211 50 24 23 57 67 102
Ancestors BCAR V S V I K E R R T T A S V
BPANDEMIC V S V T K Q R R T T A S V
Datasets D n = 18 I89 V11 S78 N17 V100 I56 T22 K100 E88 K6 K61 R39 K89 R11 T94 S6 N94 T6 E88 A6 S67 P33 I78 V16
BCAR n = 18 I61 V39 S50 N39 V61 T22 I39 T33 K89 R11 E50 A11 K50 R50 K56 R44 T83 S6 N44 T44 A55 E39 S83 P17 V100
BCAR expanded I71 V29 S50 N25 V68 T18 I54 T25 K74 R23 E48 A25 K54 R25 - - - A53 E32 - -
n = 28 n = 197 n = 59
BPANDEMIC n = 450 V69 I31 N55 S26 T66 V27 T40 I28 R75 K24 Q82 E9 R46 K44 R76 K24 S51 T45 T76 N22 G40 E27 P59 S39 I69 V28
p-values adj. D/BCAR - - - - - - 0.7563 - - 0.00391 0.0039 - 0.0001
D/BPANDEMIC 0.0172 0.0461 0.0009 0.3137 0.0073 0.0002 0.7962 0.0004 0.0311 0.00229 0.0508 0.1355 -
BCAR/BPANDEMIC 0.1084 0.3094 0.1084 0.0502 0.0200 0.0008 0.9670 0.0255 0.0015 0.0465 0.0300 0.0423 0.0300
BCAR exp/BPANDEMIC 0.0091 0.0091 0.0376 0.0376 0.0001 0.0001 0.0001 - - - 0.0001 - -

The table details positions identified as bearing amino acidic compositions significantly divergent between BCAR and BPANDEMIC strains. For each position are supplied (1) the residues present in the reconstructed BCAR and BPANDEMIC ancestors; (2) the two most common amino acid observed in that position in Subtype D, BCAR, BCAR Expanded, and BPANDEMIC datasets accompanied by a number representing its frequency in each group; (3) the adjusted p-values. The sampling range of each sub dataset is indicated in the table. Ancestor sequences were reconstructed employing FL genomes of BCAR (n = 18) and BPANDEMIC (n = 69) lineages. G (Glycine), P (Proline), A (Alanine), V (Valine), L (Leucine), I (Isoleucine), M (Methionine), C (Cysteine), F (Phenylalanine), Y (Tyrosine), W (Tryptophan), H (Histidine), K (Lysine), R (Arginine), Q (Glutamine), N (Asparagine), E (Glutamic Acid), D (Aspartic Acid), S (Serine), T (Threonine). p-values < 0.05 are in bold.