Performance of the Abbott RealTime HCV Genotype II RUO Assay

The Abbott RealTime HCV Genotype II RUO (research use only) assay was evaluated using the automated Abbott RealTime m2000 system. Concordance was 98% (81/83 samples) with samples previously typed by the Versant HCV Genotype 2.0 RUO system with manual extraction. The total assay time was reduced from 10.5 to 6.0 h and hands-on time from 13 to 4 min/patient sample.     

Multicenter Evaluation of the Abbott LCx Mycobacterium tuberculosis Ligase Chain Reaction Assay

Four Australian hospital laboratories evaluated the performance of the Abbott LCx Mycobacterium tuberculosis assay with 2,347 specimens (2,083 respiratory and 264 nonrespiratory specimens) obtained from 1, 411 patients. A total of 152 specimens (6.5%) were culture positive for Mycobacterium tuberculosis complex (MTBC); of these, 79 (52%) were smear positive. After resolution of discrepant data, the overall sensitivity, specificity, and positive and negative predictive values for the LCx assay were 69.7, 99.9, 99.1, and 97.7% respectively. For smear-positive respiratory specimens that were culture positive for MTBC, the values were 98.5, 100, 100, and 98.4%, respectively, while the values for smear-negative respiratory specimens were 41.5, 99.9, 96.4, and 98%, respectively. Relative operating characteristic curves were constructed to demonstrate the relationship between sensitivity and specificity for a range of possible cutoff values in the LCx assay. These graphs suggested that the assay sensitivity for respiratory samples could be increased from 70.2 to 78.6%, while the specificity would be reduced from 99.9 to 99.4% by inclusion of a grey zone (i.e., LCx assay values of between 0.2 and 0.99). An algorithm is presented for the handling of specimens with LCx assay values within this grey zone.     

Sequence Conservation of the Region Targeted by the Abbott RealTime HBV Viral Load Assay in Clinical Specimens

The Abbott RealTime HBV assay targets the N-terminal region of the S gene. Here we analyzed the sequence variability of the assay target region from >2,100 clinical specimens. Thermodynamic modeling of the percentage of bound primer/probe at the assay annealing temperature was performed to assess the potential effect of sequence variability.     

Evaluation of the Abbott LCx Assay for Detection of Neisseria gonorrhoeae in Endocervical Swab Specimens from Females

The Abbott LCx Neisseria gonorrhoeae assay (Abbott Laboratories, Abbott Park, Ill.) uses a ligase chain reaction (LCR) amplification in the LCx probe system for detection of a specific nucleotide sequence in the Opa-encoding gene of N. gonorrhoeae. We evaluated the LCx assay in a comparison with conventional culture employing modified Thayer-Martin media for the detection of N. gonorrhoeae from female endocervical specimens obtained from patients attending a sexually transmitted disease clinic. Discordantly LCR-positive and culture-negative specimens were further evaluated by testing with another LCR assay which used an N. gonorrhoeae-specific pilin probe. Specimens positive by both LCR assays were considered confirmed LCx-positive specimens. A specimen was considered to contain N. gonorrhoeae when it was either culture positive or culture negative and confirmed LCx positive. A total of 403 female endocervical specimens were evaluated. The prevalence of N. gonorrhoeae in this population was 8.7%. The sensitivity and specificity of the LCx assay were 94.3 and 99.4%, and those of culture were 77.1 and 100%, respectively. The Abbott LCx assay is a rapid, sensitive method for detection of N. gonorrhoeae in female endocervical specimens.     

Evaluation of the Abbott LCx Mycobacterium tuberculosis Assay for Direct Detection of Mycobacterium tuberculosis Complex in Human Samples

Seven hundred thirty-seven clinical samples from 460 patients were processed for direct detection of Mycobacterium tuberculosis complex by a semiautomated ligase chain reaction commercial assay, the LCx Mycobacterium tuberculosis Assay (LCx assay) from Abbott Laboratories. Results were compared to those of direct microscopy and standard microbiological culture. Of 26 patients (5.7%) with a culture positive for M. tuberculosis, 22 (84.6%) were found positive by the LCx assay. The sensitivity of the LCx assay was 98% for smear-positive samples and 27% for smear-negative samples. With an overall culture positivity rate for M. tuberculosis of 8.3% (61 of 737 samples) and after resolution of discrepant results according to clinical data, the sensitivity, specificity, and positive and negative predictive values of the LCx assay were 78, 100, 95, and 98%, respectively, compared to 85, 100, 100, and 98%, respectively, for culture and 67, 99, 87, and 97%, respectively, for acid-fast staining. In conclusion, the LCx assay proved satisfactory and appears to be an easy-to-use 1-day test which must be used with standard culture methods but can considerably reduce diagnosis time versus culture. However, its clinical interest appears to be limited in our population with low mycobacterial prevalence because of its cost considering the small gain in sensitivity versus direct microscopy.     

Evaluation of the Abbott Investigational Use Only RealTime Hepatitis C Virus (HCV) Assay and Comparison to the Roche TaqMan HCV Analyte-Specific Reagent Assay

The accurate and sensitive measurement of hepatitis C virus (HCV) RNA is essential for the clinical management and treatment of infected patients and as a research tool for studying the biology of HCV infection. We evaluated the linearity, reproducibility, precision, limit of detection, and concordance of viral genotype quantitation of the Abbott investigational use only RealTime HCV (RealTime) assay using the Abbott m2000 platform and compared the results to those of the Roche TaqMan Analyte-Specific Reagent (TaqMan) and Bayer Versant HCV bDNA 3.0 assay. Comparison of 216 samples analyzed by RealTime and TaqMan assays produced the following Deming regression equation: RealTime = 0.940 (TaqMan) + 0.175 log₁₀ HCV RNA IU/ml. The average difference between the assays was 0.143 log₁₀ RNA IU/ml and was consistent across RealTime''s dynamic range of nearly 7 log₁₀ HCV RNA IU/ml. There was no significant difference between genotypes among these samples. The limit of detection using eight replicates of the World Health Organization HCV standard was determined to be 7.74 HCV RNA IU/ml by probit analysis. Replicate measurements of commercial genotype panels were significantly higher than TaqMan measurements for most samples and showed that the RealTime assay is able to detect all genotypes with no bias. Additionally, we showed that the amplicon generated by the widely used Roche COBAS Amplicor Hepatitis C Virus Test, version 2.0, can act as a template in the RealTime assay, but potential cross-contamination could be mitigated by treatment with uracil-N-glycosylase. In conclusion, the RealTime assay accurately measured HCV viral loads over a broad dynamic range, with no significant genotype bias.Methods for accurate quantitation of serum and plasma hepatitis C virus (HCV) RNA levels have become key tools both for understanding the biology of HCV infection and for the clinical management of patients under treatment. The ability to predict likelihood of response to combination interferon/ribavirin therapy by assessing rates of HCV viral load decline has provided a more individualized treatment algorithm that can identify nonresponsive patients early in treatment, sparing them significant morbidity and cost. New algorithms that examine the kinetics of HCV viral decline provide an even more refined tool for management and complement the information provided by HCV genotype determination. Finally, HCV viral kinetics data are essential for the understanding of new therapeutics such as the class of protease inhibitors. For all applications, accurate quantitation of all HCV types over a broad dynamic range is critical. The advent of real-time PCR methods provides a powerful tool for a broad dynamic range of quantitation of viruses; however, targets such as HCV require careful assay design to avoid errors due to sequence variations intrinsic to RNA viruses.Abbott Molecular, Inc. (Des Plaines, IL), recently released the m2000 system and tests for human immunodeficiency virus type 1, HCV, and chlamydia/gonorrhea (Chlamydia trachomatis/Neisseria gonorrhea) in the European Union with Conformité Européene-marked certification, and the system was recently approved for human immunodeficiency virus type 1 by the U.S. Food and Drug Administration. The m2000 system consists of an eight-channel liquid handling platform (the m2000sp) for performing automated nucleic acid extraction and PCR preparation and of a real-time PCR platform (the m2000rt) for detection and quantification. We used the m2000 system to evaluate the sensitivity, reproducibility, linearity, and concordance of viral genotype quantitation of the Abbott Molecular investigational use only (IUO) RealTime HCV (RealTime) assay and compared aspects of its performance to the Roche TaqMan Analyte-Specific Reagent (ASR) (TaqMan) (Roche Molecular Systems, Inc., Branchburg, NJ) and Bayer Versant HCV bDNA 3.0 (bDNA) assay. In addition, we examined the potential for contamination by the Roche COBAS Amplicor Hepatitis C Virus Test, version 2.0 (Amplicor) (Roche Molecular Systems, Inc., Branchburg, NJ) and TaqMan amplicons and the effect of uracil-N-glycosylase (UNG) treatment in mitigating contamination from these widely used tests.     

Evaluation of the Efficiency of the Sample Inactivation Reagent in the Abbott RealTime MTB Assay for Inactivation of Mycobacterium tuberculosis

The Abbott RealTime MTB assay is a nucleic acid amplification test (NAAT) for the detection of Mycobacterium tuberculosis complex DNA. The sample inactivation procedure used in the assay, consisting of one part sample treated with 3 parts inactivation reagent for 60 min, effectively reduced viscosity and inactivated M. tuberculosis in clinical specimens.     

Evaluation of the Abbott AxSYM Cytomegalovirus (CMV) Immunoglobulin M (IgM) Assay in Conjunction with Other CMV IgM Tests and a CMV IgG Avidity Assay

The measurement of the avidity of cytomegalovirus (CMV) immunoglobulin G (IgG) antibodies has been shown by several investigators to be useful in identifying and excluding primary CMV infections in pregnant women. In this work, we examined the diagnostic utility of reflex testing of CMV IgM-positive specimens from pregnant women by using a CMV IgG avidity assay. The utility of this approach was directly dependent on the sensitivity of the CMV IgM assay employed during the initial screen. The higher initial reactivity rate of the AxSYM CMV IgM assay was necessary in order to detect CMV IgM in specimens containing low-avidity CMV IgG antibodies, indicative of a primary CMV infection, which other CMV IgM assays (Behring, Vidas, Captia, and Eurogenetics) fail to detect in some cases. The use of the AxSYM CMV IgM assay, followed by an avidity test, should result in more accurate diagnosis of CMV infection in pregnant women.     

Evaluation of Abbott TESTPACK ROTAVIRUS with clinical specimens.

TESTPACK ROTAVIRUS was compared with the Pathfinder Rotavirus assay for the detection of rotaviral antigens in feces from 137 patients. The symptomatology and ages of the patients varied from no symptoms to watery diarrhea and from less than 3 months to greater than 60 years of age. The sensitivity and specificity, before resolution, were 89.2 and 90.0%, respectively. After resolution with a blocking reagent, the results were 100% sensitivity and 98.9% specificity. The performance was similar for all age groups and in both symptomatic and asymptomatic patients. Abbott TESTPACK ROTAVIRUS is a rapid (10-min), easy-to-perform assay for the detection of rotaviral antigens and has the sensitivity and specificity of enzyme-linked immunosorbent assays that require several hours to perform.     

Evaluation of the Abbott CELL-DYN 4000 hematology analyzer

A new generation hematology analyzer, Abbott CELL-DYN 4000 (CD 4000), capable of providing 26 parameters, including fully automated reticulocyte, nucleated RBC, blast, band, and immature granulocyte, and variant lymphocyte counts, was evaluated by using the National Committee for Clinical Laboratory Standards H20-A protocol and compared with the Bayer-Technicon H-2 analyzer, which is used routinely in our laboratory. A lipid interference experiment and a sample aging study also were performed. Linearity, carryover, and precision were within the limits established by the manufacturer, and satisfactory agreement was found with the H-2 analyzer. The evaluation of leukocyte differential counts indicated an excellent correlation with the manual reference method for neutrophils and lymphocytes, a good correlation for monocytes and eosinophils, and a poor correlation for basophils in samples with low counts; for basophil counts of 2% or higher, we found an improvement of the correlation coefficient. In the lipid interference experiment, only hemoglobin determination was influenced significantly on the CD 4000, but by using a new Abbott hemoglobin reagent, the interference was eliminated. The CBC and differential counts were stable and reportable up to at least 24 hours. Intrasample viability information on leukocytes provided a quality check on each individual specimen.     

Premarket Evaluations of the IMDx C. difficile for Abbott m2000 Assay and the BD Max Cdiff Assay

Clostridium difficile-associated diarrhea is a well-recognized complication of antibiotic use. Historically, diagnosing C. difficile has been difficult, as antigen assays are insensitive and culture-based methods require several days to yield results. Nucleic acid amplification tests (NAATs) are quickly becoming the standard of care. We compared the performance of two automated investigational/research use only (IUO/RUO) NAATs for the detection of C. difficile toxin genes, the IMDx C. difficile for Abbott m2000 Assay (IMDx) and the BD Max Cdiff Assay (Max). A prospective analysis of 111 stool specimens received in the laboratory for C. difficile testing by the laboratory''s test of record (TOR), the BD GeneOhm Cdiff Assay, and a retrospective analysis of 88 specimens previously determined to be positive for C. difficile were included in the study. One prospective specimen was excluded due to loss to follow-up discrepancy analysis. Of the remaining 198 specimens, 90 were positive by all three methods, 9 were positive by TOR and Max, and 3 were positive by TOR only. One negative specimen was initially inhibitory by Max. The remaining 95 specimens were negative by all methods. Toxigenic C. difficile culture was performed on the 12 discrepant samples. True C. difficile-positive status was defined as either positive by all three amplification assays or positive by toxigenic culture. Based on this definition, the sensitivity and specificity were 96.9% and 95% for Max and 92.8% and 100% for IMDx. In summary, both highly automated systems demonstrated excellent performance, and each has individual benefits, which will ensure that they will both have a niche in clinical laboratories.     

Sequence Conservation of the Region Targeted by the Abbott RealTime HCV Viral Load Assay

The Abbott RealTime (RT) HCV assay targets the 5′ untranslated region (UTR) of the HCV genome. Here, we analyzed the sequence variability of the assay target regions from 1,092 specimens. Thermodynamic modeling of the percentage of primers/probes bound at the assay annealing temperature was performed to assess the potential effect of sequence variability. An analysis of this large data set revealed that the primer and probe binding sites of the RealTime HCV viral load assay are highly conserved and that naturally occurring sequence polymorphisms are not expected to discernibly impact assay performance.     

Evaluation of Five User-Friendly Whole Genome Sequencing Software for Mycobacterium tuberculosis in Clinical Application

BackgroundWhole genome sequencing (WGS) is an increasingly useful tool for tuberculosis (TB) diagnosis and disease management. In this study, we evaluated the utility of user-friendly WGS tools in reporting resistance profiles and identifying lineages of clinical TB isolates from South Korea.MethodsForty clinical samples from TB patients showing discrepancies between their rapid molecular and conventional drug susceptibility tests were used in this study. Among these clinical isolates, 37 strains were successfully evaluated via WGS software, using the GenTB, TB Profiler, PhyResSE, CASTB, and Mykrobe.ResultsMore accurate and faster susceptibility results could be obtained with isoniazid than with rifampin. Using the phenotypic test as the gold standard, the isoniazid concordance rate between phenotypic drug susceptibility test (DST) and WGS (GenTB: 45.9%, TB profiler: 40.5%, PhyResSE: 40.5%, CASTB: 48.6%, and Mykrobe: 43.2%) was much higher than between phenotypic DST and rapid molecular genotypic DST (18.9%) among the 37 strains. In contrast, the rifampin concordance rate between phenotypic DST and WGS and that between phenotypic DST and rapid molecular genotypic DST was similar (81.1–89.2%). We also found novel mutations associated with INH in katG and ahpC gene region, not covered by the line probe assay. In addition, lineage analysis identified 81.1% of these samples as L2 East Asian lineage strains, and 18.9% as L4 Euro-American lineage strains.ConclusionWGS may play a pivotal role in TB diagnosis and the detection of drug resistance, genetic diversity, and transmission dynamics in the near future because of its accuracy, speed, and extensibility.     

Evaluation of the Abbott RealTime HBV DNA assay and comparison to the Cobas AmpliPrep/Cobas TaqMan 48 assay in monitoring patients with chronic cases of hepatitis B

The new Abbott RealTime hepatitis B virus (HBV) assay was compared to the Cobas AmpliPrep/Cobas TaqMan assay with 128 serum samples from patients with chronic hepatitis B. There was an excellent correlation (r = 0.961) between the two assays, with the Abbott RealTime test showing at least equivalent sensitivity and a slightly wider dynamic range than the Cobas TaqMan assay. By coupling high sensitivity with a large dynamic range, the Abbott RealTime HBV assay is useful in monitoring the response to antiviral therapy.     

Evaluation of the Abbott Real-Time HIV-1 quantitative assay with dried blood spot specimens

The Abbott Real-Time HIV-1 assay was evaluated for its performance in quantification of human immunodeficiency virus type 1 (HIV-1) RNA in dried blood spot (DBS) samples. In total, 169 blood samples with detectable plasma HIV-1 RNA were used to extract RNA from paired DBS and liquid plasma samples, using the automated Abbott m Sample Preparation System (m2000sp). HIV-1 RNA was then quantitated by the m2000rt RealTime analyser. RNA samples suitable for real-time PCR were obtained from all but one (99.4%) of the DBS samples and HIV-1 RNA was detected in 163/168 (97.0%) samples. The correlation between HIV-1 RNA values measured in paired DBS and plasma samples was very high ( r  = 0.882), with 78.5% and 99.4% of cases differing by <0.5 and 1.0 log, respectively. Retesting of DBS replicates following 6 months of storage at 2–8°C showed no loss of HIV-1 RNA in a subset of 89 samples. The feasibility of DBS testing coupled with automated sample processing, and the use of a latest-generation FDA-approved real-time PCR-based system, represents an encouraging first step for viral load measurement in reference centres in developing countries where access to antiretroviral therapy is expanding.     

Comparison of detection and quantification of HBV DNA in chronic HBeAg negative and positive patients by Abbott RealTime HBV and Roche Cobas TaqMan HBV assays

Monitoring the serum hepatitis B viral DNA levels with sensitive realtime PCR assays is strongly recommended for the management of patients with chronic HBV infection. This study compares the performance of two realtime HBV quantitative PCR assays with samples from chronic HBeAg(+) and HBeAg(−) patients.     

Evaluation of Effect of Specimen-Handling Parameters for Plasma Preparation Tubes on Viral Load Measurements Obtained by Using the Abbott RealTime HIV-1 Load Assay

HIV-1 viral load testing is essential to the management of HIV-1-infected patients, and proper specimen handling ensures accurate viral load (VL) results. This study was performed to (i) evaluate the effect of freezing plasma in situ in BD Vacutainer plasma preparation tubes (PPT) on the accuracy of HIV-1 viral load results using the Abbott RealTime HIV-1 assay and (ii) evaluate the effect of whole-blood storage in the PPT for 6 h at room temperature prior to centrifugation (PPT6H) rather than 2 h as specified in the PPT product insert. Of the 64 HIV-positive subjects evaluated, 29 had average viral load counts of >40 copies/ml in at least one of the tubes tested and 35 subjects had a result of either “undetected target” or “below the limit of quantification” (LOQ) for all or some of the tubes regardless of handling condition. For the 29 subjects with VLs that were >LOQ, the mean biases between plasma from Vacutainer K₂EDTA tubes and plasma frozen in situ in PPT and between K₂EDTA tube plasma and plasma from PPT6H (log₁₀ copies/ml) were 0.005 and −0.001, respectively, and r² was >0.92 for all correlations. We conclude that VLs determined from plasma frozen in situ in PPT are equivalent to VLs in K₂EDTA tube plasma and can be used for accurate quantification of HIV-1 RNA in the Abbott RealTime HIV-1 assay. Furthermore specimens collected in PPT can be stored for 6 h at room temperature with no effect on viral load results as measured by the Abbott RealTime HIV-1 assay.Accurate quantification of human immunodeficiency virus type 1 (HIV-1), also referred to as HIV-1 viral load (VL) testing, is essential for effective management of HIV-1-infected patients. The BD Vacutainer plasma preparation tube (PPT) (BD Preanalytical Systems, Franklin Lakes, NJ) was developed to facilitate the handling of plasma specimens used for HIV-1 viral load testing. The PPT contains a K₂EDTA additive and a polyester gel which, upon centrifugation, forms a barrier that separates blood cells from plasma, allowing storage, freezing, and shipment of the plasma specimen in situ in PPT. Use of PPT also results in a decrease in the amount of labor required to process specimens, elimination of a potential source of error in specimen labeling, and reduction in the risk of HIV exposure associated with the transfer of separated plasma to secondary tubes for shipping.Earlier studies using PPT for specimen collection demonstrated compatibility of this tube with HIV-1 VL tests (1, 4, 5). Over the past few years, however, investigators have reported that freezing plasma in situ in a PPT produced higher HIV-1 viral load results compared to plasma from K₂EDTA tubes when tested in the Cobas Amplicor HIV-1 monitor system (Roche Molecular Diagnostics, Pleasanton, CA) (2, 3, 11). Elevated levels of HIV-1 VL from PPT frozen in situ after centrifugation were first reported by Squires et al., who showed that PPT yielded higher HIV RNA levels than K₂EDTA tubes. The disparity in quantification, seen in both standard and ultrasensitive assays, was more apparent in specimens with VLs between the limit of quantification (LOQ), 50 copies/ml, and 1,000 copies/ml and more pronounced in specimens close to or below 50 copies/ml (3, 10, 11). In fact, studies that compared plasma aspirated from K₂EDTA tubes with plasma frozen in situ in PPT show that VLs that are clearly below the LOQ in the former are quantifiable in the latter (3, 8, 11). Such discrepant results for plasma collected in different tubes from the same subject could be interpreted as virological failure, and these results, therefore, have therapeutic implications.Additional studies reported that specimens which were aspirated and transferred to another tube after centrifugation did not show patterns of artificially increased viral load (8, 10). Similarly, recentrifugation of specimens transported in PPT at 4°C eliminated the inaccurate quantification of HIV seen in plasmas frozen in situ in PPT (6, 9).Such observations led investigators to associate elevated viral loads in plasma in PPT with the presence of cell-associated nucleic acids released from cells trapped within or adhered to the surface of the gel barrier in PPT (6). Depletion of cellular material by recentrifugation of separated, unfrozen plasma from PPT resulted in lower VLs, indicating that cell-associated nucleic acid contributed to the elevation in VL. This finding was compatible with an earlier study which had shown that the HIV proviral DNA associated with cellular (genomic) DNA was in part responsible for the increase in viral load (13).The aim of this study was to evaluate the performance of PPT with the new automated RealTime HIV-1 assay (Abbott Molecular, Des Plaines, IL) for the quantification of HIV-1 viral load using the Abbott m2000sp and m2000rt systems for sample processing and amplification/detection, respectively. Specifically, we were interested in determining the effect of freezing plasma in situ in PPT on HIV-1 viral load analyzed using the Abbott RealTime HIV-1 assay. In addition, the study evaluated the effect on viral load of whole-blood storage in PPT for 6 h before centrifugation rather than 2 h, as specified in the PPT product insert.     

核酸序列测定技术分析HBV耐药基因与亚型鉴定

目的:用荧光标记核酸序列测定技术分析患者携带的HBV基因型,判断所携带的HBV亚型以及治疗过程中是否产生耐药性.方法:采用PCR产物直接进行核酸序列分析,使用计算机模拟核酸杂交技术分析HBV基因的亚型与耐药基因.结果:扩增产物的核酸序列分析表明,设计的引物序列在确定的条件下可以特异性的扩增HBV相应的基因片段.患者耐药基因分析结果分别为HBV YVDD变异和YIDD变异;病毒亚型分析结果提示患者携带的HBV均为adr亚型.结论:本方法能够准确判定HBV的YVDD与YIDD变异及其它类型突变,并确定患者携带HBV的基因型,能够准确、客观地反映出病原体的耐药性,可以作为合理用药的重要参考依据.