Doria-Rose NA, Learn GH, Rodrigo AG, Nickle DC, Li F, Mahalanabis M, Hensel MT, McLaughlin S, Edmonson PF, Montefiori D, Barnett SW, Haigwood NL, Mullins JI 2005 Human immunodeficiency virus type 1 subtype B ancestral envelope protein is functional and elicits neutralizing antibodies in rabbits similar to those elicited by a circulating subtype B envelope. Journal of virology791711214-24 pubmed

Supplemental Data for Doria-Rose et al.:

  1. Table S1: Model Parameters
  2. Table S2: Sequences used to derive subtype B MRCA
  3. Figure S1: Alignment of SIVBK28 (Env region) and deduced ancestor
  4. Figure S2: Nucleotide and inferred amino acid sequence of AN1env



Model Parameters for Phylogenetic Analysis
Viral gene HIV-1-B enva SIV envb
model class GTR+I+G GTR+I+G
fA 0.34857 0.3516
fC 0.17125 0.1642
fG 0.23694 0.2296
fT 0.24324 0.2546
RA<->C 1.971 1.8418
RA<->G 4.315 10.9127
RA<->T 0.8539 0.5803
RC<->G 1.021 0.9283
RC<->T 3.826 6.8499
RG<->T 1 1
p-inv 0.26035 0.471
gamma shape (α) 0.50434 0.9477

a: Model parameters estimated using hierarchical likelihood ratio test with Modeltest, version 2.0, and PAUP* version 4.0b2.
b: Model parameters estimated using Akaike Information Criterion (AIC) with Modeltest, version 3.06, and PAUP* version 4.0b10.



HIV-1 env sequences used for phylogenetic reconstruction

Sequence name Accession number Subtype
HIVELICG

K03454 D
HIVNDK

M27323 D
HIVZ2Z6

M22639 D
87USSG3X

L02317 B
88USWR27

U26546 B
89SP061

AJ006287 B
AUC18

AF042102 B
AUC18MBC

U37270 B
AUMBC200

AF042100 B
AUMBC925

AF042101 B
AUMBCC18B

AF042106 B
AUMBCC54

AF042103 B
AUMBCC98

AF042104 B
AUMBCD36

AF042105 B
USAD8

U19647 B
USDH123

AF069140 B
CNRL42CG

U71182 B
D31

U43096 B
HIVBH102

M15654 B
HIVCAM1

D10112 B
HIVF12CG

Z11530 B
HIVHAN2

U43141 B
HIVJC16

AF049494 B
HIVJRCSF

M38429 B
HIVJRFL

U63632 B
HIVLAICG

K02013 B
HIVMCK1

D86068 B
HIVMN

M17449 B
HIVNL43

M19921 B
HIVNY5CG

M38431 B
HIVOYI

M26727 B
HIVPV22

K02083 B
HIVRF

M17451 B
HIVSF2CG

K02007 B
HIVWEAU160

U21135 B
HIVYU10X

M93259 B
HIVYU2X

M93258 B
MANC

U23487 B
NLACH320A

U34603 B
NLACH320B

U34604 B
US89.6 U39362 B
Department of Microbiology
School of Medicine
University of Washington
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