Optimization of allele-specific PCR using patient-specific HIV consensus sequences for primer design

Journal of Virological Methods

Volumn 164, Issue 1-2, 2010, Pages 122-126

  Boltz, Valerie F ^a   Maldarelli, Frank ^a   Martinson, Neil ^b,d   Morris, Lynn ^c   McIntyre, James A ^b   Gray, Glenda ^b   Hopley, Mark J ^e   Kimura, Toshio ^e   Mayers, Douglas L ^f,g   Robinson, Patrick ^f   Mellors, John W ^h   Coffin, John M ^a,i   Palmer, Sarah E ^a,j  

^a NATIONAL CANCER INSTITUTE   (United States)

^b UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^c NATIONAL INSTITUTE FOR COMMUNICABLE DISEASES   (South Africa)

^d JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e BOEHRINGER INGELHEIM PHARMA GMBH AND CO KG   (Germany)

^f BOEHRINGER INGELHEIM PHARMACEUTICALS INC   (United States)

^g Idenix Pharmaceuticals Inc   (United States)

^h UNIVERSITY OF PITTSBURGH   (United States)

ⁱ TUFTS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^j KAROLINSKA INSTITUTE   (Sweden)

more..

Author keywords

Allele specific PCR; HIV 1; Low frequency variants; Patient specific HIV 1 consensus sequence; Subtype consensus sequence

Indexed keywords

ALLELE; ARTICLE; CONSENSUS SEQUENCE; GENE AMPLIFICATION; GENETIC ANALYSIS; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; NONHUMAN; PRIORITY JOURNAL; PROCESS OPTIMIZATION; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; VIRUS DETECTION;

ALLELES; CONSENSUS SEQUENCE; DNA PRIMERS; GENOTYPE; HIV INFECTIONS; HIV-1; HUMANS; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; RNA, VIRAL;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 77549086846     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2009.11.025     Document Type: Article

References (19)

1. Ambrose Z., Palmer S., Boltz V.F., Kearney M., Larsen K., Polacino P., Flanary L., Oswald K., Piatak Jr. M., Smedley J., Shao W., Bischofberger N., Maldarelli F., Kimata J.T., Mellors J.W., Hu S.L., Coffin J.M., Lifson J.D., and KewalRamani V.N. Suppression of viremia and evolution of human immunodeficiency virus type 1 drug resistance in a macaque model for antiretroviral therapy. J. Virol. 81 (2007) 12145-12155
2. Cha R.S., Zarbl H., Keohavong P., and Thilly W.G. Mismatch amplification mutation assay (MAMA): application to the c-H-ras gene. PCR Methods Appl. 2 (1992) 14-20
3. Coffin J.M. HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 267 (1995) 483-489
4. De Clercq E. HIV resistance to reverse transcriptase inhibitors. Biochem. Pharmacol. 47 (1994) 155-169
5. Deeks S.G. International perspectives on antiretroviral resistance. Nonnucleoside reverse transcriptase inhibitor resistance. J. Acquir. Immune Defic. Syndr. 26 Suppl 1 (2001) S25-S33
6. Halvas E.K., Weigand A., Boltz V.F., Kearney M., Nissley D., Wantman M., Hammer S.M., Palmer S.E., Vaida F., Coffin J.M., and Mellors J.W. Low frequency NNRTI-resistant variants contribute to failure of efavirenz-containing regimens in treatment-experienced patients. J. Infect. Dis. (2009)
7. Halvas E.K., Aldrovandi G.M., Balfe P., Beck I.A., Boltz V.F., Coffin J.M., Frenkel L.M., Hazelwood J.D., Johnson V.A., Kearney M., Kovacs A., Kuritzkes D.R., Metzner K.J., Nissley D.V., Nowicki M., Palmer S., Ziermann R., Zhao R.Y., Jennings C.L., Bremer J., Brambilla D., and Mellors J.W. Blinded, multicenter comparison of methods to detect a drug-resistant mutant of human immunodeficiency virus type 1 at low frequency. J. Clin. Microbiol. 44 (2006) 2612-2614
8. Hance A.J., Lemiale V., Izopet J., Lecossier D., Joly V., Massip P., Mammano F., Descamps D., Brun-Vezinet F., and Clavel F. Changes in human immunodeficiency virus type 1 populations after treatment interruption in patients failing antiretroviral therapy. J. Virol. 75 (2001) 6410-6417
9. Harrigan P.R., Mo T., Wynhoven B., Hirsch J., Brumme Z., McKenna P., Pattery T., Vingerhoets J., and Bacheler L.T. Rare mutations at codon 103 of HIV-1 reverse transcriptase can confer resistance to non-nucleoside reverse transcriptase inhibitors. Aids 19 (2005) 549-554
10. Johnson J.A., Li J.F., Morris L., Martinson N., Gray G., McIntyre J., and Heneine W. Emergence of drug-resistant HIV-1 after intrapartum administration of single-dose nevirapine is substantially underestimated. J. Infect. Dis. 192 (2005) 16-23
11. Kwok S., Kellogg D.E., McKinney N., Spasic D., Goda L., Levenson C., and Sninsky J.J. Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. Nucleic Acids Res. 18 (1990) 999-1005
12. Loubser S., Balfe P., Sherman G., Hammer S., Kuhn L., and Morris L. Decay of K103N mutants in cellular DNA and plasma RNA after single-dose nevirapine to reduce mother-to-child HIV transmission. Aids 20 (2006) 995-1002
13. Martinez-Picado J., and Martinez M. HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: a view from the clinic and ex vivo. Virus Res. (2008) 10.1016/j.virusres.2007.12.021
14. Metzner K.J., Bonhoeffer S., Fischer M., Karanicolas R., Allers K., Joos B., Weber R., Hirschel B., Kostrikis L.G., and Gunthard H.F. Emergence of minor populations of human immunodeficiency virus type 1 carrying the M184V and L90M mutations in subjects undergoing structured treatment interruptions. J. Infect. Dis. 188 (2003) 1433-1443
15. Palmer S., Boltz V., Maldarelli F., Kearney M., Halvas E.K., Rock D., Falloon J., Davey Jr. R.T., Dewar R.L., Metcalf J.A., Mellors J.W., and Coffin J.M. Selection and persistence of non-nucleoside reverse transcriptase inhibitor-resistant HIV-1 in patients starting and stopping non-nucleoside therapy. Aids 20 (2006) 701-710
16. Palmer S., Boltz V., Martinson N., Maldarelli F., Gray G., McIntyre J., Mellors J., Morris L., and Coffin J. Persistence of nevirapine-resistant HIV-1 in women after single-dose nevirapine therapy for prevention of maternal-to-fetal HIV-1 transmission. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 7094-7099
17. Palmer S., Boltz V., Maldarelli F., Martinson N., McIntyre J., Gray G., Hopley M., Hall D., Coffin J., and Mellors J. Addition of short-course combivir to single-dose nevirapine reduces the selection of NVP-resistant HIV-1 with infrequent emergence of 3TC-resistant variants. 14th Conference on Retroviruses and Opportunistic Infections (2007)
18. Rowley C.F., Boutwell C.L., Lockman S., and Essex M. Improvement in allele-specific PCR assay with the use of polymorphism-specific primers for the analysis of minor variant drug resistance in HIV-1 subtype C. J. Virol. Methods 149 (2008) 69-75
19. Wainberg M.A. HIV resistance to nevirapine and other non-nucleoside reverse transcriptase inhibitors. J. Acquir. Immune Defic. Syndr. 34 Suppl. 1 (2003) S2-S7