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Volumn 2015, Issue 99, 2015, Pages

Pairwise growth competition assay for determining the replication fitness of human immunodeficiency viruses

Author keywords

Fitness calculation; Growth competition; HIV 1; Immunology; Issue 99; Mutagenesis; Recombinant; Viral replication fitness

Indexed keywords

GAG PROTEIN; VIRUS DNA;

EID: 84941242961     PISSN: 1940087X     EISSN: None     Source Type: Journal    
DOI: 10.3791/52610     Document Type: Article
Times cited : (5)

References (38)
  • 1
    • 0030747157 scopus 로고    scopus 로고
    • RNA virus mutations and fitness for survival
    • Domingo, E., Holland, J. J. RNA virus mutations and fitness for survival. Annu Rev Microbiol. 51, 151-178 (1997).
    • (1997) Annu Rev Microbiol , vol.51 , pp. 151-178
    • Domingo, E.1    Holland, J.J.2
  • 2
    • 77957839777 scopus 로고    scopus 로고
    • Mechanisms of viral emergence
    • Domingo, E. Mechanisms of viral emergence. Veterinary research. 41, (6), 38 (2010).
    • (2010) Veterinary Research , vol.41 , Issue.6 , pp. 38
    • Domingo, E.1
  • 3
    • 43049095987 scopus 로고    scopus 로고
    • HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: A view from the clinic and ex vivo
    • Martinez-Picado, J., Martinez, M. A. HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: a view from the clinic and ex vivo. Virus Res. 134, (1-2), 104-123 (2008).
    • (2008) Virus Res , vol.134 , Issue.1-2 , pp. 104-123
    • Martinez-Picado, J.1    Martinez, M.A.2
  • 4
    • 84857959077 scopus 로고    scopus 로고
    • Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response
    • Troyer, R. M. Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response. PLoS Pathog. 5, (4), e1000365 (2009).
    • (2009) Plos Pathog , vol.5 , Issue.4
    • Troyer, R.M.1
  • 5
    • 77958587523 scopus 로고    scopus 로고
    • Amino-acid co-variation in HIV-1 Gag subtype C: HLA-mediated selection pressure and compensatory dynamics
    • Rolland, M. Amino-acid co-variation in HIV-1 Gag subtype C: HLA-mediated selection pressure and compensatory dynamics. PLoS One. 5, (9), e12463 (2010).
    • (2010) Plos One , vol.5 , Issue.9
    • Rolland, M.1
  • 6
    • 66149154716 scopus 로고    scopus 로고
    • CCR5- and CXCR4-tropic subtype C human immunodeficiency virus type 1 isolates have a lower level of pathogenic fitness than other dominant group M subtypes: Implications for the epidemic
    • Abraha, A. CCR5- and CXCR4-tropic subtype C human immunodeficiency virus type 1 isolates have a lower level of pathogenic fitness than other dominant group M subtypes: implications for the epidemic. J Virol. 83, (11), 5592-5605 (2009).
    • (2009) J Virol , vol.83 , Issue.11 , pp. 5592-5605
    • Abraha, A.1
  • 7
    • 0033803642 scopus 로고    scopus 로고
    • A dual infection/competition assay shows a correlation between ex vivo human immunodeficiency virus type 1 fitness and disease progression
    • Quinones-Mateu, M. E. A dual infection/competition assay shows a correlation between ex vivo human immunodeficiency virus type 1 fitness and disease progression. J Virol. 74, (19), 9222-9233 (2000).
    • (2000) J Virol , vol.74 , Issue.19 , pp. 9222-9233
    • Quinones-Mateu, M.E.1
  • 8
    • 0037223706 scopus 로고    scopus 로고
    • Comparing the ex vivo fitness of CCR5-tropic human immunodeficiency virus type 1 isolates of subtypes. B and C
    • Ball, S. C. Comparing the ex vivo fitness of CCR5-tropic human immunodeficiency virus type 1 isolates of subtypes. B and C. J Virol. 77, (2), 1021-1038 (2003).
    • (2003) J Virol , vol.77 , Issue.2 , pp. 1021-1038
    • Ball, S.C.1
  • 9
    • 84883251274 scopus 로고    scopus 로고
    • Factors affecting relative fitness measurements in pairwise competition assays of human immunodeficiency viruses
    • Lanxon-Cookson, E. C. Factors affecting relative fitness measurements in pairwise competition assays of human immunodeficiency viruses. J Virol Methods. 194, (1-2), 7-13 (2013).
    • (2013) J Virol Methods , vol.194 , Issue.1-2 , pp. 7-13
    • Lanxon-Cookson, E.C.1
  • 10
    • 19244372885 scopus 로고    scopus 로고
    • Transmitted human immunodeficiency virus type 1 carrying the D67N or K219Q/E mutation evolves rapidly to zidovudine resistance in vitro and shows a high replicative fitness in the presence of zidovudine
    • Garcia-Lerma, J. G., MacInnes, H., Bennett, D., Weinstock, H., Heneine, W. Transmitted human immunodeficiency virus type 1 carrying the D67N or K219Q/E mutation evolves rapidly to zidovudine resistance in vitro and shows a high replicative fitness in the presence of zidovudine. J Virol. 78, (14), 7545-7552 (2004).
    • (2004) J Virol , vol.78 , Issue.14 , pp. 7545-7552
    • Garcia-Lerma, J.G.1    Macinnes, H.2    Bennett, D.3    Weinstock, H.4    Heneine, W.5
  • 11
    • 0030768138 scopus 로고    scopus 로고
    • Attenuated replication of human immunodeficiency virus type 1 with a didanosine-selected reverse transcriptase mutation
    • Sharma, P. L., Crumpacker, C. S. Attenuated replication of human immunodeficiency virus type 1 with a didanosine-selected reverse transcriptase mutation. J Virol. 71, (11), 8846-8851 (1997).
    • (1997) J Virol , vol.71 , Issue.11 , pp. 8846-8851
    • Sharma, P.L.1    Crumpacker, C.S.2
  • 12
    • 0032928065 scopus 로고    scopus 로고
    • Replicative fitness of protease inhibitor-resistant mutants of human immunodeficiency virus type 1
    • Martinez-Picado, J., Savara, A. V., Sutton, L., D'Aquila, R. T. Replicative fitness of protease inhibitor-resistant mutants of human immunodeficiency virus type 1. J Virol. 73, (5), 3744-3752 (1999).
    • (1999) J Virol , vol.73 , Issue.5 , pp. 3744-3752
    • Martinez-Picado, J.1    Savara, A.V.2    Sutton, L.3    D'aquila, R.T.4
  • 13
    • 33646237789 scopus 로고    scopus 로고
    • The HIV-1 reverse transcriptase mutants G190S and G190A, which confer resistance to non-nucleoside reverse transcriptase inhibitors, demonstrate reductions in RNase H activity and DNA synthesis from tRNA(Lys, 3) that correlate with reductions in replication efficiency
    • Wang, J. The HIV-1 reverse transcriptase mutants G190S and G190A, which confer resistance to non-nucleoside reverse transcriptase inhibitors, demonstrate reductions in RNase H activity and DNA synthesis from tRNA(Lys, 3) that correlate with reductions in replication efficiency. Virology. 348, (2), 462-474 (2006).
    • (2006) Virology , vol.348 , Issue.2 , pp. 462-474
    • Wang, J.1
  • 14
    • 84867897064 scopus 로고    scopus 로고
    • Impact of immune escape mutations on HIV-1 fitness in the context of the cognate transmitted/founder genome
    • Song, H. Impact of immune escape mutations on HIV-1 fitness in the context of the cognate transmitted/founder genome. Retrovirology. 9, (89), (2012).
    • (2012) Retrovirology , vol.9 , Issue.89
    • Song, H.1
  • 15
    • 33644926105 scopus 로고    scopus 로고
    • A novel small reporter gene and HIV-1 fitness assay
    • Ali, A., Yang, O. A novel small reporter gene and HIV-1 fitness assay. Journal of Virological Methods. 133, (1), 41-47 (2006).
    • (2006) Journal of Virological Methods , vol.133 , Issue.1 , pp. 41-47
    • Ali, A.1    Yang, O.2
  • 16
    • 33645319712 scopus 로고    scopus 로고
    • A novel real-time PCR assay to determine relative replication capacity for HIV-1 protease variants and/or reverse transcriptase variants
    • Maarseveen, N. M. A novel real-time PCR assay to determine relative replication capacity for HIV-1 protease variants and/or reverse transcriptase variants. J Virol Methods. 133, (2), 185-194 (2006).
    • (2006) J Virol Methods , vol.133 , Issue.2 , pp. 185-194
    • Maarseveen, N.M.1
  • 17
    • 36049027844 scopus 로고    scopus 로고
    • Evolution of human immunodeficiency virus type 1 cytotoxic T-lymphocyte epitopes: Fitness-balanced escape
    • Liu, Y. Evolution of human immunodeficiency virus type 1 cytotoxic T-lymphocyte epitopes: fitness-balanced escape. J Virol. 81, (22), 12179-12188 (2007).
    • (2007) J Virol , vol.81 , Issue.22 , pp. 12179-12188
    • Liu, Y.1
  • 18
    • 65249151382 scopus 로고    scopus 로고
    • Resistance to CCR5 inhibitors caused by sequence changes in the fusion peptide of HIV-1 gp 41
    • Anastassopoulou, C. G., Ketas, T. J., Klasse, P. J., Moore, J. P. Resistance to CCR5 inhibitors caused by sequence changes in the fusion peptide of HIV-1 gp 41. Proc Natl Acad Sci U S A. 106, (13), 5318-5323 (2009).
    • (2009) Proc Natl Acad Sci U S A , vol.106 , Issue.13 , pp. 5318-5323
    • Anastassopoulou, C.G.1    Ketas, T.J.2    Klasse, P.J.3    Moore, J.P.4
  • 20
    • 84875544727 scopus 로고    scopus 로고
    • A sensitive real-time PCR based assay to estimate the impact of amino acid substitutions on the competitive replication fitness of human immunodeficiency virus type 1 in cell culture
    • Liu, Y. A sensitive real-time PCR based assay to estimate the impact of amino acid substitutions on the competitive replication fitness of human immunodeficiency virus type 1 in cell culture. J Virol Methods. 189, (1), 157-166 (2013).
    • (2013) J Virol Methods , vol.189 , Issue.1 , pp. 157-166
    • Liu, Y.1
  • 21
    • 78751640260 scopus 로고    scopus 로고
    • Reduced replication capacity of NL4-3 recombinant viruses encoding reverse transcriptase-integrase sequences from HIV-1 elite controllers
    • Brumme, Z. L. Reduced replication capacity of NL4-3 recombinant viruses encoding reverse transcriptase-integrase sequences from HIV-1 elite controllers. J Acquir Immune Defic Syndr. 56, (2), 100-108 (2011).
    • (2011) J Acquir Immune Defic Syndr , vol.56 , Issue.2 , pp. 100-108
    • Brumme, Z.L.1
  • 22
    • 84873042035 scopus 로고    scopus 로고
    • Significant reductions in Gag-protease-mediated HIV-1 replication capacity during the course of the epidemic in. Japan
    • Nomura, S. Significant reductions in Gag-protease-mediated HIV-1 replication capacity during the course of the epidemic in. Japan. J Virol. 87, (3), 1465-1476 (2013).
    • (2013) J Virol , vol.87 , Issue.3 , pp. 1465-1476
    • Nomura, S.1
  • 23
    • 84877321863 scopus 로고    scopus 로고
    • HIV-1 conserved-element vaccines: Relationship between sequence conservation and replicative capacity
    • Rolland, M. HIV-1 conserved-element vaccines: relationship between sequence conservation and replicative capacity. J Virol. 87, (10), 5461-5467 (2013).
    • (2013) J Virol , vol.87 , Issue.10 , pp. 5461-5467
    • Rolland, M.1
  • 24
    • 33645240933 scopus 로고    scopus 로고
    • Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1
    • Martinez-Picado, J. Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1. J Virol. 80, (7), 3617-3623 (2006).
    • (2006) J Virol , vol.80 , Issue.7 , pp. 3617-3623
    • Martinez-Picado, J.1
  • 25
    • 36048995423 scopus 로고    scopus 로고
    • Escape and Compensation from Early HLA-B57-Mediated Cytotoxic T-Lymphocyte Pressure on Human Immunodeficiency Virus Type 1 Gag Alter Capsid Interactions with Cyclophilin A
    • Brockman, M. A. Escape and Compensation from Early HLA-B57-Mediated Cytotoxic T-Lymphocyte Pressure on Human Immunodeficiency Virus Type 1 Gag Alter Capsid Interactions with Cyclophilin A. J Virol. 81, (22), 12608-12618 (2007).
    • (2007) J Virol , vol.81 , Issue.22 , pp. 12608-12618
    • Brockman, M.A.1
  • 26
    • 58149398654 scopus 로고    scopus 로고
    • HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1
    • Miura, T. HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1. J Virol. 83, (1), 140-149 (2009).
    • (2009) J Virol , vol.83 , Issue.1 , pp. 140-149
    • Miura, T.1
  • 27
    • 84941227881 scopus 로고    scopus 로고
    • Basic Methods in Cellular and Molecular Biology
    • JoVE Cambridge, MA
    • Basic Methods in Cellular and Molecular Biology, PCR: The Polymerase Chain Reaction. JoVE Cambridge, MA Available from: http://www.jove.com/science-education/5056/pcr-the-polymerase-chain-reaction (2014).
    • (2014) PCR: The Polymerase Chain Reaction
  • 29
    • 85000635686 scopus 로고    scopus 로고
    • Basic Methods in Cellular and Molecular Biology
    • JoVE Cambridge, MA
    • Basic Methods in Cellular and Molecular Biology, Restriction Enzyme Digests. JoVE Cambridge, MA Available from: http://www.jove.com/science-education/5070/restriction-enzyme-digests (2014).
    • (2014) Restriction Enzyme Digests
  • 30
    • 33847254313 scopus 로고    scopus 로고
    • Granulocyte-monocyte colony-stimulating factor upregulates HIV-1 replication in monocyte-derived macrophages cultured at low density
    • McClure, J., van't Wout, A. B., Tran, T., Mittler, J. E. Granulocyte-monocyte colony-stimulating factor upregulates HIV-1 replication in monocyte-derived macrophages cultured at low density. J Acquir Immune Defic Syndr. 44, (3), 254-261 (2007).
    • (2007) J Acquir Immune Defic Syndr , vol.44 , Issue.3 , pp. 254-261
    • McClure, J.1    Van't Wout, A.B.2    Tran, T.3    Mittler, J.E.4
  • 31
    • 33745158157 scopus 로고
    • A simple method of estimatingfifty percent endpoints
    • Reed, L. J., Muench, H. A simple method of estimatingfifty percent endpoints. Am J Hyg. 27, (3), 493-497 (1938).
    • (1938) Am J Hyg , vol.27 , Issue.3 , pp. 493-497
    • Reed, L.J.1    Muench, H.2
  • 32
    • 0037423791 scopus 로고    scopus 로고
    • Consensus and ancestral state HIV vaccines
    • Nickle, D. C. Consensus and ancestral state HIV vaccines. Science. 299, (5612), 1515-1518 (2003).
    • (2003) Science , vol.299 , Issue.5612 , pp. 1515-1518
    • Nickle, D.C.1
  • 33
    • 34547811379 scopus 로고    scopus 로고
    • Reconstruction and function of ancestral center-of-tree human immunodeficiency virus type 1 proteins
    • Rolland, M. Reconstruction and function of ancestral center-of-tree human immunodeficiency virus type 1 proteins. J Virol. 81, (16), 8507-8514 (2007).
    • (2007) J Virol , vol.81 , Issue.16 , pp. 8507-8514
    • Rolland, M.1
  • 34
    • 77954129578 scopus 로고    scopus 로고
    • Overlap extension PCR cloning: A simple and reliable way to create recombinant plasmids
    • Bryksin, A. V., Matsumura, I. Overlap extension PCR cloning: a simple and reliable way to create recombinant plasmids. Biotechniques. 48, (6), 463-465 (2010).
    • (2010) Biotechniques , vol.48 , Issue.6 , pp. 463-465
    • Bryksin, A.V.1    Matsumura, I.2
  • 35
    • 0028908784 scopus 로고
    • Effect of different donor cells on human immunodeficiency virus type 1 replication and selection in vitro
    • Spira, A. I., Ho, D. D. Effect of different donor cells on human immunodeficiency virus type 1 replication and selection in vitro. J. Virol. 69, (1), 422-429 (1995).
    • (1995) J. Virol. , vol.69 , Issue.1 , pp. 422-429
    • Spira, A.I.1    Ho, D.D.2
  • 37
    • 0031687519 scopus 로고    scopus 로고
    • Peak height pattern in dichloro-rhodamine and energy transfer dye terminator sequencing
    • Zakeri, H., Amparo, G., Chen, S. M., Spurgeon, S., Kwok, P. Y. Peak height pattern in dichloro-rhodamine and energy transfer dye terminator sequencing. Biotechniques. 25, (3), 406-410 (1998).
    • (1998) Biotechniques , vol.25 , Issue.3 , pp. 406-410
    • Zakeri, H.1    Amparo, G.2    Chen, S.M.3    Spurgeon, S.4    Kwok, P.Y.5
  • 38
    • 34548076341 scopus 로고    scopus 로고
    • Sensitive oligonucleotide ligation assay for low-level detection of nevirapine resistance mutations in human immunodeficiency virus type 1 quasispecies
    • Lalonde, M. S. Sensitive oligonucleotide ligation assay for low-level detection of nevirapine resistance mutations in human immunodeficiency virus type 1 quasispecies. J Clin Microbiol. 45, (8), 2604-2615 (2007).
    • (2007) J Clin Microbiol , vol.45 , Issue.8 , pp. 2604-2615
    • Lalonde, M.S.1


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