For in vitro diagnostic use. Others cobas MPX IVD cobas® MPX RMD-6800-8800-MPX-001 Multiplex HIV, HCV & HBV nucleic acid test for use on the cobas® 6800/8800 systems 06 997 708 190 6 997 708 190 06997708190 6997708190 06997708190 KIT COBAS 6800/8800 MPX 96T CE-IVD cobas MPX 00875197004618 Reagents, kits 1 kit 96 tests true cobas® MPX, for use on cobas® 6800 and cobas® 8800 Systems, is a qualitative in vitro nucleic acid test for the direct detection of Human Immunodeficiency Virus Type 1 (HIV-1) Group M RNA, HIV-1 Group O RNA, Human Immunodeficiency Virus Type 2 (HIV-2) RNA, Hepatitis C Virus (HCV) RNA, and Hepatitis B Virus (HBV) DNA in human plasma and serum. The cobas® MPX test simultaneously detects and discriminates for HIV, HCV, and HBV. The assay does not discriminate between HIV-1 Group M, HIV-1 Group O, and HIV-2.This test is intended for use to screen donor samples for HIV-1 Group M RNA, HCV RNA, and HBV DNA in plasma and serum samples from individual human donors, including donors of Whole Blood, blood components, Source Plasma and other living donors. This test is also intended for use to screen organ and tissue donors when donor samples are obtained while the donor's heart is still beating or from cadaveric (non-heart beating) donors. Plasma and serum from all donors may be screened as individual samples. For donations of whole blood and blood components, plasma and serum samples may be tested individually or plasma may be tested in pools comprised of not more than six individual samples. For donors of hematopoietic stem/progenitor cells (HPCs) sourced from bone marrow, peripheral blood or cord blood, and for donors of donor lymphocytes for infusion (DLI), plasma may be tested in pools comprised of not more than six individual samples. For donations of source plasma, samples may be tested in pools comprised of not more than 96 individual samples. For all other donors, samples may only be screened as individual samples.This test is intended to be used in conjunction with licensed serology tests for HIV-1, HCV, and HBV.This test is not intended for use as an aid in diagnosis of HIV, HCV, or HBV.This test is not intended for use on samples of cord blood.cobas® MPX can be considered a supplemental test that confirms HIV infection for specimens that are repeatedly reactive on a licensed donor screening test for antibodies to HIV and reactive for HIV on the cobas® MPX test.cobas® MPX can be considered a supplemental test that confirms HCV infection for specimens that are repeatedly reactive on a licensed donor screening test for antibodies to HCV and reactive for HCV on the cobas® MPX test.cobas® MPX can be considered a supplemental test that confirms HBV infection for specimens that are repeatedly reactive on a licensed donor screening test for Hepatitis B surface antigen, and reactive for HBV on the cobas® MPX test. en The cobas® MPX test, for use on cobas® 6800 and cobas® 8800 Systems is a qualitative in vitro test for the direct detection of Human Immunodeficiency Virus Type 1 (HIV-1) Group M RNA, HIV-1 Group O RNA, Human Immunodeficiency Virus Type 2 (HIV-2) RNA, Hepatitis C Virus (HCV) RNA, and Hepatitis B Virus (HBV) DNA in human plasma and serum.This test is intended for use to screen donor samples for HIV-1 Group M RNA, HIV-1 Group O RNA, HIV-2 RNA, HCV RNA, and HBV DNA in plasma and serum samples from individual human donors, including donors of whole blood, blood components, and other living donors. This test is also intended for use to screen organ and tissue donors when donor samples are obtained while the donor's heart is still beating and in testing of cadaveric (non-heart beating) donors. Plasma and serum from all donors may be screened as individual samples. For donations of whole blood and blood components, plasma and serum samples may be tested individually or plasma may be tested in pools comprised of aliquots of individual samples. For donations from cadaveric (non-heart beating) organ and tissue donors, samples may only be screened as individual sample.For an individual sample, results are simultaneously detected and discriminated for HIV, HCV, and HBV.The cobas® MPX test can be considered a supplemental test that confirms HIV infection for samples that are repeatedly reactive on a CE-IVD test for antibodies to HIV and reactive on the cobas® MPX test.The cobas® MPX test can be considered a supplemental test that confirms HCV infection for samples that are repeatedly reactive on a CE-IVD test for antibodies to HCV and reactive on the cobas® MPX test.The cobas® MPX test can be considered a supplemental test that confirms HBV infection for samples that are repeatedly reactive on a CE-IVD test for Hepatitis B surface antigen and reactive on the cobas® MPX test.This test is not intended for use as an aid in diagnosis of infection with HIV, HCV, or HBV. en cobas® MPX, for use on cobas® 6800 and cobas® 8800 Systems is a qualitative in vitro nucleic acid screening test for the direct detection of Human Immunodeficiency Virus Type 1 (HIV-1) Group M RNA, HIV-1 Group O RNA, Human Immunodeficiency Virus Type 2 (HIV-2) RNA, Hepatitis C Virus (HCV) RNA, and Hepatitis B Virus (HBV) DNA in human plasma and serum.This test is intended for use to screen do nor samples for HIV-1 Group M RNA, HIV-1 Group O RNA, HIV-2 RNA, HCV RNA, and HBV DNA in plasma and serum samples from individual human donors, including donors of whole blood, blood components, source plasma and other living donors. This test is also inte nded for use to screen organ and tissue donors when donor samples are obtained while the donor's heart is still beating and in testing of cadaveric (non -heart beating) donors. Plasma and serum from all donors may be screened as individual samples. For dona tions of whole blood and blood components, plasma and serum samples may be tested individually or plasma may be tested in pools comprised of not more than six individual samples. For donors of hematopoietic stem/progenitor cells (HPCs) sourced from bone marrow, peripheral blood or cord blood, and for donors of donor lymphocytes for infusion (DLI), plasma may be tested in pools comprised of not more than six individual samples. For donations of source plasma, samples may be tested in pools comprised of not more than 96 individual samples. For donations from cadaveric (non-heart beating) organ and tissue donors, samples may only be screened as individual sample.This test is intended to be used in conjunction with licensed serology tests for HIV, HCV, and HBV.For an individual sample, results are simultaneously detecte d and discriminated for HIV, HCV, and HBV.cobas® MPX can be considered a supplemental test that confirms HIV-1 infection for s amples that are repeatedly reactive on a licensed donor screening test for antibodies to HIV-1 and reactive for HIV on cobas® MPX. cobas® MPX is not intended to be used as a supplement test to confirm HIV -2 infection.cobas® MPX can be considered a supplemental test that confirms HCV infection for samples that are repeatedly reactive on a licensed donor screening test for antibodies to HCV and reactive for HCV on cobas® MPX.cobas® MPX can be considered a supplemental test that confirms HBV infection for samples that are repeatedly reactive on a licensed donor screening test for Hepatitis B surface antigen and reactive for HBV on cobas® MPX.This test is not intended for use as an aid in diagnosis of HIV, HCV, or HBV.This test is not intended for use on samples of cord blood. en The cobas® MPX test, for use on cobas® 6800 and cobas® 8800 Systems, is a qualitative in vitro test for the direct detection of Human Immunodeficiency Virus Type 1 (HIV-1) Group M RNA, HIV-1 Group O RNA, Human Immunodeficiency Virus Type 2 (HIV-2) RNA, Hepatitis C Virus (HCV) RNA, and Hepatitis B Virus (HBV) DNA in human plasma and serum. The cobas® MPX test simultaneously detects and discriminates for HIV, HCV, and HBV. The assay does not discriminate between HIV-1 Group M, HIV-1 Group O, and HIV-2.This test is intended for use to screen donor samples for HIV-1 Group M RNA, HIV-1 Group O RNA, HIV-2 RNA, HCV RNA, and HBV DNA in plasma and serum samples from individual human donors, including donors of whole blood, blood components, source plasma and other living donors. This test is also intended for use to screen organ and tissue donors when donor samples are obtained while the donor's heart is still beating and in testing of cadaveric (non- heart beating) donors. For donations of whole blood and blood components, plasma and serum samples are tested individually. For donations from cadaveric (non-heart beating) organ and tissue donors, samples are tested individually. For donations of source plasma, samples may be tested in pools comprised of aliquots of no more than 96 individual samples when the source plasma is intended for further manufacture into plasma derived products that undergo pathogen inactivation and/or removal procedures. The individual source plasma is collected from donors of plasma fractionation which is further manufactured into plasma-derived products which include viral inactivation and removal procedures only. This test is intended to be used in conjunction with licensed serology tests for HIV, HCV, and HBV.For an individual sample, results are simultaneously detected and discriminated for HIV, HCV, and HBV.The cobas® MPX test can be considered a supplemental test that confirms HIV infection for samples that are repeatedly reactive on a licensed donor screening test for antibodies to HIV and reactive on the cobas® MPX test.The cobas® MPX test can be considered a supplemental test that confirms HCV infection for samples that are repeatedly reactive on a licensed donor screening test for antibodies to HCV and reactive on the cobas® MPX test.The cobas® MPX test can be considered a supplemental test that confirms HBV infection for samples that are repeatedly reactive on a licensed donor screening test for Hepatitis B surface antigen and reactive on the cobas® MPX test.This test is not intended for use as an aid in diagnosis of infection with HIV, HCV, or HBV. en cobas® MPX for use on the cobas® 6800, cobas® 8800 and cobas® 5800 Systems is an in vitro test for the direct qualitative detection of human immunodeficiency virus type 1 (HIV-1) group M RNA, HIV-1 group O RNA, human immunodeficiency virus type 2 (HIV-2) RNA, hepatitis C virus (HCV) RNA and hepatitis B virus (HBV) DNA in human plasma or serum. cobas® MPX simultaneously detects and discriminates between HIV, HCV and HBV infections but is unable to discriminate between HIV-1 group M, HIV-1 group O and HIV-2.This test is mainly used to screen for HIV-1 group M RNA, HCV RNA and HBV DNA in plasma and serum samples from blood donors, including donors of whole blood, blood components and plasma as well as donors of living organs and tissues. For whole blood and all blood components that are donated, plasma and serum samples can be tested individually, or in the case of plasma, samples can be tested in pools of up to 6. For donors of hematopoietic stem/progenitor cells (HPC) from bone marrow, peripheral or cord blood, and for donors of lymphocytes for infusion (DLI), plasma can be tested in pools of up to 6 samples. For donated source plasma, samples can be tested in pools of up to 96. For all other donors, samples can only be screened individually.This test can be used in conjunction with approved serological detection reagents for HIV-1, HCV and HBV.This test may not be used as an aid in the diagnosis of HIV, HCV or HBV.This test may not be used to test samples of cord blood.For samples that get repeatedly reactive results in a confirmed HIV antibody test and HIV-reactive results in a cobas® MPX test, the cobas® MPX test can serve as a supplemental test to confirm HIV infection.For samples that get repeatedly reactive results in a certified HCV antibody test and HCV-reactive results in a cobas® MPX test, the cobas® MPX test can serve as a supplemental test to confirm HCV infection.For samples that get repeatedly reactive results in a certified HBV surface antigen test and HBV-reactive results in a cobas® MPX test, the cobas® MPX test can serve as a supplemental test to confirm HBV infection. en cobas® MPX is based on real time PCR technology on a fully automated sample preparation (nucleic acid extraction and purification) followed by PCR amplification and detection system. The cobas® 6800/8800 Systems consists of the sample supply module, the transfer module, the processing module, and the analytic module. Automated data management is performed by the cobas® 6800/8800 software which assigns test results for all tests as non-reactive, reactive, or invalid. Results can be reviewed directly on the system screen, and printed as a report, or sent to a Laboratory Information Management System (LIMS) or other result management system.Samples can either be tested individually or, optionally, can be tested in pools consisting of multiple samples. The cobas p 680 instrument, or cobas® Synergy software with the Hamilton MICROLAB® STAR IVD (cobas® Synergy Core), may optionally be used in a pre-analytical step if pooling is to be performed.Nucleic acid from the sample and added armored RNA internal control (IC) (which serve as the sample preparation and amplification/detection process control) is simultaneously extracted. In addition the test utilizes four kit controls: three positive and a negative control. Viral nucleic acid is released by addition of proteinase and lysis reagent to the sample. The released nucleic acid binds to the silica surface of the added magnetic glass particles. Unbound substances and impurities, such as denatured protein, cellular debris, and potential PCR inhibitors (such as hemoglobin) are removed with subsequent wash reagent steps and purified nucleic acid is eluted from the magnetic glass particles with elution buffer at elevated temperature.Selective amplification of target nucleic acid from the donor sample is achieved by the use of virus-specific forward and reverse primers which are selected from highly conserved regions of the viral nucleic acid. A thermostable DNA polymerase enzyme is used for both reverse-transcription and amplification. The master mix includes deoxyuridine triphosphate (dUTP), instead of deoxythimidine triphosphate (dTTP), which is incorporated into the newly synthesized DNA (amplicon).33-35 Any contaminating amplicon from previous PCR runs are eliminated by the AmpErase enzyme [uracil-N-glycosylase], which is included in the PCR master mix, when heated in the first thermal cycling step. However, newly formed amplicon are not eliminated since the AmpErase enzyme is inactivated once exposed to temperatures above 55°C.The cobas® MPX master mix contains detection probes which are specific for HIV-1 (Groups M and O), HIV-2, HCV, HBV, and IC nucleic acid. The specific HIV, HCV, HBV, and IC detection probes are each labeled with one of four unique fluorescent dyes which act as a reporter. Each probe also has a fifth dye which acts as a quencher. The four reporter dyes are measured at defined wavelengths, thus permitting simultaneous detection and discrimination of the amplified HIV, HCV, and HBV targets and the IC.36,37 When not bound to the target sequence, the fluorescent signal of the intact probes is suppressed by the quencher dye. During the PCR amplification step, hybridization of the probes to the specific singlestranded DNA template results in cleavage by the 5' to 3' nuclease activity of the DNA polymerase resulting in separation of the reporter and quencher dyes and the generation of a fluorescent signal. With each PCR cycle, increasing amounts of cleaved probes are generated and the cumulative signal of the reporter dye is concomitantly increased. Since the four specific reporter dyes are measured at defined wavelengths, simultaneous detection and discrimination of the amplified HIV, HCV and HBV targets and the IC are possible.33. Longo MC, Berninger MS, Hartley JL. Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. Gene. 1990; 93:125-128.34. Savva R, McAuley-Hecht K, Brown T, Pearl L. The structural basis of specific base-excision repair by uracil-DNA glycosylase. Nature. 1995; 373:487-493.35. Mol CD, Arvai AS, Slupphaug G, et al. Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis. Cell. 1995;80:869-878.36. Higuchi R, Dollinger G, Walsh PS, Griffith R. Simultaneous amplification and detection of specific DNA sequences. Biotechnology (NY). 1992;10:413-417.37. Heid CA, Stevens J, Livak JK, Williams PM. Real time quantitative PCR. Genome Res. 1996;6:986-994. en The cobas® MPX test is based on real time PCR technology on a fully automated sample preparation (nucleic acid extraction and purification) followed by PCR amplification and detection system. The cobas® 6800/8800 Systems consists of the sample supply module, the transfer module, the processing module, and the analytic module. Automated data management is performed by the cobas® 6800/8800 software which assigns test results for all tests as non-reactive, reactive, or invalid. Results can be reviewed directly on the system screen, and printed as a report, or sent to a Laboratory Information Management System (LIMS) or other result management system.Samples can either be tested individually or, optionally, can be tested in pools consisting of multiple samples. The cobas p 680 instrument, or cobas® Synergy software with the Hamilton MICROLAB® STAR IVD (cobas® Synergy Core), may optionally be used in a pre-analytical step if pooling is to be performed.Nucleic acid from the sample and added armored RNA internal control (IC) molecules (which serve as the sample preparation and amplification/detection process control) is simultaneously extracted. In addition the test utilizes four external controls: three positive and a negative control. Viral nucleic acid is released by addition of proteinase and lysis reagent to the sample. The released nucleic acid binds to the silica surface of the added magnetic glass particles. Unbound substances and impurities, such as denatured protein, cellular debris, and potential PCR inhibitors (such as hemoglobin) are removed with subsequent wash reagent steps and purified nucleic acid is eluted from the magnetic glass particles with elution buffer at elevated temperature.Selective amplification of target nucleic acid from the donor sample is achieved by the use of virus-specific forward and reverse primers which are selected from highly conserved regions of the viral nucleic acid. A thermostable DNA polymerase enzyme is used for both reverse-transcription and amplification. The master mix includes deoxyuridine triphosphate (dUTP), instead of deoxythimidine triphosphate (dTTP), which is incorporated into the newly synthesized DNA (amplicon).32-34 Any contaminating amplicons from previous PCR runs are eliminated by the AmpErase enzyme [uracil-N-glycosylase], which is included in the PCR master mix, when heated in the first thermal cycling step. However, newly formed amplicons are not eliminated since the AmpErase enzyme is inactivated once exposed to temperatures above 55°C.The cobas® MPX master mix contains detection probes which are specific for HIV-1 (Groups M and O), HIV-2, HCV, HBV, and IC nucleic acid. The specific HIV, HCV, HBV, and IC detection probes are each labeled with one of four unique fluorescent dyes which act as a reporter. Each probe also has a fifth dye which acts as a quencher. The four reporter dyes are measured at defined wavelengths, thus permitting simultaneous detection and discrimination of the amplified HIV, HCV, and HBV targets and the IC.35,36 When not bound to the target sequence, the fluorescent signal of the intact probes is suppressed by the quencher dye. During the PCR amplification step, hybridization of the probes to the specific single-stranded DNA template results in cleavage by the 5' to 3' nuclease activity of the DNA polymerase resulting in separation of the reporter and quencher dyes and the generation of a fluorescent signal. With each PCR cycle, increasing amounts of cleaved probes are generated and the cumulative signal of the reporter dye is concomitantly increased. Since the four specific reporter dyes are measured at defined wavelengths, simultaneous detection and discrimination of the amplified HIV, HCV and HBV targets and the IC are possible.32. Longo MC, Berninger MS, Hartley JL. Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. Gene. 1990; 93:125-128.33. Savva R, McAuley-Hecht K, Brown T, Pearl L. The structural basis of specific base-excision repair by uracil-DNA glycosylase. Nature. 1995; 373:487-493.34. Mol CD, Arvai AS, Slupphaug G, et al. Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis. Cell. 1995;80:869-878.35. Higuchi R, Dollinger G, Walsh PS, Griffith R. Simultaneous amplification and detection of specific DNA sequences. Biotechnology (NY). 1992;10:413-417.36. Heid CA, Stevens J, Livak JK, Williams PM. Real time quantitative PCR. Genome Res. 1996;6:986-994. en cobas® MPX is based on real time PCR technology on a fully automated sample preparation (nucleic acid extraction and purification) followed by PCR amplification and detection system. The cobas® 6800/8800 Systems consist of the sample supply module, the transfer module, the processing module, and the analytic module. Automated data management is performed by the cobas® 6800/8800 software which assigns test results for all tests as non-reactive, reactive, or invalid. Results can be reviewed directly on the system screen, and printed as a report , or sent to a Laboratory Information Management System (LIMS) or other result management system.Samples can either be tested individually or, optionally, can be tested in pools consisting of multiple samples. The cobas p 680 instrument may optionally be used in a pre -analytical step if pooling is to be performed.Nucleic acid from the sample and added armored RNA internal control (IC) molecules (which serve as the sample preparation and amplification/detection process control) is simultaneously extracted. In addition the test utilizes four external controls: three positive and a negative control. Viral nucleic acid is released by addition of proteinase and lysis reagent to the sample. The released nucleic acid binds to the silica surface of the added magnetic glass particles. Unbound substances and impurities, such as denatured prot ein, cellular debris, and potential PCR inhibitors (such as hemoglobin) are removed with subsequent wash reagent steps and purified nucleic acid is eluted from the magnetic glass particles with elution buffer at elevated temperature.Selective amplification of target nucleic acid from the donor sample is achieved by the use of virus-specific forward and reverse primers which are selected from highly conserved regions of the viral nucleic acid. A thermostable DNA polymerase enzyme is used for both reverse-transcription and amplification. The master mix includes deoxyuridine triphosphate (dUTP), instead of deoxythimidine triphosphate (dTTP), which is incorporated into the newly synthesized DNA (amplicon). 33-35 Any contaminating amplicon from previous PCR runs are eliminated by the AmpErase enzyme [uracil- N-glycosylase], which is included in the PCR master mix, when heated in the first thermal cycling step. However, newly formed amplicon are not eliminated since the AmpErase enzyme is inactivated once exposed to temperatures above 55°C.The cobas® MPX master mix contains detection probes which are specific for HIV -1 (Groups M and O), HIV-2, HCV, HBV, and IC nucleic acid. The specific HIV, HCV, HBV, and IC detection probes are each labeled with one of fou r unique fluorescent dyes which act as a reporter. Each probe also has a fifth dye which acts as a quencher. The four reporter dyes are measured at defined wavelengths, thus permitting simultaneous detection and discrimination of the amplified HIV, HCV, and HBV targets and the IC. 36, 37 When not bound to the target sequence, the fluorescent signal of the intact probes is suppressed by the quencher dye. During the PCR amplification step, hybridization of the probes to the specific single-stranded DNA template results in cleavage by the 5' to 3' nuclease activity of the DNA polymerase resulting in separation of the reporter and quencher dyes and the generation of a fluorescent signal. With each PCR cycle, increasing amounts of cleaved probes are generated and the cumulative signal of the reporter dye is concomitantly increased. Since the four specific reporter dyes are measured at defined wavelengths, simultaneous detection and discrimination of the amplified HIV, HCV and HBV targets and the IC are possible.33. Longo MC, Berninger MS, Hartley JL. Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. Gene. 1990; 93:125-128.34. Savva R, McAuley-Hecht K, Brown T, Pearl L. The structural basis of specific base-excision repair by uracil-DNA glycosylase. Nature. 1995; 373:487-493.35. Mol CD, Arvai AS, Slupphaug G, et al. Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis. Cell. 1995;80:869-878.36. Higuchi R, Dollinger G, Walsh PS, Griffith R. Simultaneous amplification and detection of specific DNA sequences. Biotechnology (NY). 1992;10:413-417.37. Heid CA, Stevens J, Livak JK, Williams PM. Real time quantitative PCR. Genome Res. 1996;6:986-994. en The cobas® MPX test is based on fully automated sample preparation (nucleic acid extraction and purification) followed by PCR amplification and detection. The cobas® 6800/8800 Systems consists of the sample supply module, the transfer module, the processing module, and the analytic module. Automated data management is performed by the cobas® 6800/8800 software which assigns test results for all tests as non-reactive, reactive, or invalid. Results can be reviewed directly on the system screen, and printed as a report or sent to a Laboratory Information Management System (LIMS) or other result management system.Source plasma (collected by Apheresis) samples may either be tested individually or, optionally, in pools consisting of up to 96 samples. The cobas p 680 instrument, or cobas® Synergy software with the Hamilton MICROLAB® STAR IVD system (together referred to as cobas® Synergy Core), must be used if pooling is to be performed.Nucleic acid from the sample and added armored RNA internal control (IC) molecules (which serve as the sample preparation and amplification/detection process control) is simultaneously extracted. In addition the test utilizes four external controls: three positive and a negative control. Viral nucleic acid is released by addition of proteinase and lysis reagent to the sample. The released nucleic acid binds to the silica surface of the added magnetic glass particles. Unbound substances and impurities, such as denatured protein, cellular debris, and potential PCR inhibitors (such as hemoglobin) are removed with subsequent wash reagent steps and purified nucleic acid is eluted from the magnetic glass particles with elution buffer at elevated temperature.Selective amplification of target nucleic acid from the donor sample is achieved by the use of virus-specific forward and reverse primers which are selected from highly conserved regions of the viral nucleic acid. A thermostable DNA polymerase enzyme is used for both reverse-transcription and amplification. The master mix includes deoxyuridine triphosphate (dUTP), instead of deoxythimidine triphosphate (dTTP), which is incorporated into the newly synthesized DNA (amplicon). 32-34 Any contaminating amplicons from previous PCR runs are eliminated by the AmpErase enzyme [uracil-N- glycosylase], which is included in the PCR master mix, when heated in the first thermal cycling step. However, newly formed amplicons are not eliminated since the AmpErase enzyme is inactivated once exposed to temperatures above 55°C.The cobas® MPX master mix contains detection probes which are specific for HIV-1 (Groups M and O), HIV-2, HCV, HBV, and IC nucleic acid. The specific HIV, HCV, HBV, and IC detection probes are each labeled with one of four unique fluorescent dyes which act as a reporter. Each probe also has a fifth dye which acts as a quencher. The four reporter dyes are measured at defined wavelengths, thus permitting simultaneous detection and discrimination of the amplified HIV, HCV, and HBV targets and the IC. 35,36 When not bound to the target sequence, the fluorescent signal of the intact probes is suppressed by the quencher dye. During the PCR amplification step, hybridization of the probes to the specific single- stranded DNA template results in cleavage by the 5' to 3' nuclease activity of the DNA polymerase resulting in separation of the reporter and quencher dyes and the generation of a fluorescent signal. With each PCR cycle, increasing amounts of cleaved probes are generated and the cumulative signal of the reporter dye is concomitantly increased. Since the four specific reporter dyes are measured at defined wavelengths, simultaneous detection and discrimination of the amplified HIV, HCV and HBV targets and the IC are possible.32. Longo MC, Berninger MS, Hartley JL. Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. Gene. 1990; 93:125-128.33. Savva R, McAuley-Hecht K, Brown T, Pearl L. The structural basis of specific base-excision repair by uracil-DNA glycosylase. Nature. 1995; 373:487-493.34. Mol CD, Arvai AS, Slupphaug G, et al. Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis. Cell. 1995;80:869-878.35. Higuchi R, Dollinger G, Walsh PS, Griffith R. Simultaneous amplification and detection of specific DNA sequences. Biotechnology (NY). 1992;10:413-417.36. Heid CA, Stevens J, Livak JK, Williams PM. Real time quantitative PCR. Genome Res. 1996;6:986-994. en cobas® MPX is based on real-time fluorescence PCR technology and is used on a system that fully automates sample preparation (nucleic acid extraction and purification) and PCR amplification and detection. The cobas® 5800 System consists of a single integrated instrument. The cobas® 6800/8800 Systems consist of a sample supply module, a transfer module, a processing module and an analysis module. The data is managed automatically by the cobas® 5800 or the 6800/8800 System software. For each test, the software determines whether the result is non-reactive, reactive or invalid. When using the cobas® 5800 System, the cobas® Synergy software is recommended for reviewing results and printing reports, and it is required to send results to a Laboratory Information Management System (LIMS) or other result management system. When using the cobas® 6800/8800 Systems, results can be reviewed directly on the system screen, printed as a report, or sent to a LIMS or other result management system.Samples can be tested individually or tested in pools containing multiple samples. If pooled testing is done, the cobas® Synergy software along with the Hamilton MICROLAB® STAR/STARlet IVD can be used for pooling before the analysis.The nucleic acid in the sample and the added armored RNA internal control (IC) (serving as the control for the sample preparation and amplification/detection processes) are extracted simultaneously. In addition, the test uses 4 kit controls: 3 positive controls and 1 negative control. Proteinase and lysis reagent are added to the sample to release the viral nucleic acid, and the released nucleic acid binds to the silica surface of the magnetic glass beads. Unbound substances and impurities, such as denatured protein, cellular debris and potential PCR inhibitors (such as hemoglobin) are removed in the subsequent washing steps, and purified nucleotides are eluted from the magnetic glass beads in the elution buffer using high temperature.The target nucleic acid in the sample is selectively amplified with virus-specific forward and reverse primers based on highly conserved regions of the viral nucleic acid. For HIV-1 group M, two different regions of the viral genome are amplified (dual targeting). A thermostable DNA polymerase is used for both the reverse transcription and the amplification. The master mix contains deoxyuridine triphosphate (dUTP) and AmpErase enzyme [uracil-N-glycosylase], and the dUTP instead of deoxythymidine triphosphate (dTTP) is incorporated into the newly synthesized DNA (the amplicon)33–35. In the first thermal cycling step, the AmpErase enzyme identifies the dUTP in the amplicons from previous PCR amplification reactions, thereby eliminating all amplicon contamination. After that, the temperature is raised above 55°C, and AmpErase is inactivated. Therefore newly formed amplicons are not eliminated.The cobas® MPX master mix contains detection probes that can bind specifically with the nucleic acids of HIV-1 (groups M and O), HIV-2, HCV, HBV and the IC. Detection probes for each HIV-1 Group M target are included, along with dual probes for HCV. The HIV-, HCV-, HBV- and IC-specific detection probes are each labeled with a unique fluorescent dye that acts as a reporter. Each probe is also labeled with a dye that acts as a quencher. These 4 reporter dyes are detectable at defined wavelengths. This allows for the simultaneous detection of and discrimination between the amplified HIV, HCV and HBV target sequences and the internal target (IC)36, 37. As for intact probes not bound to the target sequences, their fluorescent signals are suppressed by the quencher dye. During the PCR amplification step, these probes hybridize to the specific single-stranded DNA template, causing the DNA polymerase to cleave it through its 5' to 3' nuclease activity. This causes the reporter dye and the quencher dye to separate and generate a fluorescent signal. In each PCR cycle, as the number of cleaved probes continues to increase, the cumulative reporter dye signal also increases. The fact that the 4 specific reporter dyes are detected at defined wavelengths makes it possible to simultaneously detect and discriminate between the amplified HIV, HCV and HBV target sequences and the internal target (IC).33. Longo MC, Berninger MS, Hartley JL.Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions.Gene.1990; 93:125-128.34. Savva R, McAuley-Hecht K, Brown T, Pearl L. The structural basis of specific base-excision repair by uracil-DNA glycosylase.Nature.1995; 373:487-493.35. Mol CD, Arvai AS, Slupphaug G, et al.Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis. Cell. 1995; 80:869-878.36. Higuchi R, Dollinger G, Walsh PS, Griffith R. Simultaneous amplification and detection of specific DNA sequences. Biotechnology (NY). 1992;10:413-417.37. Heid CA, Stevens J, Livak JK, Williams PM. Real time quantitative PCR.Genome Res.1996;6:986-994. en

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