RT-PCR/MALDI-TOF Diagnostic Target Performance Reflects Circulating SARS-CoV-2 Variant Diversity in New York City.

As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate, multiple variants of concern have emerged. New variants pose challenges for diagnostic platforms because sequence diversity can alter primer/probe-binding sites (PBSs), causing false-negative results. The MassARRAY SARS-CoV-2 Panel (Agena Bioscience) uses RT-PCR and mass spectrometry to detect five multiplex targets across N and ORF1ab genes.

Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multitarget approach.

The coronavirus disease 2019 (COVID-19) pandemic has sparked the rapid development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostics. However, emerging variants pose the risk for target dropout and false-negative results secondary to primer/probe binding site (PBS) mismatches. The Agena MassARRAY® SARS-CoV-2 Panel combines reverse-transcription polymerase chain reaction and matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry to probe for five targets across N and ORF1ab genes, which provides a robust platform to accommodate PBS mismatches in divergent viruses.

Multicenter Performance Evaluation of the Simplexa Bordetella Direct Kit in Nasopharyngeal Swab Specimens.

Detection of and using molecular methods is sensitive and specific with a short turnaround time compared to other diagnostic methods. In this multicenter study, we compared the performance of the Simplexa Bordetella Direct kit to those of other molecular assays in detecting and differentiating and in nasopharyngeal swab specimens. The limits of detection (LODs) were 150 CFU/ml or 3 fg/μl of DNA for and 1,500 CFU/ml or 10 fg/μl of DNA for A total of 1,103 fresh and residual frozen specimens from eight clinical sites were tested.

Evaluation of the Luminex ARIES® system for the detection and quantification of BK virus (BKV) DNA in plasma samples from kidney transplant recipients.

BK virus (BKV) nephropathy is a serious complication in renal transplant recipients due to the need for immunosuppression. Nearly 50% of renal transplant patients with BKV nephropathy experience a significant loss of function of the transplanted kidney. It is routine practice to screen renal transplant recipients regularly for BK viremia.

Multicenter Clinical Evaluation of the Automated Aries Assay.

Molecular methods offer superior sensitivity and specificity and reduce testing turnaround time from days to hours for detection of and In this study, we evaluated the performance of the automated PCR-based Aries Assay, which detects both and directly from nasopharyngeal swab specimens. The limits of detection (LoDs) were 1,800 CFU·ml for and 213 CFU·ml for The assay detected 16/18 unique / strains. Of 71 potentially cross-reacting organisms, 5 generated false positives in 1/6 replicates; none of 6 additional spp.

Molecular pathology curriculum for medical laboratory scientists: A report of the association for molecular pathology training and education committee.

Molecular diagnostics is a rapidly growing specialty in the clinical laboratory assessment of pathology. Educational programs in medical laboratory science and specialized programs in molecular diagnostics must address the training of clinical scientists in molecular diagnostics, but the educational curriculum for this field is not well defined. Moreover, our understanding of underlying genetic contributions to specific diseases and the technologies used in molecular diagnostics laboratories change rapidly, challenging providers of training programs in molecular diagnostics to keep their curriculum current and relevant.

Molecular methods and platforms for infectious diseases testing a review of FDA-approved and cleared assays.

The superior sensitivity and specificity associated with the use of molecular assays has greatly improved the field of infectious disease diagnostics by providing clinicians with results that are both accurate and rapidly obtained. Herein, we review molecularly based infectious disease diagnostic tests that are Food and Drug Administration approved or cleared and commercially available in the United States as of December 31, 2010. We describe specific assays and their performance, as stated in the Food and Drug Administration's Summary of Safety and Effectiveness Data or the Office of In Vitro Diagnostic Device Evaluation and Safety's decision summaries, product inserts, or peer-reviewed literature.

Assessment of clinical and analytical performance characteristics of an HPV genotyping test.

Human papillomavirus (HPV), the known cause of cervical cancer, is found in essentially all cervical cancer specimens. Infection with high-risk HPV genotypes carries the greatest risk of viral persistence and the potential to develop precancerous lesions or cervical cancer. Identifying women infected with HPV 16 and/or 18, the two genotypes most commonly found in cervical cancer, helps further stratify women for either immediate referral to colposcopy or repeat cytological and HPV DNA testing in 12 months.

A comparative review of laboratory-developed tests utilizing Invader HPV analyte-specific reagents for the detection of high-risk human papillomavirus.

Background: Testing for human papillomavirus (HPV) has emerged as an important component of cervical cancer screening and disease management. Analytic performance (sensitivity, specificity, positive predictive value, negative predictive value, accuracy) and clinical relevance are important criteria by which any new test must be reviewed.

Objective: This paper compares laboratory-developed tests, utilizing Invader analyte-specific reagents (ASRs) for the detection of oncogenic HPV DNA, to the Digene Hybrid Capture 2 test (HC2).

Detection of high-risk papillomavirus DNA with commercial invader-technology-based analyte-specific reagents following automated extraction of DNA from cervical brushings in ThinPrep media.

We compared the performances of the Third Wave Technology Invader method and the Digene Hybrid Capture 2 assay to detect high-risk human papillomaviruses in 87 cervical brushing specimens submitted in Cytyc ThinPrep media. Two different methods for the extraction of DNA from squamous epithelial cells were also evaluated.

Comparative evaluation of three commercially available methodologies for hepatitis C virus genotyping.

We compared the performances of three hepatitis C virus genotyping methodologies supplied by Bayer, Abbott, and Third Wave Technologies. Genotypes were determined for 136 of 137 specimens by the Bayer method, 121 of 137 specimens by the Invader assay, and only 77 of 137 specimens by the Abbott assay. All reported genotypes were concordant by all three methods.

Smallpox: residual antibody after vaccination.

Of all the microorganisms and toxins, poxviruses (Orthopoxvirus) have the greatest potential for use by terrorists. These viruses can spread rapidly through the environment following initial infection. In 1980, the World Health Organization Eradication Program discontinued vaccination for smallpox and declared that the disease had been eliminated.

Multicenter evaluation of methods to quantitate human immunodeficiency virus type 1 RNA in seminal plasma.

We have evaluated two commercially available kits (AMPLICOR MONITOR [Roche] and NASBA HIV-1 QT or NucliSens HIV-1 QT [Organon Teknika]) and two noncommercial methods for the accurate quantitation of human immunodeficiency virus type 1 (HIV-1) RNA in seminal plasma. The same panels of coded specimens were tested on four separate occasions. Laboratories using the commercial assays employed silica beads to isolate HIV-1 RNA, which removed inhibitory factors sometimes found in seminal plasma.

Virologic and immunologic response to nucleoside reverse-transcriptase inhibitor therapy among human immunodeficiency virus-infected infants and children.

Plasma human immunodeficiency virus RNA and CD4 lymphocyte response to nucleoside reverse-transcriptase therapy were evaluated in a large, comparative pediatric trial. Both baseline values and changes in the two laboratory markers over time correlated well with clinical outcome and possessed independent predictive value. In comparison of RNA reduction from baseline between the dideoxyinosine (ddI) and zidovudine+ddI therapeutic arms, marginal superiority of the combination arm was not correlated with an observed clinical benefit.

Detection of human immunodeficiency virus type 1 proviral DNA by PCR using an electrochemiluminescence-tagged probe.

We have developed a rapid, pseudohomogeneous assay for the detection of PCR amplicons, based on the use of electrochemiluminescence generated from a Tris-bipyridine ruthenium(II) label. PCR amplification of highly conserved human immunodeficiency virus type 1 (HIV-1) gag gene sequences was performed with SK38 and SK39 primers, the latter of which was 5' biotinylated. Post-PCR reaction mixtures were combined with 10(12) copies of the SK19 probe-Tris-bipyridine ruthenium(II) conjugate, denatured by heating at 100 degrees C for 5 min, and hybridized at 55 degrees C for an additional 15 min.

Evaluation of an automated immunodiagnostic assay, VIDAS Rotavirus, for detection of rotavirus in fecal specimens.

Four hundred sixty-four fecal specimens were tested for rotavirus by three immunoassays, VIDAS Rotavirus (bioMérieux Vitek, Hazelwood, Mo.), Rotaclone (Cambridge Biotech Corporation, Worcester, Mass.), and Pathfinder Rotavirus (Sansfi Diagnostics Pasteur, Chaska, Minn.

A transcriptionally amplified DNA probe assay with ligatable probes and immunochemical detection.

Transcriptionally amplified DNA probes are valuable tools in the development of sensitive nucleic acid-based diagnostic assays. Here we describe a model assay using a novel oligonucleotide hairpin probe that encodes a T7 RNA polymerase promoter. The hairpin probe and an adjacently hybridizing biotinylated capture probe were hybridized to target DNA and the duplex was captured onto streptavidin-coated magnetic particles.

Principles and applications of the polymerase chain reaction.

The invention of the polymerase chain reaction (PCR) technique for nucleic acid amplification has had a major impact on many diverse areas of both basic and clinical research. Since its inception in 1985, reports on a wide variety of applications for PCR have received much attention in scientific and medical literature. This technology has been shown to have wide applicability to the diagnosis of human disease, including such diverse areas as infectious diseases, genetic disorders, and cancer.

Occurrence of nonspecific reactions among stool specimens tested by the Abbott TestPack rotavirus enzyme immunoassay.

Sixty-five stool specimens obtained from children suffering from gastroenteritis were tested for the presence of antigen to rotavirus by the Abbott TestPack Rotavirus (TestPack) enzyme immunoassay kit. The Kallestad Pathfinder enzyme immunoassay, polyacrylamide gel electrophoresis, immune electron microscopy, and virus isolation were utilized as reference assays. Fifty-four specimens were in accord by TestPack and Kallestad Pathfinder.

Evaluation of three immunofluorescence assays for culture confirmation and typing of herpes simplex virus.

Three pairs of monoclonal antibodies, supplied in kits by Electro-Nucleonics, Inc. (ENI), The Syva Co., and Kallestad Laboratories, Inc.

Inhibitors of human neutrophil elastase in extracts of Streptococcus pneumoniae.

Alveolar architecture is spared during most pneumococcal pneumonias, despite the presence in pneumonic exudate of many neutrophils containing a potent elastase. We explored the possibility that pneumococci might contain an inhibitor of this enzyme. We found that pneumococcal extracts prepared by sonication or by lysis with sodium deoxycholate contained 2 different inhibitors of human neutrophil elastase.