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Table 2 Genetic subtypes of HIV-1 strains determined by COMA

From: Genotyping HIV-1 and HCV Strains by a Combinatorial DNA Melting Assay (COMA)

Subtype a

Name (GenBank accession number)

Reference Pool c

A

UG271 (8), UG273 (L22957), UG275 (L22951), UG278 (8), DJ263 (L22941), UG276 (8), UG13655,b TZ940990 (U61875), TZ940992 (U61878), KE943509,b TX940996 (U61876), KE943511,b TZ941004 (U61877), KE943505b

I

B

POC367 (8), POC369 (8), POC370 (8), EG147 (8), POC366 (8), TH942705 (U22552), TH942728 (U22600), TH942706 (U22554), TH942664 (U22581), TH942698 (U22543), TH942711 (U22560), TH942670 (U22587), TH942699 (U22604), TH942723 (U22595)

I

C

SE145 (L22946), DJ259 (L22940), DJ260 (8), BR15 (M74984), MW6510 (L15733), MW12199 (L15721), MW12233 (L15730), MW12205 (L15723), MW6506 (L15731), MW12225 (L15727), MW6512 (L15734), MW6518 (L15735), MW12203 (L15722)

I

D

UG272 (8), UG274 (L22950), UG267 (8), UG269 (L22949), SE365 (L22945), UG279 (8), UG35 (8), UG24 (8), TAN372 (8), UG5428,b UG13671,b KE943513,b KE943384,b KE943382b

I

E

TH942095 (U22611), TH942123 (U22557), TH942113 (U22625), TH942125 (U22561), TH942093 (U22609), BZ162 (L11751), BZ163 (L22946)

I

F

BZ126 (L22082), RO18556,b RO18572,b RO18596,b RO18578b

I

A

KE943507b

II

B

TH942700 (U22545), TH942724 (U22596)

II

C

MW12227 (L15728)

II

E

TH942115 (U22542), TH942127 (U22567), TH942129 (U22575), TH942111 (U22624), TH942105 (U22617), TH942686 (U22604), TH942121 (U22553), TH942117 (U22548), TH942097 (U22612)

II

F

RO18558,b RO18576,b RO18568,b RO18584,b RO18552,b RO18570,b RO18594b

II

A

UG29 (8), UG31 (L34667)

III

B

BZ195 (8)

III

C

DJ261 (8), DJ262 (8)

III

D

TAN371 (8), UG277 (8)

III

A

UG13673,b UG13675,b UG13669b

IV

C

MW6508 (L15732), MW12215 (L15727), MW6514b

IV

D

TZ940994 (U61879)

IV

A

92UG037 (U09127), 92RW020 (U08794)

V

B

91US005 (U27434), 92HT953 (U08444), 92HT954 (U08445), 91HT651 (U08441), 92HT596 (U08446), 91HT652 (U08443), 92HT599 (U08447), 92US716 (U08453), 92US712 (U08449), 92US715 (U08451), 92US714 (U08448), 92US714 (U08450)

V

C

93MW960 (U08454), 93MW959 (U08453), 93MW956 (U08455)

V

D

92UG021 (U27399)

V

E

93TH975 (U08457), 93TH966 (U08456), 93TH975 (U08458)

V

F

93BR019 (U27401), 93BR020 (U27408)

V

G

92RU131 (U27445)

V

  1. aHIV-1 genetic subtypes had been previously determined by phylogenetic analyses of nucleotide sequences or by heteroduplex mobility assay (8,9).
  2. bUnpublished sequences communicated by M. L. Kalish. The following HIV-1 env sequences were used as subtype reference pools: A1: (RW20, IC144 and SF170); A2: (RW20, IC144, SF170, UG278, and DJ263); A3: (RW20, IC144, SF170, UG278, DJ263, UG273, UG275, UG13655, TZ940990, TZ940992, KE943509, TZ940996, KE943511, and TZ941004); A4: (RW20, UG271, UG273, and UG31); B1: (BR20, TH14, CYHO401, CYHO111, CYHO503, CYH0481, and CYH0271); B2: (BR20, TH14, CYHO401, CYHO111, CYHO503, CYH0481, CYH0271, TH942705, TH942728, TH942706, TH942664, TH942698, and TH942711); B3: (BR20, TH14, and SF162); C1: (MA959, IN868, and BR25); C2: (MA959, IN868, BR25, DJ259, and DJ260); C3: (MA959, IN868, BR25, DJ259, DJ260, SM145, MW6510, MW12199, MW12233, MW6512, MW12203, and MW12205); C4: (MA959, BR25, MW6508, MW12227, and MW12215); D1: (UG21, UG38, and UG46); D2: (UG21, UG38, UG46, UG272, UG274, UG279, TAN371, UG35, and UG24); D3: (UG21, UG38, UG46, UG269, UG274, UG5428, and KE943382); E1: (TH22 and TH06); E2: (TH22, TH06, and TH942105); E3: (TH22, TH06, TH942105, TH942095, TH942123, TH942113, TH942125, TH942111, TH942115, TH942127, TH942093, and TH942686); F1: (BZ126, BZ162, and BZ163); F2: (BZ126, BZ162, BZ163, RO18596, and RO18578); F3: (BZ126, BZ162, BZ163, RO18596, RO18578, RO942095, RO942123, RO18596, RO18588, RO18576, and RO18566); G1: (RU131, LBV21-7, and V1525); G2: (RU131B1); H1: (CA13 and VI557).
  3. cThe following subtype-reference pools were used in the combinatorial melting assay: I(A1, B1, C1, D1, E1, F1, G1, and H1); II (A2, B1, C2, D1, E2, F2, G1, and H1); III (A2, B1, C2, D2, E2, F2, G1, and H1); IV (A3, B2, C3, D3, E3, F3, G1, and H1); V (A4, B3, C4, D1, E1, F1, and G2).