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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]