Professional oversight of centralized laboratories can be provided by individuals from a wide variety of backgrounds, but the individual charged with that responsibility must have strong ...collaborative relationships with the clinical specialists in the other laboratory disciplines to help establish the test menu, testing priorities and integration with other test methods, and to help with the interpretation of molecular test results (matrix management scheme). Historically, molecular diagnostic laboratories were limited to academic medical centers or specialized references laboratories because of unique laboratory design and workflow requirements, lack of adequately trained technical and professional staff, complexity of the tests, and reliance on the development and validation of laboratory-developed assays owing to the lack of US Food and Drug Administration (FDA)2-approved/ cleared assays. ...in many laboratories, including my own, these services are offered in a clinical genomics laboratory because they are closely aligned by technology, need for a strong knowledge base in genetics, and bioinformatics requirements. ...molecular pathology is a collection of related methods and procedures not a separate discipline within laboratory medicine.
Over the past 2 decades there have been substantial improvements in the methods used to quantify viral nucleic acid in body fluids and in our understanding of how to use viral load measurements in ...the diagnosis and management of patients with a number of viral infections. These methods are now integrated into a wide range of diagnostic and treatment guidelines and commonly deployed in a variety of clinical settings.
Quantitative nucleic acid amplification methods that are used to measure viral load are described along with key issues and important variables that affect their performance. Particular emphasis is placed on those methods used in clinical laboratories as US Food and Drug Administration-cleared or laboratory-developed tests. We discuss the clinical applications of these methods in patients with HIV-1, hepatitis C virus, hepatitis B virus, cytomegalovirus, Epstein-Barr virus, and BK polyomavirus infections. Finally, the current challenges and future directions of viral load testing are examined.
Quantitative nucleic acid amplification tests provide important information that can be used to predict disease progression, distinguish symptomatic from asymptomatic infection, and assess the efficacy of antiviral therapy. Despite the advances in technology, large challenges remain for viral testing related to accuracy, precision, and standardization. Digital PCR, a direct method of quantification of nucleic acids that does not rely on rate-based measurements or calibration curves, may address many of the current challenges.
Traditional microbiological methods for detection of respiratory tract pathogens can be slow, are often not sensitive, may not distinguish infection from colonization, and are influenced by previous ...antibiotic therapy. Molecular diagnostic tests for common and atypical causative pathogens of community-acquired pneumonia have the potential to dramatically increase the diagnostic yield and decrease the time required to render results. Unfortunately, these tests often lack standardization and are not widely available. Consideration should be given to the development and evaluation of companion molecular diagnostic tests for detection of respiratory pathogens in future clinical trials of antimicrobials intended to treat community-acquired pneumonia.
We compared two rapid, point-of care nucleic acid amplification tests for detection of influenza A and B viruses (Alere i Alere and cobas Liat Roche Diagnostics) with the influenza A and B virus test ...components of the FilmArray respiratory panel (BioFire Diagnostics) using 129 respiratory specimens collected in universal viral transport medium (80 influenza A virus and 16 influenza B virus positive) from both adult and pediatric patients. The sensitivities of the Alere test were 71.3% for influenza A virus and 93.3% for influenza B virus, with specificities of 100% for both viruses. The sensitivities and specificities of the Liat test were 100% for both influenza A and B viruses. The poor sensitivity of the Alere test for detection of influenza A virus was likely due to a study set that included many low-positive samples that were below its limit of detection.
BackgroundThe goal of the present study was to assess risk factors for perinatal hepatitis C virus (HCV) transmission and the natural history of infection among HCV-infected infants MethodsIn a ...cohort study, 244 infants born to HCV-positive mothers were followed from birth until age ⩾12 months. Maternal serum was collected at enrollment and delivery; infant serum was collected at birth and at 8 well-child visits. Testing included detection of antibody to HCV, detection of HCV RNA (qualitative and quantitative), and genotyping. HCV-infected infants were followed annually until age 5 years ResultsOverall, 9 of 190 (4.7% 95% confidence interval {CI}, 2.3%–9.1%) infants born to mothers who were HCV RNA positive at delivery became infected, compared with 0 of 54 infants born to HCV RNA–negative mothers (P=.10). Among HCV RNA–positive mothers, the rate of transmission was 3.8% (95% CI, 1.7%–8.1%) from the 182 who were human immunodeficiency virus (HIV) negative, compared with 25.0% (95% CI, 4.5%–64.4%) from the 8 who were HIV positive (P<.05). Three infected infants resolved their infection (i.e., became HCV RNA negative). In multivariate analysis restricted to HCV RNA–positive mothers, membrane rupture ⩾6 h (odds ratio OR, 9.3 95% CI, 1.5–179.7) and internal fetal monitoring (OR, 6.7 95% CI, 1.1–35.9) were associated with transmission of HCV to infants ConclusionIf duration of membrane rupture and internal fetal monitoring are confirmed to be associated with transmission, interventions may be possible to decrease the risk of transmission
We verified the analytical performance of the Abbott RealTime SARS-CoV-2 assay on the m2000 system and compared its clinical performance to the CDC 2019-nCoV real-time PCR diagnostic panel and the ...Thermo Fisher TaqPath RT-PCR COVID-19 kit. We also performed a bridging study comparing the RealTime SARS-CoV-2 assay with the new Abbott Alinity m SARS-CoV-2 assay. A number of standards, reference materials, and commercially available controls were used for the analytical verification to confirm the limit of detection, linearity, and reproducibility. We used nasopharyngeal (NP) swab specimens collected in saline for the clinical verification and bridging studies. Overall, we found 91.2% positive percent agreement (PPA; 95% confidence interval CI = 76.2 to 98.14%) and a 100% negative percent agreement (NPA; 95% CI = 97.97 to 100%) between the results of the RealTime SARS-CoV-2 and CDC tests with 217 NP specimens (P = 0.13). We found a PPA of 100% (95% CI = 90.26 to 100%) and an NPA of 95.15% (95% CI = 83.47 to 99.4%) between the results of the RealTime and TaqPath tests with 77 NP specimens (P = 0.24). Finally, we tested 203 NP swab specimens for SARS-CoV-2 on the m2000 on the Alinity m systems. The PPA and NPA were 92.2% (95% CI = 85.3 to 96.59%) and 92% (95% CI = 84.8 to 96.5%), respectively (P = 0.4). Although cycle number (Cn) values obtained for the concordant positive samples were highly correlated (R2 = 0.95), the Cn values were on average 14.14 higher on the Alinity m system due to the unread cycles with the RealTime SARS-CoV-2 assay.
Abstract
Background
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody testing is an important tool in assessment of pandemic progress, contact tracing, and identification of ...recovered coronavirus disease 2019 (COVID-19) patients. We evaluated an orthogonal testing algorithm (OTA) to improve test specificity in these use cases.
Methods
A two-step OTA was applied where individuals who initially tested positive were tested with a second test. The first-line test, detecting IgG antibodies to the viral nucleocapsid protein, was validated in 130 samples and the second-line test, detecting IgG antibodies to the viral spike protein in 148 samples. The OTA was evaluated in 4333 clinical patient specimens. The seropositivity rates relative to the SARS-CoV-2 PCR positivity rates were evaluated from our entire patient population data (n = 5102).
Results
The first-line test resulted in a clinical sensitivity of 96.4% (95% CI; 82.3% to 99.4%), and specificity of 99.0% (95% CI; 94.7% to 99.8%), whereas the second-line test had a sensitivity of 100% (95% CI; 87.1% to 100%) and specificity of 98.4% (95% CI; 94.2% to 99.5%). Using the OTA, 78/98 (80%) of initially positive SARS-CoV-2 IgG results were confirmed with a second-line test, while 11/42 (26%) of previously diagnosed COVID-19 patients had no detectable antibodies as long as 94 days post PCR diagnosis.
Conclusion
Our results show that an OTA can be used to identify patients who require further follow-up due to potential SARS CoV-2 IgG false positive results. In addition, serological testing may not be sufficiently sensitive to reliably detect prior COVID-19 infection.
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