Real-Time, Multiplexed SHERLOCK for in Vitro Diagnostics.

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the need for simple, low-cost, and scalable diagnostics that can be widely deployed for rapid testing. Clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics have emerged as a promising technology, but its implementation in clinical laboratories has been limited by the requirement of a separate amplification step prior to CRISPR-associated (Cas) enzyme-based detection. This article reports the discovery of two novel Cas12 enzymes (SLK9 and SLK5-2) that exhibit enzymatic activity at 60°C, which, when combined with loop-mediated isothermal amplification (LAMP), enable a real-time, single-step nucleic acid detection method [real-time SHERLOCK (real-time SLK)]. Real-time SLK was demonstrated to provide accurate results comparable to those from real-time quantitative RT-PCR in clinical samples, with 100% positive and 100% negative percent agreement. The method is further demonstrated to be compatible with direct testing (real-time SLK Direct) of samples from anterior nasal swabs, without the need for standard nucleic acid extraction. Lastly, SLK9 was combined with either Alicyclobacillus acidoterrestris AacCas12b or with SLK5-2 to generate a real-time, multiplexed CRISPR-based diagnostic assay for the simultaneous detection of SARS-CoV-2 and a human-based control in a single reaction, with sensitivity down to 5 copies/µL and a time to result of under 30 minutes.

Does the variant positivity and negativity affect the clinical course in COVID-19?: A cohort study.

The primary aim of the current study is to analyze the clinical, laboratory, and demographic data comparing the patients with Coronavirus Disease 2019 (COVID-19) admitted to our intensive care unit before and after the UK variant was first diagnosed in December 2020. The secondary objective was to describe a treatment approach for COVID-19. Between Mar 12, 2020, and Jun 22, 2021, 159 patients with COVID-19 were allocated into 2 groups: the variant negative group (77 patients before December 2020) and the variant positive group (82 patients after December 2020). The statistical analyses included early and late complications, demographic data, symptoms, comorbidities, intubation and mortality rates, and treatment options. Regarding early complications, unilateral pneumonia was more common in the variant (-) group (P = .019), whereas bilateral pneumonia was more common in the variant (+) group (P < .001). Regarding late complications, only cytomegalovirus pneumonia was observed more frequently in the variant (-) group (P = .023), whereas secondary gram (+) infection, pulmonary fibrosis (P = .048), acute respiratory distress syndrome (ARDS) (P = .017), and septic shock (P = .051) were more common in the variant (+) group. The therapeutic approach showed significant differences in the second group such as plasma exchange and extracorporeal membrane oxygenation which is more commonly used in the variant (+) group. Although mortality and intubation rates did not differ between the groups, severe challenging early and late complications were observed mainly in the variant (+) group, necessitating invasive treatment options. We hope that our data from the pandemic will shed light on this field. Regarding the COVID-19 pandemic, it is clear that there is much to be done to deal with future pandemics.

Increases in CLIA-Waived Testing Sites Since the Start of the COVID-19 Pandemic.

The number of testing sites receiving their first Certificate of Waiver (CoW) under the Clinical Laboratory Improvement Amendments of 1988 (CLIA) increased significantly after the start of the COVID-19 pandemic. We compared the first-time CoWs in 2020-2021 to those in 2018-2019. The total number of first-time CoWs during 2020-2021 was more than twice what it was in 2018-2019, corresponding to population testing needs during the COVID-19 pandemic, especially in assisted living facility, pharmacy, physician office, and school/student health service settings. This study highlighted the need to strengthen clinical testing strategies to be better prepared for future public health emergencies.

Performance Characteristics of High-Throughput Serologic Assays for Severe Acute Respiratory Syndrome Coronavirus 2 with Food and Drug Administration Emergency Use Authorization: A Review.

This review provides a broad summary of the performance characteristics of high-throughput severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serologic assays with Food and Drug Administration Emergency Use Authorization, which are commonly found in central clinical laboratories. In addition, this review discusses the current roles of serologic testing for SARS-CoV-2 and provides a perspective for the future.

Biosafety protection and workflow of clinical microbiology laboratory under COVID-19: A review.

This paper mainly discusses how to do a good job of daily biosafety protection measures in clinical microbiology laboratories during the epidemic of COVID-19, so as to ensure the safe development of routine clinical microbiology testing items. According to the microbiological and epidemiological characteristics of the novel coronavirus, this paper analyzed the potential risks of the laboratory from the perspective of personal protection before, during, and after testing. Combined with the actual work situation, the improved biosafety protection measures and optimized work flow are introduced to ensure the safety of medical staff and the smooth development of daily work. Danyang People's Hospital of Jiangsu Province, clinical microbiology laboratory of clinical laboratory in strict accordance with the relevant laws and regulations, technical specifications and the expert consensus, combined with their own conditions, the biosafety measures to perfect the working process was optimized, effectively prevent the laboratory exposure, and maintain strict working condition for a long time, continue to improve. We found that the biosafety protection measures of clinical microbiology laboratory have good prevention and control effect on preventing infection of medical staff, which will greatly reduce the risk of infection of medical staff, form good working habits, and provide reference for biosafety protection of microbiology laboratory during the epidemic of COVID-19.

Technical and health governance aspects of the External Quality Assessment Scheme for the SARS-CoV-2 molecular tests: institutional experience performed in all clinical laboratories of a Regional Health Service.

OBJECTIVES: Since December 2019, the worldwide public health has been threatened by a severe acute respiratory syndrome caused by Coronavirus-2. From the beginning, a turning point has been the identification of new cases of infection, in order to minimize the virus spreading among the population. For this reason, it was necessary introducing a panel of tests able to identify positive cases, which became crucial for all countries. METHODS: As a Regional Reference Centre, the CRQ Laboratory (Regional Laboratory for the Quality Control) developed and conducted an External Quality Assessment (EQA) panel of assay, so as to evaluate the quality of real-time reverse transcription polymerase chain reaction (PCR), which were used by 62 Sicilian laboratories, previously authorized to issue certificates for the COVID-19 diagnosis, on behalf of the Public Health Service. RESULTS: The qualitative performance test was based on pooled samples with different viral loads of SARS-CoV-2 or human Coronavirus OC43. 75% of the participating laboratories tested all core samples correctly, while the remaining 25% interpreted incorrectly the EQA exercise samples matching negatively the standards required. CONCLUSIONS: Subsequent inspection visits confirmed the issue of incorrect positive and negative certifications for COVID-19 by private and public laboratories, despite the possession of the authorization requirements currently provided for by current regulations, with a significant impact on the SSR.

Отчет по итогам первого совещания Европейской региональной лабораторной специальной группы по особо опасным патогенам: г. Вена, Австрия, 26–27 февраля 2020 г.

Международные сети по лабораторному надзору, обеспечению готовности и ответным действиям представляют собой важный механизм усиления лабораторных служб, поскольку они могут служить как платформой для обмена информацией и экспертными знаниями, так и системой направления клинических образцов на первичное и подтверждающее тестирование. Из числа приоритетных стран Программы ВОЗ по чрезвычайным ситуациям в области здравоохранения в Европейском регионе остается ряд стран, которые не участвуют в деятельности международных сетей по обеспечению лабораторной готовности и реагирования в связи с особо опасными патогенами (ООП), что рассматривается как серьезный пробел. Для его восполнения Европейское региональное бюро ВОЗ сформировало Европейскую региональную лабораторную специальную группу по особо опасным патогенам (Лабораторную специальную группу). Настоящее совещание явилось первой официальной встречей членов и партнеров Лабораторной специальной группы. Совещание дало возможность представить информацию о глобальной и региональной ситуации с распространением вируса, вызывающего COVID-19, в том числе, о готовности лабораторных служб.

Report first meeting of the European Region laboratory task force for high threat pathogens: Vienna, Austria, 26–27 February 2020

International networks for laboratory surveillance, preparedness and response are an important tool for laboratory strengthening, because they can serve both as a platform for sharing information and expertise, and as a system for the referral of diagnostic specimens for primary and confirmatory testing. Among the European Region priority countries of the WHO Health Emergencies Programme a number do not participate in international laboratory preparedness and response networks for High Threat Pathogens (HTPs), which represents a key gap. To address this gap, the WHO Regional Office for Europe is establishing the European Regional Laboratory Task Force for High Threat Pathogens (Lab Task Force). This was the first official meeting of the Lab Task Force’s members and partners and the opportunity to provide information on COVID-19 virus globally and in the Region, including laboratory readiness, was taken.

Changes in Test Volumes During Coronavirus Disease 2019 (COVID-19): A Laboratory Stewardship Opportunity.

CONTEXT.­: Coronavirus disease 2019 (COVID-19) changed the dynamics of health care delivery, shifting patient priorities and deferring care perceived as less urgent. Delayed or eliminated care may place patients at risk for adverse outcomes. OBJECTIVE.­: To identify opportunities for laboratory test stewardship to close potential gaps in care created by the COVID-19 pandemic. DESIGN.­: The study was a retrospective time series design examining laboratory services received before and during the COVID-19 pandemic at a large metropolitan health system serving women and children. RESULTS.­: Laboratory test volumes displayed 3 distinct patterns: (1) a decrease during state lockdown, followed by near-complete or complete recovery; (2) no change; and (3) a persistent decrease. Tests that diagnose or monitor chronic illness recovered only partially. For example, hemoglobin A1c initially declined 80% (from 2232 for April 2019 to 452 for April 2020), and there was a sustained 16% drop (28-day daily average 117 at August 30, 2019, to 98 at August 30, 2020) 4 months later. Blood lead dropped 39% (from 2158 for April 2019 to 1314 for April 2020) and remained 23% lower after 4 months. CONCLUSIONS.­: The pandemic has taken a toll on patients, practitioners, and health systems. Laboratory professionals have access to data that can provide insight into clinical practice and identify pandemic-related gaps in care. During the pandemic, the biggest patient threat is underuse, particularly among tests to manage chronic diseases and for traditionally underserved communities and people of color. A laboratory stewardship program, focused on peri-pandemic care, positions pathologists and other laboratory professionals as health care leaders with a commitment to appropriate, equitable, and efficient care.

Impact of the COVID-19 pandemic on clinical research activities: Survey of study participants and health care workers participating in a hypertension trial in Vietnam.

BACKGROUND: The COVID-19 pandemic has had a profound worldwide impact. Vietnam, a lower middle-income country with limited resources, has successfully slowed this pandemic. The objectives of this report are to explore the impact of the COVID-19 pandemic on the research activities of an ongoing hypertension trial using a storytelling intervention in Vietnam. METHODS: Data were collected in a mixed-methods study among 86 patients and 10 health care workers participating in a clinical trial designed to improve hypertension control. Several questions related to the impact of COVID-19 on patient's daily activities and adherence to the study interventions were included in the follow-up visits. A focus group discussion was conducted among health care workers to discuss the impact of COVID-19 on research related activities. RESULTS: Fewer patients in the intervention group reported that they faced difficulties in adhering to prescribed study interventions, wanted to receive a call from a dedicated hotline, or have a visit from a community health worker as compared with those in the comparison group. Most study patients are willing to participate in future health research studies. When asked about the potential use of mobile phones in health research studies, fewer patients in the intervention group felt comfortable using a mobile phone for the delivery of intervention and interviews compared with those in the comparison condition. Community health workers shared that they visited patient's homes more often than previously due to the pandemic and health care workers had to perform more virus containment activities without a corresponding increase in ancillary staff. CONCLUSIONS: Both patients and health care workers in Vietnam faced difficulties in adhering to recommended trial interventions and procedures. Multiple approaches for intervention delivery and data collection are needed to overcome these difficulties during future health crises and enhance the implementation of future research studies. TRIAL REGISTRATION: ClinicalTrials.gov. Registration number: https://clinicaltrials.gov/ct2/show/NCT03590691 (registration date July 17, 2018).

Comparative Performance of Four Nucleic Acid Amplification Tests for SARS-CoV-2 Virus.

BACKGROUND: COVID-19 is caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was discovered in 2019 and spread around the world in a short time. SARS-CoV-2 nucleic acid amplification tests (NAATs) have been rapidly developed and quickly applied to clinical testing of COVID-19. Aim of this study was to evaluate the performance of four NAAT assays. METHODS: Limit of detection (LOD), precision, accuracy, analytical specificity and analytical interference studies on four NAATs (Daan, Sansure, Hybribio, and Bioperfectus) were performed according to Clinical Laboratory Standards Institute protocols and guidelines. The four NAATs were compared using 46 clinical samples. RESULTS: The LOD of the N gene for Daan, Sansure, and Hybribio was 500 copies/mL, and that for Bioperfectus was 1,000 copies/mL. The LOD of the ORF1ab gene for Daan, Bioperfectus, and Hybribio was 3,000 copies/mL, and that for Sansure was 2,000 copies/mL. A good precision was shown at the concentration above 20% of the LOD for all four NAATs, with all individual coefficients of variation below 3.6%. Satisfactory results were also observed in the accuracy, analytical specificity, and analytical interference tests. The results of the comparison test showed that Daan, Sansure, and Hybribio NAATs could detect the samples with a specificity of 100% (30/30) and a sensitivity of 100% (16/16), whereas Bioperfectus NAAT detected the samples with a specificity of 100% (30/30) and a sensitivity of 81.25% (13/16). However, no significant difference in sensitivity was found between Bioperfectus NAAT and the three other NAATs (p > 0.05). CONCLUSIONS: The four SARS-CoV-2 NAATs showed comparable performance, with the LOD of the N gene lower than the LOD of the ORF1ab gene.

Evaluation of the Clinical Performance of 7 Serological Assays for SARS-CoV-2 for Use in Clinical Laboratories.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serological assays have emerged as a response to the global pandemic, warranting studies evaluating their clinical performance. This study investigated 7 commercially available SARS-CoV-2 serological assays in samples from noninfected individuals and hospitalized patients. METHODS: SARS-CoV-2 qualitative serological assays by Abbott (IgG), Beckman (IgG), DiaSorin (IgG), EUROIMMUN (IgG and IgA), Roche and Bio-Rad (Total) were evaluated using specimens collected pre-December 2019 (n = 393), from nucleic acid amplification testing (NAAT) negative patients (n = 40), and from 53 patients with COVID-19 by NAAT collected 3-21 days post-onset of symptoms (POS) (N = 83). Negative agreement (NA), positive agreement (PA), and positive and negative predictive values (PPV and NPV) at prevalences of 5% and 10% were calculated. RESULTS: The overall %NA; 95% CI in the negative samples were: Roche 99.8%; 99.3-100.2, Beckman 99.8%; 98.7-100.0, Abbott and Bio-Rad 99.3%; 98.0-99.9, DiaSorin 98.4; 97.2-99.6, EUROIMMUN IgG 97.5%; 95.5-98.7, and EUROIMMUN IgA 79.7%; 75.9-83.5), accounting for positive/equivocal results as false positives. The %PA; 95% CI in samples collected 14+ days POS (n = 24) were: Bio-Rad 83.3%; 68.4-98.2, Abbott and Roche 79.2%; 62.9-95.4, EUROIMMUN IgA 70.8%; 52.6-89.0, Beckman 58.3%; 38.6-78.1, DiaSorin 54.2; 34.2-74.1, and EUROIMMUN IgG 50.0%; 30.0-70.0, accounting for negative/equivocal results as false negatives. NPVs ranged from 97.4%-98.9% and 94.7%-97.7% for prevalences 5% and 10%, respectively. PPVs ranged from 15.5%-94.8% and 27.9%-97.4% for prevalences 5% and 10%, respectively. CONCLUSION: The Roche and Beckman assays resulted in fewer false positives, followed by the Bio-Rad and Abbott assays. While the Bio-Rad assay demonstrated higher antibody detection in COVID-19-positive patients, PA claims cannot be established with a high level of confidence in our sample population.

Strategies to ensure efficient laboratory functioning while navigating through the COVID-19 crisis in developing countries: An early experience from a tertiary care centre in India.

BACKGROUND: The coronavirus disease 2019 (COVID 19) is a zoonotic viral infection that originated in Wuhan, China, in December 2019. It was declared a pandemic by the World Health Organization shortly thereafter. This pandemic is going to have a lasting impact on the functioning of pathology laboratories due to the frequent handling of potentially infectious samples by the laboratory personnel. To deal with this unprecedented situation, various national and international guidelines have been put forward outlining the precautions to be taken during sample processing from a potentially infectious patient. PURPOSE: Most of these guidelines are centered around laboratories that are a part of designated COVID 19 hospitals. However, proper protocols need to be in place in all laboratories, irrespective of whether they are a part of COVID 19 hospital or not as this would greatly reduce the risk of exposure of laboratory/hospital personnel. As part of a laboratory associated with a rural cancer hospital which is not a dedicated COVID 19 hospital, we aim to present our institute's experience in handling pathology specimens during the COVID 19 era. CONCLUSION: We hope this will address the concerns of small to medium sized laboratories and help them build an effective strategy required for protecting the laboratory personnel from risk of exposure and also ensure smooth and optimum functioning of the laboratory services.

COVID-19-another influential event impacts on laboratory medicine management.

BACKGROUND: Before public health emergencies became a major challenge worldwide, the scope of laboratory management was only related to developing, maintaining, improving, and sustaining the quality of accurate laboratory results for improved clinical outcomes. Indeed, quality management is an especially important aspect and has achieved great milestones during the development of clinical laboratories. CURRENT STATUS: However, since the coronavirus disease 2019 (COVID-19) pandemic continues to be a threat worldwide, previous management mode inside the separate laboratory could not cater to the demand of the COVID-19 public health emergency. Among emerging new issues, the prominent challenges during the period of COVID-19 pandemic are rapid-launched laboratory-developed tests (LDTs) for urgent clinical application, rapid expansion of testing capabilities, laboratory medicine resources, and personnel shortages. These related issues are now impacting on clinical laboratory and need to be effectively addressed. CONCLUSION: Different from traditional views of laboratory medicine management that focus on separate laboratories, present clinical laboratory management must be multidimensional mode which should consider consolidation of the efficient network of regional clinical laboratories and reasonable planning of laboratories resources from the view of overall strategy. Based on relevant research and our experience, in this review, we retrospect the history trajectory of laboratory medicine management, and also, we provide existing and other feasible recommended management strategies for laboratory medicine in future.