Skip to main content
. 2014 Dec 11;9(12):e114441. doi: 10.1371/journal.pone.0114441

Table 5. V3 amino acid sequences and predicted phenotypes of different HIV-1 isolates in Taiwan.

Isolate Consensus V3 region amino acid sequences 11 1819 232425 CTRPNNNTRKSIHIGPGRAFYTTGEIIGDIRQAHC Genetic subtype Biotype MT-2 assay Predictions
Sequencea Geno2phenob PSSMc
TW_D78 CTRPGNNTRKSIRIGPGQTFYATGDIIGDIRQAHC CRF07_BC R5 NSI R5 R5 R5
TW_D83 CTRPGNNTRKSIRIGPGQTFYATGDIIGDIRQAHC CRF07_BC R5 NSI R5 R5 R5
TW_D590 CTRPGNNTRKSIRIGPGQTFYATGDIIGDIRQAHC CRF07_BC R5 NSI R5 R5 R5
TW_D592 CTRPGNNTRKSIRIGPGQTFYATGDIIGDIRQAHC CRF07_BC R5 NSI R5 R5 R5
TW_D848 CTRPGNNTRKSIRIGPGQTFYATGEIIGNIRQAHC CRF07_BC R5 NSI R5 R5 R5
TW_D854 CTRPGNNTRKSIRIGPGQTFYATGDIIGDIRQAHC CRF07_BC R5 NSI R5 R5 R5
TW_D855 CTRPGNNTRKSIRIGPGQTFYATGDIIGDIRQAHC CRF07_BC R5 NSI R5 R5 R5
TW_D40 CTRPNNNTRRSIPIGPGRAFYTSE-IIGDIRKAHC B R5 NSI R5 R5 R5
TW_D257 CTRPNNNTRKSISMGPGKAFFATGDIIGDIRAAYC B R5 NSI R5 R5 R5
TW_D573 CTRPNNNTRKSIPIGPGRAFYTTN-IIGDIRKAHC B R5 NSI R5 R5 R5

A dash indicated a deletion or lack of an insertion.

a

The phenotype prediction based on 2 amino acid insertion/deletion between position 14 and 15, as well as variable amino acid positions (11, 18, 19, 23, 24 and 25) of V3 regions.

b

Geno2pheno (http://coreceptor.bioinf.mpi-inf.mpg.de/index.php), false-positive rate of 0.01.

c

Position-Specific Scoring Matrix (PSSM) (http://indra.mullins.microbiol.washington.edu/webpssm/).