Performance of the automated Abbott RealTime™ HIV-1 assay on a genetically diverse panel of specimens from London: Comparison to VERSANT HIV-1 RNA 3.0, AMPLICOR HIV-1 MONITOR v1.5, and LCx® HIV RNA Quantitative assays

Journal of Virological Methods

Volumn 137, Issue 2, 2006, Pages 184-192

  Swanson, Priscilla ^a   Holzmayer, Vera ^a   Huang, Shihai ^b   Hay, Phillip ^c   Adebiyi, Ade ^c   Rice, Philip ^c   Abravaya, Klara ^b   Thamm, Sven ^b   Devare, Sushil G ^a   Hackett Jr , John ^a  

^a ABBOTT LABORATORIES   (United States)

^b Abbott Molecular Inc   (United States)

^c ST GEORGE S HOSPITAL   (United Kingdom)

Author keywords

HIV 1 genetic diversity; HIV 1 viral load; Real time RT PCR

Indexed keywords

GAG PROTEIN; GLYCOPROTEIN GP 41; VIRUS RNA;

ARTICLE; ASSAY; CONTROLLED STUDY; GENE SEQUENCE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTED PATIENT; MAJOR CLINICAL STUDY; NUCLEOTIDE SEQUENCE; PLASMA; PRIORITY JOURNAL; SAMPLE; STRUCTURAL GENE; UNITED KINGDOM; VIRUS LOAD; VIRUS STRAIN;

AUTOMATION; GENOTYPE; HIV INFECTIONS; HIV-1; HUMANS; OBSERVER VARIATION; PLASMA; REAGENT KITS, DIAGNOSTIC; RNA, VIRAL; SENSITIVITY AND SPECIFICITY; STATISTICS; STATISTICS AS TOPIC; VIRAL LOAD;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 33748879967     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2006.06.010     Document Type: Article

References (37)

1. Aggarwal I., Smith M., Tatt I.D., Murad S., Osner N., Geretti A.M., and Easterbrook P.J. Evidence for onward transmission of HIV-1 non-B subtype strains in the United Kingdom. J. Acquir. Immune Defic. Syndr. 41 (2006) 201-209
2. Barlow K.L., Tosswill J.H.C., Parry J.V., and Clewley J.P. Performance of the Amplicor human immunodeficiency virus type 1 PCR and analysis of specimens with false-negative results. J. Clin. Microbiol. 35 (1997) 2846-2853
3. Beuselinck K., van Ranst M., and van Eldere J. Automated extraction of viral-pathogen RNA and DNA for high-throughput quantitative real-time PCR. J. Clin. Microbiol. 43 (2005) 5541-5546
4. Bland J.M., and Altman D.G. Statistical methods for assessing agreement between two methods of clinical measurement. Lancet 1 (1986) 307-310
5. Böni J., Pyra H., Gebhardt M., Perrin L., Bürgisser P., Matter L., Fierz W., Erb P., Piffaretti J.-C., Minder E., Grob P., Burckhardt J.J., Zwahlen M., and Schüpbach J. High frequency of non-B subtypes in newly diagnosed HIV-1 infections in Switzerland. J. Acq. Immune Defic. Syndr. 22 (1999) 174-179
6. Bustin S.A. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J. Mol. Endocrinol. 25 (2000) 169-193
7. Christopherson C., Sninsky J., and Kwok S. The effects of internal primer-template mismatches on RT-PCR: HIV-1 model studies. Nucleic Acids Res. 25 (1997) 654-658
8. Clarke J.R., Galpin S., Braganza R., Ashraf A., Russell R., Churchill D.R., Weber J.N., and McClure M.O. Comparative quantification of diverse serotypes of HIV-1 in plasma from a diverse population of patients. J. Med. Virol. 62 (2000) 445-449
9. Collins M.L., Irvine B., Tyner D., Fine E., Zayati C., Chang C., Horn T., Ahle D., Detmer J., Shen L.-P., Kolberg J., Bushnell S., Urdea M.S., and Ho D.D. A branched DNA signal amplification assay for quantification of nucleic acid targets below 100 molecules/ml. Nucleic Acids Res. 25 (1997) 2979-2984
10. de Mendoza C., Alcamí J., Sainz M., Folgueira D., and Soriano V. Evaluation of the Abbott LCx quantitative assay for measurement of human immunodeficiency virus RNA in plasma. J. Clin. Microbiol. 40 (2002) 1518-1521
11. de Mendoza C., Koppelman M., Montès B., Ferre V., Soriano V., Cuypers H., Segondy M., and Oosterlaken T. Multicenter evaluation of the NucliSens EasyQ HIV-1 v1.1 assay for the quantitative detection of HIV-1 RNA in plasma. J. Virol. Methods 127 (2005) 54-59
12. Esteves A., Parreira R., Piedade J., Venenno T., Franco M., De Sousa J.G., Patrício L., Brum P., Costa A., and Canas-Ferreira W.F. Spreading of HIV-1 subtype G and envB/gagG recombinant strains among injecting drug users in Lisbon Portugal. AIDS Res. Hum. Retrovir. 19 (2003) 511-517
13. Gardner S.N., Kuczmarski T.A., Vitalis E.A., and Slezak T.R. Limitations of TaqMan PCR for detecting divergent viral pathogens illustrated by Hepatitis A, B, C, and E, viruses and human immunodeficiency virus. J. Clin. Microbiol. 41 (2003) 2417-2427
14. Geelen S., Lange J., Borleffs J., Wolfs T., Weersink A., and Schuurman R. Failure to detect a non-B HIV-1 subtype by the HIV-1 Amplicor Monitor test, version 1.5: a case of unexpected vertical transmission. AIDS 17 (2003) 781-782
15. Germer J.J., Lins M.M., Jensen M.E., Harmsen W.S., Ilstrup D.M., Mitchell P.S., Cockerill III F.R., and Patel R. Evaluation of the MagNA Pure LC instrument for extraction of hepatitis C virus RNA for the COBAS Amplicor hepatitis C virus test, Version 2.0. J. Clin. Microbiol. 41 (2003) 3503-3508
16. Johanson J., Abravaya K., Caminiti W., Erickson D., Flanders R., Leckie G., Marshall E., Mullen C., Ohhashi Y., Perry R., Ricci J., Salituro J., Smith A., Tang N., Vi M., and Robinson J. A new ultrasensitive assay for quantitation of HIV-1 RNA in plasma. J. Virol. Methods 95 (2001) 81-92
17. Katsoulidou A., Petrodaskalaki M., Sypsa V., Papachristou E., Anastassopoulou C.G., Gargalianos P., Karafoulidou A., Lazanas M., Kordossis T., Andoniadou A., and Hatzakis A. Evaluation of the clinical sensitivity for the quantification of human immunodeficiency virus type 1 RNA in plasma: comparison of the new COBAS TaqMan HIV-1 with three current HIV-RNA assays - LCX HIV RNA quantitative, VERSANT HIV-1 RNA 3.0 (bDNA) and COBAS AMPLICOR HIV-1 Monitor v1.5. J. Virol. Methods 131 (2006) 168-174
18. Kievits T., van Gemen B., van Strijp D., Schukkink R., Dircks M., Adriaanse H., Malek L., Sooknanan R., and Lens P. NASBA isothermal enzymatic in vitro nucleic acid amplification optimized for the diagnosis of HIV-1 infection. J. Virol. Methods 35 (1991) 273-286
19. Lot F., Semaille C., Cazein F., Barin F., Pinget R., Pillonel J., and Desenclos J.C. Preliminary results from the new HIV surveillance system in France. Eurosurveillance 9 (2004) 34-37
20. Maljkovic I., Wilbe K., Sölver E., Alaeus A., and Leitner T. Limited transmission of drug-resistant HIV type 1 in 100 Swedish newly detected and drug-naïve patients infected with subtypes A, B, C, D, G, U and CRF01_AE. AIDS Res. Hum. Retrovir. 19 (2003) 989-997
21. + lymphocytes as prognostic markers of HIV-1 infection. Ann. Intern. Med. 126 (1997) 946-954
22. Michael N.L., Herman S.A., Kwok S., Dreyer K., Wang J., Christopherson C., Spadoro J.P., Young K.K.Y., Polonis V., McCutchan F.E., Carr J., Mascola J.R., Jagodzinski L.L., and Robb M.L. Development of calibrated viral load standards for group M subtypes of human immunodeficiency virus type 1 and performance of an improved AMPLICOR HIV-1 MONITOR test with isolates of diverse subtypes. J. Clin. Microbiol. 37 (1999) 2557-2563
23. Nye M.B., Leman A.R., Meyer M.E., Menegus M.A., and Rothberg P.G. Sequence diversity in the glycoprotein B gene complicates real-time PCR assays for detection and quantification of cytomegalovirus. J. Clin. Microbiol. 43 (2005) 4968-4971
24. Op de Coul E.L.M., Coutinho R.A., van der Schoot A., van Doornum G.J.J., Lukashov V.V., Goudsmit J., Cornelissen M., and for the Dutch HIV-1 subtype surveillance. The impact of immigration on env HIV-1 subtype distribution among heterosexuals in the Netherlands: influx of subtype B and non-B strains. AIDS 15 (2001) 2277-2286
25. Osmanov S., Pattou C., Walker N., Schwardländer B., Esparza J., and the WHO-UNAIDS Network for HIV Isolation and Characterization. Estimated global distribution and regional spread of HIV-1 genetic subtypes in the year 2000. J. Acq. Immune Defic. Syndr. 29 (2002) 184-190
26. Parry J.V., Murphy G., Barlow K.L., Lewis K., Rogers P.A., Belda F.J., Nicoll A., McGarrigle C., Cliffe S., Mortimer P.P., and Clewley J.P. National surveillance of HIV-1 subtypes for England and Wales: design, methods, and initial findings. J. Acq. Immune Defic. Syndr. 26 (2001) 381-388
27. Plantier J.-C., Gueudin M., Damond F., Braun J., Mauclère P., and Simon F. Plasma RNA quantification and HIV-1 divergent strains. J. Acq. Immune Defic. Syndr. 33 (2003) 1-7
28. Rouet F., Ekouevi D.K., Chaix M.-L., Burgard M., Inwoley A., Tony T.D., Danel C., Anglaret X., Leroy V., Msellati P., Dabis F., and Rouzioux C. Transfer and evaluation of an automated, low-cost real-time reverse transcription-PCR test for diagnosis and monitoring of human immunodeficiency virus type 1 infection in a Western African resource-limited setting. J. Clin. Microbiol. 43 (2005) 2709-2717
29. Sun R., Ku J., Jayakar H., Kuo J.-C., Brambilla D., Herman S., Rosenstraus M., and Spadoro J. Ultrasensitive reverse transcription-PCR assay for quantitation of human immunodeficiency virus type 1 RNA in plasma. J. Clin. Microbiol. 36 (1998) 2964-2969
30. Swanson P., Harris B.J., Holzmayer V., Devare S.G., Schochetman G., and Hackett Jr. J. Quantification of HIV-1 group M (subtypes A-G) and group O by the LCx HIV RNA Quantitative Assay. J. Virol. Methods 89 (2000) 97-108
31. Swanson P., Devare S.G., and Hackett Jr. J. Molecular characterization of 39 HIV-1 isolates representing group M (subtypes A-G) and group O: Sequence analysis of gag p24, pol integrase, and env gp41. AIDS Res. Hum. Retrovir. 19 (2003) 625-629
32. Swanson P., de Mendoza C., Joshi Y., Golden A., Hodinka R.L., Soriano V., Devare S.G., and Hackett Jr. J. Impact of human immunodeficiency virus type 1 (HIV-1) genetic diversity on performance of four commercial viral load assays: LCx HIV RNA Quantitative, AMPLICOR HIV-1 MONITOR v1.5, VERSANT HIV-1 RNA 3.0, and NucliSens HIV-1 QT. J. Clin. Microbiol. 43 (2005) 3860-3868
33. Swanson P., Huang S., Holzmayer V., Bodelle P., Yamaguchi J., Brennan C., Badaro R., Brites C., Abravaya K., Devare S.G., and Hackett Jr. J. Performance of the Automated Abbott RealTime™ HIV-1 Assay on a Genetically Diverse Panel of Specimens from Brazil. J. Virol. Methods 134 (2006) 237-243
34. Tatt I.D., Barlow K.L., Clewley J.P., Gill O.N., and Parry J.V. Surveillance of HIV-1 subtypes among heterosexuals in England and Wales, 1997-2000. J. Acq. Immune Defic. Syndr. 36 (2004) 1092-1099
35. ® HIV RNA quantitative assay - a new competitive reverse transcriptase-PCR which targets pol genomic region of HIV-1 for the measurement of type B, non-type B and group O HIV-1 RNA. Clin. Chem. Lab. Med. 40 (2002) 698-704
36. Whiley D.M., and Sloots T.P. Sequence variation in primer targets affects the accuracy of viral quantitative PCR. J. Clin. Virol. 34 (2005) 104-107
37. Wong M.L., and Medrano J.F. Real-time PCR for mRNA quantitation. BioTechniques 39 (2005) 75-85