Performance of applied biosystems ViroSeq HIV-1 genotyping system for sequence-based analysis of non-subtype B human immunodeficiency virus type 1 from Uganda

M. Mracna, G. Becker-Pergola, J. Dileanis, L. A. Guay, S. Cunningham, J. B. Jackson, Susan Eshleman

Research output: Contribution to journalArticle

Abstract

The Applied Biosystems ViroSeq HIV-1 Genotyping System is a commercially available, integrated system for sequence-based analysis of drug resistance mutations in human immunodeficiency virus type 1 (HIV-1) protease and reverse transcriptase (RT). We evaluated the performance of this system for analysis of non subtype B HIV-1 by analyzing plasma samples from Ugandan women and infants. Plasma samples were obtained from 105 women and 25 infants enrolled in a Ugandan clinical trial. HIV-1 analysis was performed with the ViroSeq system according to the manufacturer's instructions, except that the volume of plasma used for analysis was less than the recommended 0.5 ml for some samples. Viral loads ranged from 2,313 to 2,336,400 copies/ml. PCR products suitable for sequencing were amplified from all samples tested. Complete sequences for protease (amino acids 1 to 99) and RT (amino acids 1 to 320) were obtained for 102 of 105 (97%) of the maternal samples tested and all 25 of the infant samples tested. Complete double-stranded sequences were obtained for 90 of 105 (86%) of the maternal samples tested and 22 of 25 (88%) of the infant samples tested. The sequences obtained with this system were used for HIV-1 subtyping. The subtypes identified were A, C, D, and A/D recombinant HIV-1. The performances of the seven sequencing primers were similar for the subtypes examined. The ViroSeq system performs well for analysis of Ugandan plasma samples with subtypes A, C, D, and A/D recombinant HIV-1. The availability of this genotyping system should facilitate studies of HIV-1 drug resistance in countries where these subtypes are prevalent.

Original languageEnglish (US)
Pages (from-to)4323-4327
Number of pages5
JournalJournal of Clinical Microbiology
Volume39
Issue number12
DOIs
StatePublished - 2001

Fingerprint

Cercopithecine Herpesvirus 1
Uganda
Sequence Analysis
HIV-1
Drug Resistance
Peptide Hydrolases
Mothers
Plasma Volume
RNA-Directed DNA Polymerase
Systems Analysis
Viral Load
Amino Acid Sequence
Clinical Trials
Amino Acids
Polymerase Chain Reaction
Mutation

ASJC Scopus subject areas

  • Microbiology (medical)
  • Microbiology

Cite this

Performance of applied biosystems ViroSeq HIV-1 genotyping system for sequence-based analysis of non-subtype B human immunodeficiency virus type 1 from Uganda. / Mracna, M.; Becker-Pergola, G.; Dileanis, J.; Guay, L. A.; Cunningham, S.; Jackson, J. B.; Eshleman, Susan.

In: Journal of Clinical Microbiology, Vol. 39, No. 12, 2001, p. 4323-4327.

Research output: Contribution to journalArticle

Mracna, M. ; Becker-Pergola, G. ; Dileanis, J. ; Guay, L. A. ; Cunningham, S. ; Jackson, J. B. ; Eshleman, Susan. / Performance of applied biosystems ViroSeq HIV-1 genotyping system for sequence-based analysis of non-subtype B human immunodeficiency virus type 1 from Uganda. In: Journal of Clinical Microbiology. 2001 ; Vol. 39, No. 12. pp. 4323-4327.
@article{7d2ec0d09b874a8fb26a45f710a55a39,
title = "Performance of applied biosystems ViroSeq HIV-1 genotyping system for sequence-based analysis of non-subtype B human immunodeficiency virus type 1 from Uganda",
abstract = "The Applied Biosystems ViroSeq HIV-1 Genotyping System is a commercially available, integrated system for sequence-based analysis of drug resistance mutations in human immunodeficiency virus type 1 (HIV-1) protease and reverse transcriptase (RT). We evaluated the performance of this system for analysis of non subtype B HIV-1 by analyzing plasma samples from Ugandan women and infants. Plasma samples were obtained from 105 women and 25 infants enrolled in a Ugandan clinical trial. HIV-1 analysis was performed with the ViroSeq system according to the manufacturer's instructions, except that the volume of plasma used for analysis was less than the recommended 0.5 ml for some samples. Viral loads ranged from 2,313 to 2,336,400 copies/ml. PCR products suitable for sequencing were amplified from all samples tested. Complete sequences for protease (amino acids 1 to 99) and RT (amino acids 1 to 320) were obtained for 102 of 105 (97{\%}) of the maternal samples tested and all 25 of the infant samples tested. Complete double-stranded sequences were obtained for 90 of 105 (86{\%}) of the maternal samples tested and 22 of 25 (88{\%}) of the infant samples tested. The sequences obtained with this system were used for HIV-1 subtyping. The subtypes identified were A, C, D, and A/D recombinant HIV-1. The performances of the seven sequencing primers were similar for the subtypes examined. The ViroSeq system performs well for analysis of Ugandan plasma samples with subtypes A, C, D, and A/D recombinant HIV-1. The availability of this genotyping system should facilitate studies of HIV-1 drug resistance in countries where these subtypes are prevalent.",
author = "M. Mracna and G. Becker-Pergola and J. Dileanis and Guay, {L. A.} and S. Cunningham and Jackson, {J. B.} and Susan Eshleman",
year = "2001",
doi = "10.1128/JCM.39.12.4323-4327.2001",
language = "English (US)",
volume = "39",
pages = "4323--4327",
journal = "Journal of Clinical Microbiology",
issn = "0095-1137",
publisher = "American Society for Microbiology",
number = "12",

}

TY - JOUR

T1 - Performance of applied biosystems ViroSeq HIV-1 genotyping system for sequence-based analysis of non-subtype B human immunodeficiency virus type 1 from Uganda

AU - Mracna, M.

AU - Becker-Pergola, G.

AU - Dileanis, J.

AU - Guay, L. A.

AU - Cunningham, S.

AU - Jackson, J. B.

AU - Eshleman, Susan

PY - 2001

Y1 - 2001

N2 - The Applied Biosystems ViroSeq HIV-1 Genotyping System is a commercially available, integrated system for sequence-based analysis of drug resistance mutations in human immunodeficiency virus type 1 (HIV-1) protease and reverse transcriptase (RT). We evaluated the performance of this system for analysis of non subtype B HIV-1 by analyzing plasma samples from Ugandan women and infants. Plasma samples were obtained from 105 women and 25 infants enrolled in a Ugandan clinical trial. HIV-1 analysis was performed with the ViroSeq system according to the manufacturer's instructions, except that the volume of plasma used for analysis was less than the recommended 0.5 ml for some samples. Viral loads ranged from 2,313 to 2,336,400 copies/ml. PCR products suitable for sequencing were amplified from all samples tested. Complete sequences for protease (amino acids 1 to 99) and RT (amino acids 1 to 320) were obtained for 102 of 105 (97%) of the maternal samples tested and all 25 of the infant samples tested. Complete double-stranded sequences were obtained for 90 of 105 (86%) of the maternal samples tested and 22 of 25 (88%) of the infant samples tested. The sequences obtained with this system were used for HIV-1 subtyping. The subtypes identified were A, C, D, and A/D recombinant HIV-1. The performances of the seven sequencing primers were similar for the subtypes examined. The ViroSeq system performs well for analysis of Ugandan plasma samples with subtypes A, C, D, and A/D recombinant HIV-1. The availability of this genotyping system should facilitate studies of HIV-1 drug resistance in countries where these subtypes are prevalent.

AB - The Applied Biosystems ViroSeq HIV-1 Genotyping System is a commercially available, integrated system for sequence-based analysis of drug resistance mutations in human immunodeficiency virus type 1 (HIV-1) protease and reverse transcriptase (RT). We evaluated the performance of this system for analysis of non subtype B HIV-1 by analyzing plasma samples from Ugandan women and infants. Plasma samples were obtained from 105 women and 25 infants enrolled in a Ugandan clinical trial. HIV-1 analysis was performed with the ViroSeq system according to the manufacturer's instructions, except that the volume of plasma used for analysis was less than the recommended 0.5 ml for some samples. Viral loads ranged from 2,313 to 2,336,400 copies/ml. PCR products suitable for sequencing were amplified from all samples tested. Complete sequences for protease (amino acids 1 to 99) and RT (amino acids 1 to 320) were obtained for 102 of 105 (97%) of the maternal samples tested and all 25 of the infant samples tested. Complete double-stranded sequences were obtained for 90 of 105 (86%) of the maternal samples tested and 22 of 25 (88%) of the infant samples tested. The sequences obtained with this system were used for HIV-1 subtyping. The subtypes identified were A, C, D, and A/D recombinant HIV-1. The performances of the seven sequencing primers were similar for the subtypes examined. The ViroSeq system performs well for analysis of Ugandan plasma samples with subtypes A, C, D, and A/D recombinant HIV-1. The availability of this genotyping system should facilitate studies of HIV-1 drug resistance in countries where these subtypes are prevalent.

UR - http://www.scopus.com/inward/record.url?scp=0035209291&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0035209291&partnerID=8YFLogxK

U2 - 10.1128/JCM.39.12.4323-4327.2001

DO - 10.1128/JCM.39.12.4323-4327.2001

M3 - Article

C2 - 11724839

AN - SCOPUS:0035209291

VL - 39

SP - 4323

EP - 4327

JO - Journal of Clinical Microbiology

JF - Journal of Clinical Microbiology

SN - 0095-1137

IS - 12

ER -