Human Leukocyte Antigen Diversity: A Southern African Perspective

Table 1

Contemporary studies which provide insight into HLA diversity in southern Africa. HLA allele frequency from the studies cited was extracted from the AFND [35, 48] to assess HLA diversity in southern Africa. The AFND curated allele frequency data was generated from Mozambique, South Africa, Zambia, and Zimbabwe as shown in (a) with the most and least frequent classical HLA alleles in these populations as shown in (b) and (c).

(a) General description of studies used in this review

Country	Year	Population		Typing method	Loci typed	Comments
Bots	2005		55	SSP	DRB, DQB1	55 HIV negative compared to 74 HIV positive [7]
Moza	2010	Mostly Black	202	SSOP	A, B, DRB1	91.8% Black, rest admixture. Assane et al. [35, 48, 55]
RSA	2012	Black	200	SBT, SSP	A, B, C, DRB1	Blacks from different ethnolinguistic groups in RSA. Paximadis et al. [18, 35, 48]
RSA	2012	Caucasians	102	SBT, SSP	A, B, C, DRB1	English and Afrikaner ancestry. Paximadis et al. [18, 35, 48]
RSA	2002	Tamil/Natal	51	SSOP	A, B, C	Hammond [35, 48, 56]
RSA	2000	Black Zulu/Natal	100	SSOP	A, B	Could not distinguish A0301 from A0303N, and B0705 from B0706 [35, 37, 48, 57]
RSA	2006	Black/Tswana	41		A, B	Coetzee et al. [35, 48, 58]
RSA	2004	Black	112	SSP	DRB1, DQB1, DPB1	112 Sclerosis controls compared to cases [59]
Zam	2002	Black/Lusaka	44	SSOP	A, B, C	Alleles similar at exons 2 and 3 could not be distinguished [35, 48, 60, 61]
Zim	2002	Shona/Harare	230	SSOP	A, B, C, DPB1, DQA1, DQB1, DRB1	Louie [35, 48, 62]

(b) Most frequent alleles in different southern African populations [35, 48]

Population	Loci
	A	B	C	DP	DQ	DRB1
Black RSA	A30:01 (0.101)	B42:01 (0.089), B58:02 (0.094)	C06:02 (0.149)	DPB113:01 (0.148) [59]	DQB106 (0.555) [59]	DRB111 (0.366) [59], DRB113:01 (0.124)
Bots					DQB116 (0.509) [7]	DRB111 (0.364) [7]
Caucasian RSA	A01:01:01 (0.2), A02:01:01 (0.26)	B07:02:01 (0.149)	C07:01 (0.172), C07:02:01 (0.137)			DRB103:01 (0.122)
Moza	A30 (0.239)	B15 (0.156)				DRB111 (0.196), DRB113 (0.198)
Shona Zim	A30:02 (0.147)	B45:01 and B53:01 (0.093)	C04:01 (0.148)	DPB101:01:01 (0.355)	DQA101:02 (0.343), DQB105:01 (0.227), DQB106:02 (0.247)	DRB111:01 (0.144), DRB115:03 (0.153)
Tamil RSA	A01:01 (0.17), A11:01 (0.18)	B40:06 (0.143)	C06:02 (0.177)
Tswana RSA	A02 (0.146), A30 (0.159)	B58 (0.22)
Venda RSA					DQB106 (0.437)	DRB111 (0.184)
Zam	A30:02 (0.233)	B42:01 (0.148)	C17:01 (0.156)
Zulu RSA	A30 (0.195)	B15 (0.15), B58 (0.145)

(c) Least frequent alleles in different southern African populations [35, 48]

Population	Loci
	A	B	C	DP	DQ	DRB1
Bots					DQB102 (0.127) [7]	DRB110 and DRB112 (0.074) [7]
Caucasian RSA	A02:05, A02:17, A11:12, A24:07, A25:01:01, A33:03:01 and A69:01 (0.005)	B07:06, B14:01, B15:02, B15:03, B15:10, B15:13, B15:16, B15:24, B27:02, B35:05, B40:06:01, B41:01, B44:04, B44:27, B45:01, B49:01, B50:01 and B58:02 (0.005)	C02:05, C03:16, C04:08, C04:09N, C06:11, C07:22, C08:01, C14:04 and C17:01 (0.005)			DRB103:02, DRB104:08, DRB112:02,; DRB114:04 and DRB115:07 (0.005)
Moza	A32 (0.002)	B27, B37, B73 and B82 (0.002)				DRB116 (0.002)
Shona Zim	A02:17, A32:02, A34:01, A80:01, A66:02, A66:03 and A74 (0.002)	B07:12, B13:04, B14:04, B15:17, B15:18, B35:02, B39:10, B40:01, B40:16, B50:02 and B73:01 (0.002)	C03:04:01, C07:08, C12:04:02 and C15:05 (0.02)	DPB101:01:02, DPB102:02, DPB162:01, DPB165:01 and DPB180:01 (0.002)	DQA105:02 (0.004), DQB106:08 and DQB106:15 (0.002)	DRB103, DRB104:04, DRB112:04,; DRB113 and DRB115:01 (0.002)
Tamil RSA	A02:01, A02:03, A03:02, A24:07, A30:01 and A32:01 (0.001)	B15:25, B27:05, B44:07, B50:01 and B56:01 (0.01)	C02:02:01, C12:03, C15:02 and C16:01 (0.01)
Tswana RSA	A01, A31, A32, A36 and A80 (0.012)	B35, B40, B50 and B53 (0.012)
Venda RSA					DQB104 (0.094)	DRB110:01 (0.004)
Zam	A02:06, A02:14, A26:01, A33:01, A34:02, A43:01 and A66:01 (0.012)	B07:05, B13:02, B15:18, B18:03, B41:01, B44:05, B47:01, B49:01 and B57:01 (0.011)	C03:03 and C07:04 (0.022)
Zulu RSA	A31, A31:01:02, A33 and A33:03 (0.005)	B15:01, B15:16, B41:01, B41:02, B67, B67:01, B82 and B82:01 (0.005)

= sample size, Bots = Botswana, Moza = Mozambique, RSA = Republic of South Africa, Zam = Zambia, Zim = Zimbabwe, SSP = sequence specific primers, SBT = sequence based typing, SSOP = sequence specific oligonucleotide primers, and (number) is allele frequency in the population stated. Blanks indicate no alleles reported in the population or ethnicity not defined or typing method not specified.