Hybridized face-to-face and online laboratory content in the time of COVID-19.

This article describes strategies to adapt and ensure equivalency of content coverage for an existing protein assay laboratory practical for concurrent face-to-face and online deliveries during COVID-19 and beyond.

Pathogen genomics in public health laboratories: successes, challenges, and lessons learned from California's SARS-CoV-2 Whole-Genome Sequencing Initiative, California COVIDNet.

The capacity for pathogen genomics in public health expanded rapidly during the coronavirus disease 2019 (COVID-19) pandemic, but many public health laboratories did not have the infrastructure in place to handle the vast amount of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequence data generated. The California Department of Public Health, in partnership with Theiagen Genomics, was an early adopter of cloud-based resources for bioinformatics and genomic epidemiology, resulting in the creation of a SARS-CoV-2 genomic surveillance system that combined the efforts of more than 40 sequencing laboratories across government, academia and industry to form California COVIDNet, California's SARS-CoV-2 Whole-Genome Sequencing Initiative. Open-source bioinformatics workflows, ongoing training sessions for the public health workforce, and automated data transfer to visualization tools all contributed to the success of California COVIDNet. While challenges remain for public health genomic surveillance worldwide, California COVIDNet serves as a framework for a scaled and successful bioinformatics infrastructure that has expanded beyond SARS-CoV-2 to other pathogens of public health importance.

Successful Detection of Delta and Omicron Variants of SARS-CoV-2 by Veterinary Diagnostic Laboratory Participants in an Interlaboratory Comparison Exercise.

BACKGROUND: Throughout the COVID-19 pandemic, veterinary diagnostic laboratories have tested diagnostic samples for SARS-CoV-2 both in animals and over 6 million human samples. An evaluation of the performance of those laboratories is needed using blinded test samples to ensure that laboratories report reliable data to the public. This interlaboratory comparison exercise (ILC3) builds on 2 prior exercises to assess whether veterinary diagnostic laboratories can detect Delta and Omicron variants spiked in canine nasal matrix or viral transport medium. METHODS: The ILC organizer was an independent laboratory that prepared inactivated Delta variant at levels of 25 to 1000 copies per 50 µL of nasal matrix for blinded analysis. Omicron variant at 1000 copies per 50 µL of transport medium was also included. Feline infectious peritonitis virus (FIPV) RNA was used as a confounder for specificity assessment. Fourteen test samples were prepared for each participant. Participants used their routine diagnostic procedures for RNA extraction and real-time reverse transcriptase-PCR. Results were analyzed according to International Organization for Standardization (ISO) 16140-2:2016. RESULTS: Overall, laboratories demonstrated 93% detection for Delta and 97% for Omicron at 1000 copies per 50 µL. Specificity was 97% for blank samples and 100% for blank samples with FIPV. No differences in Cycle Threshold (Ct) values were significant for samples with the same virus levels between N1 and N2 markers, nor between the 2 variants. CONCLUSIONS: The results indicated that all ILC3 participants were able to detect both Delta and Omicron variants. The canine nasal matrix did not significantly affect SARS-CoV-2 detection.

Advancements in portable instruments based on affinity-capture-migration and affinity-capture-separation for use in clinical testing and life science applications.

The shift from testing at centralized diagnostic laboratories to remote locations is being driven by the development of point-of-care (POC) instruments and represents a transformative moment in medicine. POC instruments address the need for rapid results that can inform faster therapeutic decisions and interventions. These instruments are especially valuable in the field, such as in an ambulance, or in remote and rural locations. The development of telehealth, enabled by advancements in digital technologies like smartphones and cloud computing, is also aiding in this evolution, allowing medical professionals to provide care remotely, potentially reducing healthcare costs and improving patient longevity. One notable POC device is the lateral flow immunoassay (LFIA), which played a major role in addressing the COVID-19 pandemic due to its ease of use, rapid analysis time, and low cost. However, LFIA tests exhibit relatively low analytical sensitivity and provide semi-quantitative information, indicating either a positive, negative, or inconclusive result, which can be attributed to its one-dimensional format. Immunoaffinity capillary electrophoresis (IACE), on the other hand, offers a two-dimensional format that includes an affinity-capture step of one or more matrix constituents followed by release and electrophoretic separation. The method provides greater analytical sensitivity, and quantitative information, thereby reducing the rate of false positives, false negatives, and inconclusive results. Combining LFIA and IACE technologies can thus provide an effective and economical solution for screening, confirming results, and monitoring patient progress, representing a key strategy in advancing diagnostics in healthcare.

Анализ уроков, извлеченных из лабораторных мер реагирования на COVID-19 в Европейском регионе ВОЗ. Париж, Франция, 25–26 октября 2022 г. Отчет о совещании

На этом совещании обсуждались меры реагирования национальных лабораторий на пандемию COVID-19 и уроки, извлеченные за последние два года. Пандемия COVID-19 привела к значительной нагрузке на лаборатории общественного здравоохранения во всем мире. Государства-члены и территории сталкивались с множеством проблем, в том числе в отношении технического потенциала лабораторий, инфраструктуры, закупок и людских и финансовых ресурсов. Они не были готовы к кризисной ситуации такого масштаба в области общественного здравоохранения, и эта ситуация высветила важность готовности и ответных мер лабораторных служб.

First Round of External Quality Assessment Scheme for SARS-CoV-2 Laboratories During the COVID-19 Pandemic in Thailand.

The emergence of SARS-CoV-2 necessitated the rapid deployment of tests to diagnose COVID-19. To monitor the accuracy of testing across the COVID-19 laboratory network in Thailand, the Department of Medical Sciences under the Ministry of Public Health launched a national external quality assessment (EQA) scheme using samples containing inactivated SARS-CoV-2 culture supernatant from a predominant strain in the early phase of the Thailand outbreak. All 197 laboratories in the network participated; 93% (n=183) of which reported correct results for all 6 EQA samples. Ten laboratories reported false-negative results, mostly for samples with low viral concentrations, and 5 laboratories reported false-positive results (1 laboratory reported false positives and false negatives). An intralaboratory investigation of 14 laboratories reporting incorrect results revealed 2 main causes of error: (1) RNA contamination of the rRT-PCR reaction and (2) poor-quality RNA extraction. Specific reagent combinations were significantly associated with false-negative reports. Thailand's approach to national EQA for SARS-CoV-2 can serve as a roadmap for other countries interested in implementing a national EQA program to ensure laboratories provide accurate testing results, which is crucial in diagnosis, prevention, and control strategies. A national EQA program can be less costly and thus more sustainable than commercial EQA programs. National EQA is recommended to detect and correct testing errors and provide postmarket surveillance for diagnostic test performance.

Lessons learned from public health laboratory responses to COVID-19 across the WHO European Region: Paris, France, 25–26 October 2022: meeting report

This meeting discussed national laboratory responses to coronavirus disease (COVID-19) and the lessons learned from the past two years. The COVID-19 pandemic placed great stresses upon public health laboratories globally. Member States and territories faced many challenges, including laboratory technical capacity, infrastructure, procurement and human and financial resources. A public health crisis of this magnitude, while never anticipated, highlighted the importance of laboratory preparedness and response.

Diagnostics for Viral Pathogens in Veterinary Diagnostic Laboratories.

Laboratory testing is one part of clinical diagnosis, and quick and reliable testing results provide important data to support treatment decision and develop control strategies. Clinical viral testing has been shifting from traditional virus isolation and electron microscopy to molecular polymerase chain reaction and point-of-care antigen tests. This shift in diagnostic methodology also means change from looking for infectious virions or viral particles to hunting viral antigens and genomes. With technological development, it is predicted that metagenomic sequencing will be commonly used in veterinary clinical diagnosis for unveiling the whole picture of microbes involved in diseases in the future.

Insights from establishing a high throughput viral diagnostic laboratory for SARS-CoV-2 RT-PCR testing facility: challenges and experiences.

Background: The World Health Organization declared the coronavirus disease 2019 (COVID-19) a global pandemic on 11 March 2020. Identifying the infected people and isolating them was the only measure that was available to control the viral spread, as there were no standardized treatment interventions available. Various public health measures, including vaccination, have been implemented to control the spread of the virus worldwide. India, being a densely populated country, required laboratories in different zones of the country with the capacity to test a large number of samples and report test results at the earliest. The Indian Council of Medical Research (ICMR) took the lead role in developing policies, generating advisories, formulating guidelines, and establishing and approving testing centers for COVID-19 testing. With advisories of ICMR, the National Institute of Cancer Prevention and Research (NICPR) established a high-throughput viral diagnostic laboratory (HTVDL) for RT-PCR-based diagnosis of SARS-CoV-2 in April 2020. HTVDL was established during the first lockdown to serve the nation in developing and adopting rapid testing procedures and to expand the testing capacity using "Real-Time PCR." The HTVDL provided its testing support to the national capital territory of Delhi and western Uttar Pradesh, with a testing capacity of 6000 tests per day. The experience of establishing a high-throughput laboratory with all standard operating procedures against varied challenges in a developing country such as India is explained in the current manuscript which will be useful globally to enhance the knowledge on establishing an HTVDL in pandemic or non-pandemic times.

Global Veterinary Diagnostic Laboratory Equipment Management and Sustainability and Implications for Pandemic Preparedness Priorities1.

Substantial investments into laboratories, notably sophisticated equipment, have been made over time to detect emerging diseases close to their source. Diagnostic capacity has expanded as a result, but challenges have emerged. The Equipment Management and Sustainability Survey was sent to the Veterinary Services of 182 countries in mid-2019. We measured the status of forty types of laboratory equipment used in veterinary diagnostic laboratories. Of the 68,455 items reported from 227 laboratories in 136 countries, 22% (14,894/68,455) were improperly maintained, and 46% (29,957/65,490) were improperly calibrated. Notable differences were observed across World Bank income levels and regions, raising concerns about equipment reliability and the results they produce. Our results will advise partners and donors on how best to support low-resource veterinary laboratories to improve sustainability and fulfill their mandate toward pandemic prevention and preparedness, as well as encourage equipment manufacturers to spur innovation and develop more sustainable products that meet end-users' needs.

From Biowaste to Lab-Bench: Low-Cost Magnetic Iron Oxide Nanoparticles for RNA Extraction and SARS-CoV-2 Diagnostics.

The gold standard for diagnostics of SARS-CoV-2 (COVID-19) virus is based on real-time polymerase chain reaction (RT-PCR) using centralized PCR facilities and commercial viral RNA extraction kits. One of the key components of these kits are magnetic beads composed of silica coated magnetic iron oxide (Fe2O3 or Fe3O4) nanoparticles, needed for the selective extraction of RNA. At the beginning of the pandemic in 2019, due to a high demand across the world there were severe shortages of many reagents and consumables, including these magnetic beads required for testing for SARS-CoV-2. Laboratories needed to source these products elsewhere, preferably at a comparable or lower cost. Here, we describe the development of a simple, low-cost and scalable preparation of magnetic nanoparticles (MNPs) from biowaste and demonstrate their successful application in viral RNA extraction and the detection of COVID-19. These MNPs have a unique nanoplatelet shape with a high surface area, which are beneficial features, expected to provide improved RNA adsorption, better dispersion and processing ability compared with commercial spherical magnetic beads. Their performance in COVID-19 RNA extraction was evaluated in comparison with commercial magnetic beads and the results presented here showed comparable results for high throughput PCR analysis. The presented magnetic nanoplatelets generated from biomass waste are safe, low-cost, simple to produce in large scale and could provide a significantly reduced cost of nucleic acid extraction for SARS-CoV-2 and other DNA and RNA viruses.

Design of external quality assessment schemes and definition of the roles of their providers in future epidemics.

During an epidemic, individual test results form the basis of epidemiological indicators such as case numbers or incidence. Therefore, the accuracy of measures derived from these indicators depends on the reliability of individual results. In the COVID-19 pandemic, monitoring and evaluating the performance of the unprecedented number of testing facilities in operation, and novel testing systems in use, was urgently needed. External quality assessment (EQA) schemes are unique sources of data reporting on testing performance, and their providers are recognised contacts and support for test facilities (for technical-analytical topics) and health authorities (for planning the monitoring of infection diagnostics). To identify information provided by SARS-CoV-2 genome detection EQA schemes that is relevant for public health microbiology, we reviewed the current literature published in PubMed between January, 2020, and July, 2022. We derived recommendations for EQA providers and their schemes for best practices to monitor pathogen-detection performance in future epidemics. We also showed laboratories, test facilities, and health authorities the information and benefits they can derive from EQA data, and from the non-EQA services of their providers.

Impact of COVID-19 on access to laboratories and human participants: exercise science faculty perspectives.

Restrictions due to the coronavirus (COVID-19) pandemic impacted the ability of faculty and students in exercise science to work in lab settings with human participants. The purpose of this study was to determine how exercise science faculty were impacted by COVID-19 restrictions with respect to access and use of exercise science lab and research facilities. Of the 100 surveyed participants categorized as requiring access to people and lab spaces (lab-based faculty), 61% (n = 61) reported decreased research productivity with 87% (n = 53) of those faculty in one or more of the following subdisciplines: exercise physiology, clinical exercise physiology, or biomechanics. Of all lab-based faculty, 40% (n = 40) participants reported having access to students and lab spaces and 55% (n = 55) indicated they were allowed to conduct in-person research. Of tenure-track lab-based faculty, 80% (n = 20) reported a decrease in research productivity, of which 60.0% (n = 12) identified as female. Among faculty with 5 or less years of teaching experience (n = 23), 69.6% (n = 16) reported a decrease in productivity, with 68.8% (n = 11) of those being female. All exercise science faculty surveyed reported issues with safety and social distancing, modified lab and research procedures, faculty workload, and research productivity. This information can be leveraged to create better infrastructure to support faculty and develop and implement strategies to reduce workload inequities.

A scoping review on laboratory surveillance in the WHO Southeast Asia Region: Past, present and the future.

Background: The South-East Asia (SEA) region bears a significant proportion of the world's communicable disease burden. The onset of the COVID-19 pandemic has further affected the situation. A well-established laboratory-based surveillance (LBS) can reduce the burden of infectious diseases. In light of this, the review collated the existing literature on LBS system in the region and the modifications adopted by the surveillance systems during the pandemic. Methodology: We followed the guidelines for scoping review as prescribed by Arskey and O'Malley. We comprehensively searched three databases (PubMed, Scopus and CINAHL) and supplemented it with grey literature search. The screening of the articles was conducted at the title and abstract followed by full-text screening. This was followed by data extraction using a pre-tested data extraction tool by two independent reviewers. The results were presented narratively. Results: Including 75 relevant articles and documents, we compiled a list of surveillance systems. A shift from paper to dual (paper and electronic) modalities was identified across the countries. This largely low- and middle-income countries (LMIC) area face challenges in reporting, resources, and collaboration-related issues. While some countries have well-established National Reference Laboratories; others have more private than public-owned laboratories. Given the COVID-19 pandemic, modifications to the existing laboratory capacities to enable real-time surveillance was identified. Laboratory capacity complemented with genomic surveillance can indubitably aid in disease detection and control. Limitations due to inaccessible government portals, and language barriers are acknowledged. This review identified a comprehensive list of surveillance systems in the region, challenges faced in using these surveillance systems and inform the decision makers about the benefits of integrating fragmented surveillance systems. Conclusion: Regionally and nationally integrated genomic and laboratory surveillance systems justify capital investments, as their payoffs rationalise such costs owing to economies of scale over time. Further, as data flows are harmonized and standardized, algorithm- and computing-based pattern recognition methods allow for targeted and accurate disease prediction when integrated with, potentially, climate and weather systems data. Trained human resources are a sine qua non to optimize such investments, but in the medium to long run, such investments will buttress initiatives in other arenas at the regional level.

The effects of enhanced formaldehyde clearance in a gross anatomy laboratory by floor plan redesign and dissection table adjustment.

Formaldehyde has carcinogenic properties. It is associated with nasopharyngeal cancer and causes irritation of the eyes, nose, throat, and respiratory system. Formaldehyde exposure is a significant health concern for those participating in the gross anatomy laboratory, but no learning method can substitute cadaver dissection. We performed a formaldehyde level study in 2018, which found that most of the breathing zone (S-level) and environment (R-level) formaldehyde levels during laboratory sessions at the Faculty of Medicine Siriraj Hospital exceeded international ceiling standards. In the academic year 2019, we adapted the engineering rationale of the NIOSH hierarchy of controls to facilitate formaldehyde clearance by opening the dissection table covers and increasing the area per dissection table, then measured formaldehyde ceiling levels by formaldehyde detector tube with a gas-piston hand pump during (1) body wall, (2) upper limb, (3) head-neck, (4) thorax, (5) spinal cord removal, (6) lower limb, (7) abdomen, and (8) organs of special senses dissection sessions and comparing the results with the 2018 study. The perineum region data were excluded from analyses due to the laboratory closure in 2019 from the COVID-19 outbreak. There were statistically significant differences between the 2018 and 2019 S-levels (p < 0.001) and R-levels (p < 0.001). The mean S-level decreased by 64.18% from 1.34 ± 0.71 to 0.48 ± 0.26 ppm, and the mean R-level decreased by 70.18% from 0.57 ± 0.27 to 0.17 ± 0.09 ppm. The highest formaldehyde level in 2019 was the S-level in the body wall region (1.04 ± 0.3 ppm), followed by the S-level in the abdomen region (0.56 ± 0.08 ppm) and the spinal cord removal region (0.51 ± 0.29 ppm). All 2019 formaldehyde levels passed the OSHA 15-min STEL standard (2 ppm). The R-level in the special sense region (0.06 ± 0.02 ppm) passed the NIOSH 15-min ceiling limit (0.1 ppm). Three levels for 2019 were very close: the R-level in the head-neck region (0.11 ± 0.08 ppm), the abdomen region (0.11 ± 0.08), the body wall region (0.14 ± 0.12 ppm), and the S-level in the special sense region (0.12 ± 0.04 ppm). In summary, extensive analysis and removal of factors impeding formaldehyde clearance can improve the general ventilation system and achieve the OSHA 15-min STEL standard.

A Public Health Laboratory Information System in Support of Health Emergencies: The Nebraska Public Health Laboratory COVID-19 Experience.

OBJECTIVES: Public health laboratories (PHLs) are essential components of US Public Health Service operations. The health information technology that supports PHLs is central to effective and efficient laboratory operations and overall public health response to infectious disease management. This analysis presents key information on how the Nebraska Public Health Laboratory (NPHL) information technology system evolved to meet the demands of the COVID-19 pandemic. MATERIALS AND METHODS: COVID-19 presented numerous, unforeseen information technology system challenges. The most notable challenges requiring changes to NPHL software systems and capability were improving efficiency of the laboratory operation due to high-volume testing, responding daily to demands for timely data for analysis by partner systems, interfacing with multiple testing (equipment) platforms, and supporting community-based specimen collection programs. RESULTS: Improvements to the NPHL information technology system enabled NPHL to perform >121 000 SARS-CoV-2 polymerase chain reaction tests from March 2020 through January 2022 at a sustainable rate of 2000 SARS-CoV-2 tests per day, with no increase in laboratory staffing. Electronic reporting of 62 000 rapid antigen tests eliminated paper reporting and extended testing services throughout the state. Collection of COVID-19 symptom data before specimen collection enabled NPHL to make data-driven decisions to perform pool testing and conserve testing kits when supplies were low. PRACTICE IMPLICATIONS: NPHL information technology applications proved essential for managing health care provider workload, prioritizing the use of scarce testing supplies, and managing Nebraska's overall pandemic response. The NPHL experience provides useful examples of a highly capable information technology system and suggests areas for additional attention in the PHL environment, including a focus on end users, collaboration with various partners, and investment in information technology.