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Table 3 Haplotypes frequencies for A3D, A3F, A3G and A3H

From: Characterization of APOBEC3 variation in a population of HIV-1 infected individuals in northern South Africa

Variation (amino acid and its position) Frequency (%) Haplotypes within individuals
Confirmed APOBEC3D Haplotypes (n = 168)
 97R, 238 T, 248R 88 (52.3) i/i
 97C, 238 T, 248R 1 (0.6) ii/ii
 97C(het), 238 T, 248R 18 (10.7) i/ii
 97R, 238A(het), 248R 10 (6) i/iii
 97R, 238 T, 248 K 1 (0.6) iv/iv
 97R, 238 T, 248 K(het) 27 (16) i/iv
 Minor variant frequency < 5% 7 (4.1) Not assigned
 Othersa 16 (9.7) Not assigned
Unconfirmed APOBEC3D Haplotypes
 None
Confirmed APOBEC3F Haplotypes (n = 154)
 48R, 78A, 87I, 108A, 231 V, 307Y 5 (3.2) i/i
 48R, 78A, 87I, 108S, 231 V, 307Y 2 (1.3) iii/iii
 48R, 78A, 87I, 108S(het), 231 V, 307Y 32 (20.8) i/iii
 48R, 78A, 87I, 108A, 231 V, 307C(het) 5 (3.2) i/iv
 48R, 78 V, 87I, 108S, 231 V, 307Y 1 (0.6) vi/vi
 48R, 78 V (het), 87I, 108S, 231 V, 307Y 2 (1.3) vi/iii
 Minor variant frequency < 5% 5 (3.2) Not assigned
 Othersa 51 (33.1) Not assigned
Unconfirmed APOBEC3F Haplotypes
 48R, 78 V (het), 87I, 108S (het), 231 V, 307Y 21 (13.6) Not assigned
 48R, 78 V (het), 87I, 108S (het), 231I (het), 307Y 14 (9.1) Not assigned
 48R, 78 V (het), 87I, 108S, 231I (het), 307Y 8 (5.2) Not assigned
 48R, 78 V (het), 87I, 108S (het), 231I, 307Y 2 (1.3) Not assigned
 48P (het), 78A, 87I, 108S (het), 231 V, 307Y 6 (3.9) Not assigned
Confirmed APOBEC3G Haplotypes (n = 165)
 186H, 275Q, 363G 5 (3.1) i/i
 186R, 275Q, 363G 20 (12.1) ii/ii
 186R (het), 275Q, 363G 43 (26.1) i/ii
 186H, 275E, 363G 3 (1.8) iii/iii
 186H, 275E(het), 363G 22 (13.3) i/iii
 186H, 275Q, 363R(het) 9 (5.5) iv/iv
 Minor variant frequency < 5% 11 (6.6) Not assigned
 Othersa 52 (31.5) Not assigned
Unconfirmed APOBEC3G Haplotypes
 None
Confirmed APOBEC3H Haplotypesb (n = 133)
 15 N, 18R, 105R, 121E, 178D 38 (28.6) ii/ii
 15Δ,18R, 105R, 121E,178E 25 (18.8) x/x
 15Δ(het), 18R, 105R, 121E, 178D 36 (27.1) ii/iii
 15Δ, 18 L, 105R, 121E, 178D 6 (4.5) iv/iv
 15Δ, 18 L(het), 105R, 121E, 178D 7 (5.3) iv/iii
 Othera 10 (7.4) Not assigned
Unconfirmed APOBEC3H Haplotypesb
 15Δ(het), 18R, 105R, 121E(het), 178D 4 (3) Not assigned
 15Δ(het), 18 L(het), 105R, 121E, 178D 7 (5.3) Not assigned
  1. Bold defines variants that are different from those listed in haplotype I in each gene
  2. All variants marked by (het) are heterozygous. All others are homozygous
  3. Haplotypes are called unconfirmed in our population due to more than 1 heterozygous SNP in the cluster
  4. aRefers to the haplotypes with synonymous changes and those of novel SNPs (not reported on the dbSNP)
  5. bA3H haplotypes were determined using previous classification from references [11, 12, 37]
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