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Table 1.

Table 1A Updated Proposal of Reference Sequences of HIV-1 Genetic Subtypes and Circulating Recombinant

Subtype

Sequence IDs

Region

A

U455

92UG037.1

Q2317

SE7253

complete genome

B

HXB2

JRFL

RF

WEAU.160

complete genome

C

ETH2220

92BR025

IN21068

96BW05.02

complete genome

D

NDK

ELI

94UG1141

84ZR085

complete genome

F

93BR020.1

FIN6393

VI850


complete genome


BZ162

VI69



gag


BZ163

BZ126



env

G2

SE6165

HH8793

DRCBL


complete genome

H

90CF056.1

VI991

VI997


complete genome


VI5573




gag, env

J

SE9280.9

SE9173.3



complete genome

Circulating Recombinant Forms

AB(KAL153)

KAL1534




complete genome

AE(CM240)

CM2405

90CR402.1

93TH253.3


complete genome


TN235




env

AG(IbNG)

IBNG6

DJ263

DJ264


complete genome

AGI(CY032)

CY032.37

PVMY

PVCH


complete genome

Group

N

YBF30




complete genome

O

MVP5180

ANT70



complete genome

Chimpanzee SIV Isolates

CPZ

CPZANT8

CPZGAB



complete genome

Footnotes:

1 The sequence 94UG114.1 is the most distant complete genome subtype D sequence (see trees), tending to branch off closest to the B/D root in most analyses. In some subgenomic regions, it may even move outside theB/D cluster.

2 The G reference sequences may show resemblance to subtype A in regions of pol, vif, and env [2, 8]. The sequence NG083.2, characterized as an AG in [8]shares a similar genetic structure with the three sequences listed as G here.

3 Full length gene sequences of gag, pol, or env are not yet available, see Table 1B.

4 A circulating recombinant form with A and B subtype subregions in an epidemic strain in an outbreak in Kaliningrad. Only one full-length genome is available at this time [14].

5 Circulating Recombinant Form AE was called subtype E in previous compendia and the previous literature, but it is E in most of env, A in gag and pol, mixture of A \E in regulatory genes [3, 8, 14].

6 Circulating Recombinant Form AG(IBNG) recombination breakpoints are described in [2].

7 Circulating Recombinant Form AGI(CY032) recombination breakpoints are described in [7].

8 A 275 bp insert in CPZANT, near the 3' end of the pol gene was deleted from the subtype reference set alignment, because this insert is not related to any HIV or SIV sequence, and likely represents a cloning or sequencing artifact. See pages I-54 to I-55 of the 1997 HIV SequenceCompendium.


Table 1B Description of sequences in alignments

Subtype

Sequence

Acc. No.

Source

Region

Sampling year

Sampling country (origin)

A

U455

M62320

Oram, J.D. ARHR 6:1073-1078 (1990)

complete

NA

Uganda

A

92UG037.1

U51190

Gao, F. J Virol 70:7013-7029 (1996)

complete

1992

Uganda

A

Q2317

AF004885

Poss, M. J Virol 72:8240-8251 (1998)

complete

1994

Kenya

A

SE7253

AF069670

Carr, J.K. Unpublished. (1998)

complete

1994

Sweden (Somalia)

B

HXB2

K03455, M38432

Wong-Staal, F. Nature313:277-284 (1985)

complete

NA

France

B

JRFL

U63632

O'Brien, W.A. Nature 348:69 (1990)

complete

NA

U.S.A.

B

RF

M17451, M12508

Starcich, B.R. Cell 45:637-648 (1986)

complete

1983

U.S.A. (Haiti)

B

WEAU160

U21135

Ghosh, S.K. Unpublished (1995)

complete

NA

U.S.A.

C

ETH2220

U46016

Salminen, M.O. ARHR 12:1329-1339 (1996)

complete

1986

Ethiopia

C

92BR025.8

U52953

Gao, F. J Virol 70:1651-1657 (1996)

complete

1992

Brazil

C

IN21068

AF067155

Lole, K.S. Unpublished (1998)

complete

NA

India

C

96BW05.02

AF110967

Novitsky, V. J Virol submitted (1998)

complete

1996

Botswana

D

NDK

M27323

Spire, B. Gene 81:275-284 (1989)

complete

NA

Zaire/DRC*

D

ELI

K03454, X04414

Alizon, M. Cell 46:63-74 (1986)

complete

NA

Zaire/DRC*

D

94UG114.1

U88824

Gao, F. J Virol 72:5680-5698 (1998)

complete

1994

Uganda

D

84ZR085

U88822

Gao, F. J Virol 72:5680-5698 (1998)

complete

1984

Zaire/DRC*

F

93BR020.1

AF005494

Gao, F. J Virol 72:5680-5698 (1998)

complete

1993

Brazil

F

VI850

AF077336

Carr, J. et al., Unpublished (1998)

complete

1993

Belgium (Zaire/DRC*)

F

FIN9363

AF075703

Laukkanen, T. Unpublished (1998)

complete

NA

Finland

F

BZ162

L11751

Louwagie, J. AIDS 7:769-780 (1993)

gag

NA

Brazil

F

VI69

L11796

Louwagie, J. AIDS 7:769-780 (1993)

gag

NA

Belgium (Rwanda)

F

BZ163

L22085

Louwagie, J. ARHR 10:561-567 (1994)

env-nef

NA

Brazil

F

BZ126

L22082

Louwagie, J. ARHR 10:561-567 (1994)

env-nef

NA

Brazil

G**

SE6165

AF061642

Carr, J.K. Virology 247:22-31 (1998)

complete

1993

Sweden (Zaire/DRC*)

G**

HH8793.1.1

AF061640

Carr, J.K. Virology 247:22-31 (1998)

complete

NA

Finland (Kenya)

G**

DRCBL

AF084936

Oelrichs, R. ARHR in press (1999)

complete

NA

Belgium

H

90CF056.1

AF005496

Gao, F. J Virol 72:5680-5698 (1998)

complete

1990

Cent. Afr. Rep.

H

VI991

none yet

Laukkanen, T. Unpublished (1998)

complete

NA

Belgium

H

VI997

none yet

Laukkanen, T. Unpublished (1998)

complete

NA

Belgium

H

VI557

U09666

Janssens, W. ARHR 10:877-879 (1994)

V3-V5

NA

Zaire/DRC*

H

VI557

L11793

Louwagie, J. AIDS 7:769-780 (1993)

gag

NA

Zaire/DRC*

J

SE9280.9

AF082394

Laukkanen, T. ARHR in press (1999)

complete

NA

Sweden

J

SE9173.3

AF082395

Laukkanen, T. ARHR in press (1999)

complete

NA

Sweden (Zaire/DRC*)

AB

KAL153

none yet

Salminen, M.O., Unpublished (1998)

complete

NA

Russia

AE

CM240

U54771

Carr, J.K. J Virol 70:5935-5943 (1996)

complete

1990

Thailand

AE(like CM240)

90CF402.1

U51188

Gao, F. J Virol 70: 7013-7029 (1996)

complete

1990

Cent. Afr. Rep.

AE(like CM240)

93TH253.3

U51189

Gao, F. J Virol 70: 7013-7029 (1996)

complete

1993

Thailand

AE(like CM240)

TN235

L03698

McCutchan, F.E. ARHR 8:1887-1895 (1992)

env

NA

Thailand

AG

IBNG

L39106

Howard, T.M. ARHR 10:1755-1757 (1994)

complete

NA

Nigeria

AG(like IBNG)

DJ264

AF063224

Carr, J.K. Virology 247:22-31 (1998)

complete

NA

France (Djibouti)

AG(like IBNG)

DJ263

AF063223

Carr, J.K. Virology 247:22-31 (1998)

complete

NA

France (Djibouti)

AGI

CY032.3

AF049337

Gao, F. J Virol in press (1998)

complete

1994

Cyprus (Greece)

AGI(like CY032)

PVMY

AF119819

Nasioulas, G. ARHR in press (1999)

complete

NA

Greece

AGI(like CY032)

PVCH

AF119820

Nasioulas, G. ARHR in press (1999)

complete

NA

Greece

N

YBF30

AJ006022

Simon, F. Nature Medicine 4:1032-1037 (1998)

complete

1995

Cameroon

O

MVP5180

L20571

Gurtler, L.G. J Virol 68:1581-1585 (1994)

complete

1991

Cameroon

O

ANT70

L20587

Haesevelde, M. J Virol 68:1586-1596 (1994)

complete

NA

Cameroon

CPZ

CPZGAB

X52154

Huet, T. Nature 345:356-359 (1990)

complete

NA

Gabon

CPZ

CPZANT

U42720

Haesevelde, M. Virol 221:346-350 (1996)

complete

NA

Zaire/DRC*

* The former Zaire is now called the Democratic Republic of Congo

** These G viruses are difficult to classify, as they contain some possibly "A" like regions.

last modified: Tue Apr 20 10:01 2010


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