Clinical impact of molecular point-of-care testing for suspected COVID-19 in hospital (COV-19POC): a prospective, interventional, non-randomised, controlled study

Analysis and mapping of global research publications on point-of-care testing for infectious diseases

RATIONALE

This study presents the first comprehensive analysis and mapping of scientific research on point-of-care testing (POCT) in infectious diseases, filling a gap in understanding the evolving landscape of this field. The identification of research themes and global contributions offers valuable insights.

AIMS AND OBJECTIVES

This manuscript aims to analyse and map scientific research on POCT in the context of infectious diseases.

METHODS

The study employed a comprehensive search strategy using terms related to POCT and infectious diseases. The search was conducted on the Scopus database, refining results based on inclusion and exclusion criteria. The dataset of 1719 research articles was then subjected to descriptive analysis and mapping using VOSviewer.

RESULTS

The research findings indicate an exponential growth in POCT-related publications, with 46.8% published post the COVID-19 pandemic. Plos One journal led in publication frequency, and Biosensors and Bioelectronics received the highest citations per article. North America and Western Europe dominated contributions, with notable participation from China, South Africa, and India. The research landscape revealed the following research themes: detection technologies, human immunodeficiency virus (HIV)/sexually transmitted infection (STI) diagnosis, antibiotic optimisation, and schistosomiasis. Clinical trials focused on antibiotic prescribing, HIV, STIs, and specific infections. The findings suggest a shifting landscape towards POCT, emphasising the need for future planning and investment in healthcare systems. The research identifies areas for future exploration, such as the impact of POCT on antibiotic prescribing and its role in combating infectious diseases in low- and middle-income countries.

CONCLUSION

Implementation of POCT has the potential to revolutionise infectious disease management, improve patient outcomes, and reduce the global burden of diseases. Better public awareness, healthcare team management, and planning for POCT at entry points are crucial for societal benefit. Results demonstrated the evolving role of POCT in infectious disease management and prevention.

Effects of Different SARS-CoV-2 Testing Strategies in the Emergency Department on Length of Stay and Clinical Outcomes: A Randomised Controlled Trial

The turn-around-time (TAT) of diagnostic and screening measures such as testing for SARS-CoV-2 can affect a patient's length of stay (LOS) in the hospital as well as the emergency department (ED). This, in turn, can affect clinical outcomes. Therefore, a reliable and time-efficient SARS-CoV-2 testing strategy is necessary, especially in the ED. In this randomised controlled trial, n = 598 ED patients presenting to one of three university hospital EDs in Berlin, Germany, and needing hospitalisation were randomly assigned to two intervention groups and one control group. Accordingly, different SARS-CoV-2 testing strategies were implemented: rapid antigen and point-of-care (POC) reverse transcription polymerase chain reaction (rtPCR) testing with the Roche cobas® Liat® (LIAT) (group one n = 198), POC rtPCR testing with the LIAT (group two n = 197), and central laboratory rtPCR testing (group three, control group n = 203). The median LOS in the hospital as an inpatient across the groups was 7 days. Patients' LOS in the ED of more than seven hours did not differ significantly, and furthermore, no significant differences were observed regarding clinical outcomes such as intensive care unit stay or death. The rapid and POC test strategies had a significantly (p < 0.01) shorter median TAT (group one 00:48 h, group two 00:21 h) than the regular central laboratory rtPCR test (group three 06:26 h). However, fast SARS-CoV-2 testing strategies did not reduce ED or inpatient LOS significantly in less urgent ED admissions. Testing strategies should be adjusted to the current circumstances including crowding, SARS-CoV-2 incidences, and patient cohort. This trial is registered with DRKS00023117.

Routine, molecular point-of-care testing for SARS-CoV-2 and other respiratory viruses within an acute oncology service improves patient care

OBJECTIVES

COVID-19 has caused significant challenges for infection prevention measures and patient flow in hospital admission pathways. We aimed to assess the impact of replacing laboratory PCR with molecular point-of-care testing (mPOCT) for respiratory viruses including SARS-CoV-2, within an Acute Oncology Service (AOS).

METHODS

This pre- and post-implementation study took place in the AOS of a large teaching hospital, in Southampton, UK. We collected data from two periods: November 25th, 2019 to November 24th, 2020, when respiratory virus testing utilised laboratory PCR, and December 1st, 2020 to May 31st, 2021 following the introduction of mPOCT. The primary outcome was the time to results.

RESULTS

2189 patients were tested in the pre-implementation period and 1540 in the post implementation period. Median (IQR) time to results was 5.8 h (4.2-10.6) pre-implementation and 1.9 h (1.5-3.0) post-implementation (difference -3.6 h [95%CI to -3.8 to -3.5]; p < 0.0001). Median time spent in assessment areas was 6.0 h (4.1-7.9) pre-implementation and 5.5 h (3.8-7.4) post-implementation (p < 0.0001). 20 (0.9%) patients admitted via AOS assessment unit developed hospital-acquired respiratory virus infection pre-implementation versus 0 (0%) post-implementation (p = 0.031).

CONCLUSIONS

Routine mPOCT for respiratory viruses, including SARS-CoV-2, was associated with a reduced time to results, reduced time in assessment areas, and a reduction in the rates of hospital-acquired respiratory virus infection in an acute oncology assessment unit.

Point of Care Tests: Changing Paradigms in the Diagnosis of SARS-CoV-2

Background

Point of care tests provide rapid information about the patient's condition, with a turnaround time of 15 min. During the COVID-19 pandemic, many such point of care tests were developed, to aid in the rapid diagnosis of SARS-Cov-2 infection.

Aim

To describe and synthesize the available literature on point of care tests for diagnosis of SARS-CoV-2.

Methodology

This narrative review was done through online literature search, using Google Scholar and PubMed.

Result

There were 51 point of care tests for diagnosis of SARS-CoV-2 which were validated using different samples, such as such as nasopharyngeal swabs(42), oropharyngeal and naso-pharyngealswabs(2), oropharyngeal swab in VTM(1) nasal swabs(5) and throat swab(1).

Conclusion

There was global developement of point of care tests on a war footing. The Indian states of Delhi, Maharashtra, Gujarat, Uttar Pradesh, Tamil Nadu, Karnataka, Haryana, Rajasthan, Kerala, Himachal Pradesh, Goa and Uttarakhand, were in the forefront of these developments, as also the USA, Belgium, Taiwan, Korea and South Korea.

Preparing for the next pandemic: lessons learnt from the implementation of point-of-care SARS-CoV-2 testing in an emergency department

Point-of-care testing (POCT) provides rapid, accurate results that facilitate diagnosis and patient management. POCT for infectious agents allows timely infection prevention and control interventions and informs decisions around safe patient placement. However, POCT implementation requires careful governance as they are primarily operated by staff with limited prior education on laboratory quality control and assurance processes. Here, we describe our experience implementing SARS-CoV-2 POCT in the emergency department of a large tertiary referral hospital during the COVID-19 pandemic. We describe collaborative governance between pathology and clinical specialities, quality assurance, testing (volume and positivity rates), impact on patient flow and focus on lessons learnt during implementation that should be incorporated into revised pandemic preparedness planning.

An Innovative Workshop Embedding Pathology Service Users into the Undergraduate Biomedical Science Curriculum

The integration of pathology service users into the biomedical science curriculum has been driven by the refinement of the Health and Care Professions Council (HCPC) Standards of Proficiency. This study aimed to design and implement a novel and innovative service user event with a reflective assessment to enhance students' knowledge and understanding of the impact of pathology laboratory results on the patient pathway. The 4-h workshop consisted of a series of service users. Patients discussed how pathology services had contributed to their diagnosis and treatment, while service providers-a Microbiology Consultant, a director of primary care, and the patient referral optimisation officer-discussed their roles and their interactions with pathology services. Post-event, students completed a 750-word reflective assessment, highlighting challenges experienced by service users and providing suggestions for improving the delivery of pathology services. In total, 57.5% of respondents (57/99) completed a post-reflection survey, which included open- and closed-ended questions. Quantitative analysis of the survey data revealed that over 87.7% of respondents had increased knowledge and understanding of the revised HCPC standards. Following the assessment, students reported a significant increase in their confidence with respect to reflective writing (p < 0.001), with over 90% of respondents agreeing that the reflective assessment had increased their knowledge and understanding of the limitations that may negatively impact service users and patient care. Moreover, respondents highlighted how advancements in point-of-care testing (POCT) and improvements in communication can improve patient experiences. Thematic analysis revealed that respondents agreed that embedding patients into the curriculum reinforced the importance of there being a patient behind every sample. Respondents reported that reflecting upon service user experiences enabled them to identify improvements to the delivery of pathology services while recognising the essential role that Biomedical Scientists play in the patient pathway. This successful workshop has created a platform encompassing a range of pathology service users in the undergraduate curriculum. We recommend that other accredited biomedical science programmes adopt and embed this innovative workshop and reflective assessment into their programmes to help them meet these standards relating to service users while fostering important transferable skills in their students.

Point-of-Care Testing for SARS-CoV-2: A Prospective Study in a Primary Health Centre

BACKGROUND

In 2020, health systems across the world responded to the COVID-19 pandemic by making rapid changes to reduce the risk of exposure in patients and healthcare professionals. The use of point-of-care tests (POCT) has been a central strategy in dealing with the COVID-19 pandemic. The aims of this study were to evaluate the impact of POCT strategy (1) on maintaining elective surgeries by removing the risk of delayed pre-appointment testing and turn-around times and (2) on time dedicated for end-to-end appointment and management, and (3) to assess the feasibility of using the ID NOW^® among healthcare professionals and patients in a primary care setting, requiring pre-surgical appointment and minor ENT surgery in the Townsend House Medical Centre (THMC), Devon, United Kingdom.

METHODS

A logistic regression was performed to identify factors associated with the risk of canceled or delayed surgeries and medical appointments. Second, a multivariate linear regression analysis was conducted to calculate changes in the time dedicated to administrative tasks. A questionnaire was developed to assess the acceptance of POCT in patients and staff.

RESULTS

274 patients were included in this study; 174 (63.5%) in Group 1 (Usual Care) and 100 (36.5%) in Group 2 (Point of Care). Multivariate logistic regression showed that the percentage of postponed or canceled appointments was similar between the two groups (adjusted OR = 0.65, [95%CI: 0.22-1.88]; p = 0.42). Similar results were observed for the percentage of postponed or canceled scheduled surgeries (adjusted OR = 0.47, [95%CI: 0.15-1.47]; p = 0.19). The time dedicated to administrative tasks was significantly lowered by 24.7 min in G2 compared to G1 (p < 0.001). 79 patients in G2 (79.0%) completed the survey, and the majority agreed or strongly agreed that it improved care management (79.7%), decreased administrative time (65.8%), reduced the risk of canceled appointments (74.7%) and the traveling time to do COVID-19 test (91.1%). Having point-of-care testing in the clinic in the future seemed more than welcome by 96.6% of patients; 93.6% declared to be less stressed by having the test at the clinic than waiting for the results of the test realized elsewhere. The five healthcare professionals of the primary care center completed the survey, and all agreed that the POCT positively influences the workflow and can be successfully implemented into routine primary care.

CONCLUSIONS

Our study shows that NAAT-based point-of-care SARS-CoV-2 testing significantly improved flow management in a primary care setting. POC testing was a feasible and well-accepted strategy by patients and providers.

Performance of the VitaPCR rapid molecular test for SARS-CoV-2 screening at hospital admission

OBJECTIVE

To evaluate the diagnostic accuracy of rapid VitaPCR™ (Credo) assay as screening test in emergency department (ED) patients prior to transfer or medical interventions.

METHODS

In this prospective study 6642 oropharyngeal swabs from nonpreselected ED patients were tested for SARS-CoV-2 with (1) extraction-free VitaPCR and (2) extraction-based reference assays (Aptima®, cobas®, Xpert®Xpress).

RESULTS

The median TAT of VitaPCR was 47 minutes (IQR: 38-59), while reference assays required 6.2 hours (IQR: 4.4-13.3). VitaPCR's sensitivity, specificity, PPV and NPV was 77.9%, 99.9%, 97.9%, and 98.9% in relation to Hologic Panther TMA; 78.3%, 99.8%, 96.4%, and 98.5% compared to Roche cobas6800 PCR; 71.2%, 99.2%, 94.9%, and 94.3% using Cepheid GeneXpert PCR as reference.

CONCLUSION

High-sensitivity testing is needed to limit nosocomial spread and identify asymptomatic COVID-19 patients. However, time advantage of the VitaPCR must be weighed against its significantly lower sensitivity, especially when used in high-risk environments such as hospitals.

Clinical impact of syndromic molecular point-of-care testing for gastrointestinal pathogens in adults hospitalised with suspected gastroenteritis (GastroPOC): a pragmatic, open-label, randomised controlled trial

BACKGROUND

Single-occupancy isolation rooms are a finite resource in UK hospitals but are crucial in preventing transmission of infection. Patients with suspected gastroenteritis are nursed in single-occupancy rooms, but delays in laboratory testing lead to non-infectious patients remaining isolated for prolonged periods unnecessarily. Rapid molecular test panels for gastrointestinal pathogens have a run time of around 1 h but their clinical impact is unknown. We aimed to evaluate the clinical impact of syndromic molecular point-of-care testing (mPOCT) for gastrointestinal pathogens in adult patients presenting to hospital with suspected gastroenteritis on single-occupancy room use and a range of other outcome measures.

METHODS

In this pragmatic, open-label, randomised controlled trial, we enrolled adults hospitalised with suspected gastroenteritis in a large UK hospital. Patients were randomly allocated (1:1) to receive syndromic mPOCT of stool or rectal samples, or to routine clinical care (control) with laboratory testing. The primary outcome was the duration of time in single-occupancy rooms assessed on a modified intention-to-treat basis. Secondary outcomes included the time to results, time to de-isolation, antibiotic use, and safety outcomes. The study was registered with ISRCTN, ISRCTN88918395, and is complete.

FINDINGS

Between March 20, 2017 and March 17, 2020, from 455 patients assessed for eligibility, we enrolled 278 patients, 138 assigned to mPOCT (one withdrawal) and 140 to the control group. The duration (geometric mean) of single-occupancy room isolation was 1·8 days (95% CI 1·5-2·2) in the mPOCT group compared with 2·6 days (2·2-3·0) in the control group (exponentiated coefficient 0·70 [95% CI 0·56 to 0·87]; p=0·0017). The median (IQR) time to results was 1·7 h (1·5-2·0) for mPOCT and 44·7 h (21·2-66·1) for the control group (p<0·0001). Time to de-isolation was 0·6 days (0·3-1·8) in the mPOCT group compared with 2·2 days (1·2-3·2) in the control group, (p<0·0001). Antibiotics were given in 89 (65%) of 137 in the mPOCT group and 66 (47%) of 140 in the control group (p=0·0028). There were no differences between groups in length of hospital stay, or in safety outcomes including mortality, intensive care unit admission, or readmission to hospital.

INTERPRETATION

mPOCT for gastrointestinal pathogens in patients with suspected gastroenteritis returned results more rapidly than conventional testing and was associated with a reduction in single-occupancy room use. However, these benefits need to be balanced against a potential increase in antibiotic use.

FUNDING

University Hospital Southampton NHS Foundation Trust.

Rapid Multiplex PCR for Respiratory Viruses Reduces Time to Result and Improves Clinical Care: Results of a Systematic Review and Meta-Analysis

OBJECTIVES

The clinical impact of rapid sample-to-answer 'syndromic' multiplex polymerase chain reaction (PCR) testing for respiratory viruses is not clearly established. We performed a systematic literature review and meta-analysis to evaluate this impact for patients with possible acute respiratory tract infection in the hospital setting.

METHODS

We searched EMBASE, MEDLINE, and Cochrane databases from 2012 to present and conference proceedings from 2021 for studies comparing clinical impact outcomes between multiplex PCR testing and standard testing.

RESULTS

Twenty-seven studies with 17,321 patient encounters were included in this review. Rapid multiplex PCR testing was associated with a reduction of -24.22hours (95% CI -28.70 to -19.74hours) in the time to results. Hospital length of stay was decreased by -0.82 days (95% CI -1.52 to -0.11 days). Among influenza positive patients, antivirals were more likely to be given (RR 1.25, 95% CI 1.06 to 1.48) and appropriate infection control facility use was more common with rapid multiplex PCR testing (RR 1.55, 95% CI 1.16 to 2.07).

CONCLUSIONS

Our systematic review and meta-analysis demonstrates a reduction in time to results and length of stay for patients overall along with improvements in appropriate antiviral and infection control management among influenza positive patients. This evidence supports the routine use of rapid sample-to-answer multiplex PCR testing for respiratory viruses in the hospital setting.

Performance of point-of care molecular and antigen-based tests for SARS-CoV-2: a living systematic review and meta-analysis

BACKGROUND

Molecular and antigen point-of-care tests (POCTs) have augmented our ability to rapidly identify and manage SARS-CoV-2 infection. However, their clinical performance varies among individual studies.

OBJECTIVES

The evaluation of the performance of molecular and antigen-based POCTs in confirmed, suspected, or probable COVID-19 cases compared with that of laboratory-based RT-PCR in real-life settings.

DATA SOURCES

MEDLINE/PubMed, Scopus, Embase, Web of Science, Cochrane Library, Cochrane COVID-19 study register, and COVID-19 Living Evidence Database from the University of Bern.

STUDY ELIGIBILITY CRITERIA

Peer-reviewed or preprint observational studies or randomized controlled trials that evaluated any type of commercially available antigen and/or molecular POCTs for SARS-CoV-2, including multiplex PCR panels, approved by the United States Food and Drug Administration, with Emergency Use Authorization, and/or marked with Conformitè Europëenne from European Commission/European Union.

PARTICIPANTS

Close contacts and/or patients with symptomatic and/or asymptomatic confirmed, suspected, or probable COVID-19 infection of any age.

TEST/S

Molecular and/or antigen-based SARS-CoV-2 POCTs.

REFERENCE STANDARD

Laboratory-based SARS-CoV-2 RT-PCR.

ASSESSMENT OF RISK OF BIAS

Eligible studies were subjected to quality-control and risk-of-bias assessment using the Quality Assessment of Diagnostic Accuracy Studies 2 tool.

METHODS OF DATA SYNTHESIS

Summary sensitivities and specificities with their 95% CIs were estimated using a bivariate model. Subgroup analysis was performed when at least three studies informed the outcome.

RESULTS

A total of 123 eligible publications (97 and 26 studies assessing antigen-based and molecular POCTs, respectively) were retrieved from 4674 initial records. The pooled sensitivity and specificity for 13 molecular-based POCTs were 92.8% (95% CI, 88.9-95.4%) and 97.6% (95% CI, 96.6-98.3%), respectively. The sensitivity of antigen-based POCTs pooled from 138 individual evaluations was considerably lower than that of molecular POCTs; the pooled sensitivity and specificity rates were 70.6% (95% CI, 67.2-73.8%) and 98.9% (95% CI, 98.5-99.2%), respectively.

DISCUSSION

Further studies are needed to evaluate the performance of molecular and antigen-based POCTs in underrepresented patient subgroups and different respiratory samples.

Reduction in cycle time for a rapid polymerase chain reaction diagnostic test at the point of care

Background

Rapid testing facilitates safe and effective diagnosis, but the true speed of the process is the time from collection of a sample to delivery of an accurate and reliable test result - 'end-to-end' time. Transport, unpacking and relaying of information can extend this time considerably beyond the minimum laboratory turnaround times as stipulated by PCR testing protocols.

Aim/Objective

This study aimed to minimise time needed to ascertain SARS-CoV-2 status prior to treatment in a UK Dental Hospital using a novel, mobile, direct to polymerase chain reaction (PCR) workflow.

Methods

Process flow analysis and PDSA (Plan, Do, Study, Act) cycles for rapid continuous improvement were employed in a service improvement programme. Primerdesign™ q16 rapid PCR instruments and PROmate® COVID-19 direct assays were used for molecular testing.

Findings/Results

We showed a reduction in real-world end-to-end time for a diagnostic test from 240 min to 85 min (65% reduction) over a 4-week period.

Discussion

New rapid technologies have become available that reduce analytical time to under 90 min, but the real-world clinical implementation of the test requires a fully integrated workflow from clinic to reporting.

Clinical Evaluation of a Multiplex PCR Assay for Simultaneous Detection of 18 Respiratory Pathogens in Patients with Acute Respiratory Infections

Reliable diagnostics are necessary to identify influenza infections, and coronavirus disease 2019 (COVID-19) highlights the need to develop highly specific and sensitive viral detection methods to distinguish severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory pathogens to prevent their further spread. In this prospective study, 1070 clinical respiratory samples were collected from patients with acute respiratory infections from January 2019 to February 2021 to evaluate the diagnostic performance of a multiplex probe amplification (MPA) assay, designed to screen 18 pathogens, mainly those causing acute respiratory infections. Ninety-six positive samples and twenty negative samples for the 18 respiratory pathogens defined by the MPA assay and reverse transcription polymerase chain reaction (RT-PCR) were further confirmed by reference next-generation sequencing (NGS). The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the MPA assay were 95.00%, 93.75%, 98.96% and 75.00%, respectively. Additionally, the co-infection rate for these positive samples were 25% (24/95). The MPA assay demonstrated a highly concordant diagnostic performance with NGS in the diagnosis of 18 respiratory pathogens and might play an important role in clinical respiratory pathogen diagnosis.

How to design and implement a university-based COVID-19 testing programme? An evaluation of a novel RT-LAMP COVID-19 testing programme in a UK university

BACKGROUND

Little is known about how asymptomatic testing as a method to control transmission of COVID-19 can be implemented, and the prevalence of asymptomatic infection within university populations. The objective of this study was to investigate how to effectively set-up and implement a COVID-19 testing programme using novel reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) technology and to quantify the scale of asymptomatic infection on a university campus.

METHODS

An observational study to describe the set-up and implementation of a novel COVID-19 testing programme on a UK university campus between September and December 2020. RT-LAMP testing was used to identify asymptomatic cases.

RESULTS

A total of 1,673 tests were performed using RT-LAMP during the study period, of which 9 were positive for COVID-19, giving an overall positivity rate of 0.54%, equivalent to a rate in the tested population of 538 cases per 100,000 over the duration of testing. All positive tests were found to be positive on RT-PCR testing, giving a false positive rate of 0%.

CONCLUSIONS

This study shows that it is possible to rapidly setup a universal university testing programme for COVID-19 in collaboration with local healthcare providers using RT-LAMP testing. Positive results were comparable to those in the local population, though with a different peak of infection. Further research to inform the design of the testing programme includes focus groups of those who underwent testing and further interrogation of the demographics of those opting to be tested to identify potential access problems or inequalities.

Utilization of point-of-care tests among general practitioners, a cross-sectional study

Background

Point-of-care testing (POCT) has numerous potential benefits to improve health care service, especially in resource-limited settings. We aim to identify which POC-tests (POCTs) of laboratory parameters are known, employed, and rated as useful by general practitioners (GPs).

Methods

A questionnaire with 27 POCTs was posted to a random selection of GPs (n = 451) in Saxony, Germany.

Results

A total of 208 GPs replied (response rate 46.1%). Out of 27 POCTs, each GP knew an average of 20.3 as laboratory parameters and 9.2 as POCTs. Urine test strips (99.0%), blood glucose test (98.1%), and Troponin I/T (86.4%) were the best-known, followed by INR/Quick (82.5%), Microalbumin (79.1%), and D-dimer (78.6%) POCTs. Yet, solely 0 to 13 POC tests were actually used (mean value 4.6). Urine test strips were employed most frequently (97.6%), followed by blood glucose test (94.7%), Troponin I/T (57.8%), Microalbumin (57.3%), and INR/Quick POCTs (41.7%). Heart fatty binding protein (H-FABP), Syphilis, Coeliac disease, and Malaria appeared as the least frequently used POCTs. The majority of the GPs declared 14 of the 27 POCTs to be useful.

Discussion/conclusion

The most recurrently employed POCTs are those for diagnosing or monitoring diabetes mellitus, ensued by POCTs addressing acute cardiovascular diseases (Troponin I/T, D-dimer) or monitoring the therapy of infectious diseases or the anticoagulant therapy. POCTs most often rated as useful by GPs are also widely known and frequently used. Nonetheless, the majority of GPs rate only a very limited number of POCTs as useful. Frequent concerns might be low economic benefit, over-reliance, and test accuracy coming along with the complex implementation of the tests requiring technical skills, accurate storage, and the correct interpretation of test results.

Trial registration

In accordance with the (Model) Professional Code for Physicians in Germany, neither human body materials nor data that can be assigned to a specific human being are used in our study. A declaration of no objection from the Ethics Committee of the Martin-Luther University Halle-Wittenberg (Medical Faculty) confirms no professional or ethical concerns due to completely anonymized data collection and analysis. Our study was therefore not registered in a corresponding registry.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12875-022-01643-9.

Molecular point-of-care testing for lower respiratory tract pathogens improves safe antibiotic de-escalation in patients with pneumonia in the ICU: results of a randomised controlled trial

BACKGROUND

Effective treatment of pneumonia requires timely administration of appropriate antimicrobials but standard diagnostic tests take around 48 hours to generate results. Highly accurate, rapid molecular tests have been developed for identifying organisms in lower respiratory tract samples, however their impact on antibiotic use is unknown. The aim of this study was to assess the impact of syndromic molecular point-of-care testing compared to conventional diagnostic testing, on antibiotic use.

METHODS

In this pragmatic, randomised controlled trial, we enrolled critically ill adults with pneumonia. Patients were assigned (1:1) to molecular testing of samples at the point-of-care or routine clinical care. The primary outcome was the proportion of patients who received results-directed antimicrobial therapy.

RESULTS

200 patients were randomly assigned to point-of-care testing (n=100) or the control group (n=100). 85 patients had community acquired pneumonia (42 in the mPOCT group and 43 in the control group), 69 hospital acquired pneumonia (30 in mPOCT and 39 in control) and 46 ventilator associated pneumonia (28 in mPOCT and 18 in control). The median [IQR] time to results was 1.7 [1.6-1.9] hours for point-of-care testing and 66.7 [56.7-88.5] hours for standard diagnostics (difference of -65.0 hours, 95%CI -68.0 to -62.0; p<0.0001). 71 (71%) patients in the point-of-care testing arm had pathogens detected compared to 51 (51%) in the control arm (difference of 20%, 95%CI 7 to 33; p=0.004). 80 (80%) of patients in the point-of-care group received results-directed therapy, compared with 29 (29%) of 99 in the control group (difference of 51%, 95%CI 39-63; p<0.0001). Time to results-directed therapy was 2.3 [1.8-7.2] hours in the mPOCT group and 46.1 [23.0-51.5] hours in the control group (difference of -43.8 hours, 95% CI -48.9 to -38.6; p<0.0001). 42 (42%) patients in mPOCT group had antibiotics de-escalated compared with 8 (8%) of 98 in the control group (difference of 34%, 95%CI 23-45; p<0.0001). Time to de-escalation was 4.8 [2.4-13.0] hours in the mPOCT group compared with 46.5 [26.3-48.6] hours in the control group (difference of -41.4 hours, 95%CI -53 to -29.7; p<0.0001). There was no major difference in antibiotic duration or in clinical or safety outcomes between the two groups.

CONCLUSIONS

Use of molecular point-of-care testing in patients with pneumonia returned results more rapidly and identified more pathogens than conventional testing. This was associated with improvements in appropriate antimicrobial use and appeared safe.

Point of care SARS-CoV-2 nucleic acid testing in schools improves school attendance

Background: National lockdowns have led to significant interruption to children’s education globally. In the Autumn term in 2020, school absence in England and Wales was almost five times higher than the same period in 2019. Transmission of SARS-CoV-2 in schools and ongoing interruption to education remains a concern. However, evaluation of rapid point of care (POC) polymerase chain reaction (PCR) testing in British schools has not been undertaken.

Methods: This is a survey of secondary schools in England that implemented PCR-based rapid POC testing. The study aims to measure the prevalence of SARS-CoV-2 infection in schools, to assess the impact of this testing on school attendance and closures, and to describe schools experiences with testing. All schools utilised the SAMBA II SARS-CoV-2 testing platform.

Results: 12 fee-paying secondary schools in England were included. Between September 1 ^st 2020 and December 16 ^th 2020, 697 on site rapid POC PCR tests were performed and 6.7% of these were positive for SARS-CoV-2 infection. There were five outbreaks in three schools during this time which were contained. Seven groups of close contacts within the school known as bubbles had to quarantine but there were no school closures. 84% of those tested were absent from school for less than one day whilst awaiting their test result. This potentially saved between 1047 and 1570 days off school in those testing negative compared to the NHS PCR laboratory test. Schools reported a positive impact of having a rapid testing platform as it allowed them to function as fully as possible during this pandemic.

Conclusions: Rapid POC PCR testing platforms should be widely available and utilised in school settings. Reliable positive tests will prevent outbreaks and uncontrolled spread of infection within school settings. Reliable negative test results will reassure students, parents and staff and prevent disruption to education.

A rapid RT-LAMP SARS-CoV-2 screening assay for collapsing asymptomatic COVID-19 transmission

PURPOSE

To demonstrate the diagnostic performance of rapid SARS-CoV-2 RT-LAMP assays, comparing the performance of genomic versus sub-genomic sequence target with subsequent application in an asymptomatic screening population.

METHODS

RT-LAMP diagnostic specificity (DSe) and sensitivity (DSe) was determined using 114 RT-PCR clinically positive and 88 RT-PCR clinically negative swab samples processed through the diagnostic RT-PCR service within the University Hospitals of Leicester NHS Trust. A swab-based RT-LAMP SARS-CoV-2 screening programme was subsequently made available to all staff and students at the University of Leicester (Autumn 2020), implemented to ISO 15189:2012 standards using NHS IT infrastructure and supported by University Hospital Leicester via confirmatory NHS diagnostic laboratory testing of RT-LAMP 'positive' samples.

RESULTS

Validation samples reporting a Ct < 20 were detected at 100% DSe and DSp, reducing to 95% DSe (100% DSp) for all samples reporting a Ct < 30 (both genomic dual sub-genomic assays). Advisory screening identified nine positive cases in 1680 symptom free individuals (equivalent to 540 cases per 100,000) with results reported back to participants and feed into national statistics within 48 hours.

CONCLUSION

This work demonstrates the utility of a rapid RT-LAMP assay for collapsing transmission of SARS-CoV-2 in an asymptomatic screening population.

FebriDx host response point-of-care testing improves patient triage for coronavirus disease 2019 (COVID-19) in the emergency department

Objectives:

Patients presenting to hospital with suspected coronavirus disease 2019 (COVID-19), based on clinical symptoms, are routinely placed in a cohort together until polymerase chain reaction (PCR) test results are available. This procedure leads to delays in transfers to definitive areas and high nosocomial transmission rates. FebriDx is a finger-prick point-of-care test (PoCT) that detects an antiviral host response and has a high negative predictive value for COVID-19. We sought to determine the clinical impact of using FebriDx for COVID-19 triage in the emergency department (ED).

Design:

We undertook a retrospective observational study evaluating the real-world clinical impact of FebriDx as part of an ED COVID-19 triage algorithm.

Setting:

Emergency department of a university teaching hospital.

Patients:

Patients presenting with symptoms suggestive of COVID-19, placed in a cohort in a ‘high-risk’ area, were tested using FebriDx. Patients without a detectable antiviral host response were then moved to a lower-risk area.

Results:

Between September 22, 2020, and January 7, 2021, 1,321 patients were tested using FebriDx, and 1,104 (84%) did not have a detectable antiviral host response. Among 1,104 patients, 865 (78%) were moved to a lower-risk area within the ED. The median times spent in a high-risk area were 52 minutes (interquartile range [IQR], 34–92) for FebriDx-negative patients and 203 minutes (IQR, 142–255) for FebriDx-positive patients (difference of −134 minutes; 95% CI, −144 to −122; P < .0001). The negative predictive value of FebriDx for the identification of COVID-19 was 96% (661 of 690; 95% CI, 94%–97%).

Conclusions:

FebriDx improved the triage of patients with suspected COVID-19 and reduced the time that severe acute respiratory coronavirus virus 2 (SARS-CoV-2) PCR-negative patients spent in a high-risk area alongside SARS-CoV-2–positive patients.

Caring for COVID-19 patients through a pandemic in the intensive care setting: A narrative review

Since the declaration of the novel SARS-CoV-2 virus pandemic, health systems/ health-care-workers globally have been overwhelmed by a vast number of COVID-19 related hospitalizations and intensive care unit (ICU) admissions. During the early stages of the pandemic, the lack of formalized evidence-based guidelines in all aspects of patient management was a significant challenge. Coupled with a lack of effective pharmacotherapies resulted in unsatisfactory outcomes in ICU patients. The anticipated increment in ICU surge capacity was staggering, with almost every ICU worldwide being advised to increase their capacity to allow adequate care provision in response to multiple waves of the pandemic. This increase in surge capacity required advanced planning and reassessments at every stage, taking advantage of experienced gained in combination with emerging evidence. In University Hospital Southampton General Intensive Care Unit (GICU), despite the initial lack of national and international guidance, we enhanced our ICU capacity and developed local guidance on all aspects of care to address the rapid demand from the increasing COVID-19 admissions. The main element of this success was a multidisciplinary team approach intertwined with equipment and infrastructural reorganization. This narrative review provides an insight into the approach adopted by our center to manage patients with COVID-19 critical illness, exploring the initial planning process, including contingency preparations to accommodate (360% capacity increment) and adaptation of our management pathways as more evidence emerged throughout the pandemic to provide the most appropriate levels of care to our patients. We hope our experience will benefit other intensive care units worldwide. This article is categorized under: Infectious Diseases > Genetics/Genomics/Epigenetics.

The role of routine SARS-CoV-2 screening of healthcare-workers in acute care hospitals in 2020: a systematic review and meta-analysis

Background

Healthcare workers (HCW) are at increased risk of infection with SARS-CoV-2. Vulnerable patient populations in particular must be protected, and clinics should not become transmission hotspots to avoid delaying medical treatments independent of COVID. Because asymptomatic transmission has been described, routine screening of asymptomatic HCW would potentially be able to interrupt chains of infection through early detection.

Methods

A systematic search was conducted in the Cochrane COVID-19 Study Register, Web of Science and WHO COVID‐19 Global literature on coronavirus with regard to non-incident related testing of healthcare workers using polymerase chain reaction on May 4th 2021. Studies since January 2020 were included. An assessment of risk of bias and representativeness was performed.

Results

The search identified 39 studies with heterogeneous designs. Data collection of the included studies took place from January to August 2020. The studies were conducted worldwide and the sample size of the included HCW ranged from 70 to 9449 participants. In total, 1000 of 51,700 (1.9%) asymptomatic HCW were tested positive for SARS-CoV-2 using PCR testing. The proportion of positive test results ranged between 0 and 14.3%. No study reported on HCW-screening related reductions in infected person-days.

Discussion and conclusions

The heterogeneous proportions might be explained by different regional incidences, lock-downs, and pre-analytical pitfalls that reduce the sensitivity of the nasopharyngeal swab. The very high prevalence in some studies indicates that screening HCW for SARS-CoV-2 may be important particularly in geographical regions and pandemic periods with a high-incidence. With low numbers and an increasing rate of vaccinated HCW, a strict cost–benefit consideration must be made, especially in times of low incidences. Since we found no studies that reported on HCW-screening related reductions in infected person-days, re-evaluation should be done when these are available.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07554-5.

A retrospective cohort study of the effect of SARS-CoV-2 point of care rapid RT-PCR at the Emergency Department on targeted admission

Background

To prevent nosocomial transmission of SARS-CoV-2, infection prevention control (IPC) measures are implemented for patients with symptoms compatible with COVID-19 until reliable test results are available. This delays admission to the most appropriate ward based on the medical condition. SARS-CoV-2 rapid antigen detection (RAD) tests and point-of-care (POC) rapid RT-PCR (VitaPCR) were introduced at emergency department (ED) at Skåne University Hospital, Sweden in late 2020, but the consequence on patient flow and targeted admission is unknown.

Methods

Patients presenting at the emergency department of a referral hospital (N = 2940) between 13-Nov-2020 and 12-Jan-2021 were included. The study period was delimited into three periods by the introduction of RAD tests and the VitaPCR. Participant data was collected from hospital records, and outcome variables were Length-of-Stay (LoS), intrahospital transfers and targeted admission to COVID-19 ward.

Results

Compared to baseline (RT-PCR only), RAD tests reduced ED Length-of-Stay (LoS) for participants with positive tests. Negative VitaPCR results reduced mean hospital LoS by 1.5 (95% CI 0.3–2.7) days and admissions to COVID-19 wards from 34.5 (95% CI 28.9–40.5) to 14.7 (95% CI 11.1–19.1) per 100 admissions and reduced transfers between hospital wards in the first 5 days from 50.0 (95% CI 45.0–55.0) to 34.0 (95% CI 30.3–37.9) per 100 admissions.

Conclusion

RAD tests enabled prompt detection of SARS-CoV-2 infection which had pronounced effects on LoS at the ED. Negative VitaPCR enabled cessation of IPC measures and a negative test was associated with increased targeted admissions, reduced intrahospital transfers and shorter LoS at the hospital.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07497-x.

Evaluating the Immune Response in Treatment-Naive Hospitalised Patients With Influenza and COVID-19

The worldwide COVID-19 pandemic has claimed millions of lives and has had a profound effect on global life. Understanding the body’s immune response to SARS-CoV-2 infection is crucial in improving patient management and prognosis. In this study we compared influenza and SARS-CoV-2 infected patient cohorts to identify distinct blood transcript abundances and cellular composition to better understand the natural immune response associated with COVID-19, compared to another viral infection being influenza, and identify a prognostic signature of COVID-19 patient outcome. Clinical characteristics and peripheral blood were acquired upon hospital admission from two well characterised cohorts, a cohort of 88 patients infected with influenza and a cohort of 80 patients infected with SARS-CoV-2 during the first wave of the pandemic and prior to availability of COVID-19 treatments and vaccines. Gene transcript abundances, enriched pathways and cellular composition were compared between cohorts using RNA-seq. A genetic signature between COVID-19 survivors and non-survivors was assessed as a prognostic predictor of COVID-19 outcome. Contrasting immune responses were detected with an innate response elevated in influenza and an adaptive response elevated in COVID-19. Additionally ribosomal, mitochondrial oxidative stress and interferon signalling pathways differentiated the cohorts. An adaptive immune response was associated with COVID-19 survival, while an inflammatory response predicted death. A prognostic transcript signature, associated with circulating immunoglobulins, nucleosome assembly, cytokine production and T cell activation, was able to stratify COVID-19 patients likely to survive or die. This study provides a unique insight into the immune responses of treatment naïve patients with influenza or COVID-19. The comparison of immune response between COVID-19 survivors and non-survivors enables prognostication of COVID-19 patients and may suggest potential therapeutic strategies to improve survival.

Clinical analysis on diagnostic accuracy of Bosch Vivalytic SARS-CoV-2 point-of-care test and evaluation of cycle threshold at admission for COVID-19 risk assessment

BACKGROUND

Point-of-care (POC) polymerase chain reaction (PCR) tests have the ability to improve testing efficiency in the Coronavirus disease 2019 (COVID-19) pandemic. However, real-world data on POC tests is scarce.

OBJECTIVE

To evaluate the efficiency of a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) POC test in a clinical setting and examine the prognostic value of cycle threshold (CT) on admission on the length of hospital stay (LOS) in COVID-19 patients.

METHODS

Patients hospitalised between January and May 2021 were included in this prospective cohort study. Patients' nasopharyngeal swabs were tested for SARS-CoV-2 with Allplex™2019-nCoV (Seegene Inc.) real-time (RT) PCR assay as gold standard as well as a novel POC test (Bosch Vivalytic SARS-CoV-2 [Bosch]) and the SARS-CoV-2 Rapid Antigen Test (Roche) accordingly. Clinical sensitivity and specificity as well as inter- and intra-assay variability were analyzed.

RESULTS

120 patients met the inclusion criteria with 46 (38%) having a definite COVID-19 diagnosis by RT-PCR. Bosch Vivalytic SARS-CoV-2 POC had a sensitivity of 88% and specificity of 96%. The inter- and intra- assay variability was below 15%. The CT value at baseline was lower in patients with LOS ≥ 10 days when compared to patients with LOS < 10 days (27.82 (± 4.648) vs. 36.2 (25.9-39.18); p = 0.0191). There was a negative correlation of CT at admission and LOS (r[44]s = - 0.31; p = 0.038) but only age was associated with the probability of an increased LOS in a multiple logistic regression analysis (OR 1.105 [95% CI, 1.03-1.19]; p = 0.006).

CONCLUSION

Our data indicate that POC testing with Bosch Vivalytic SARS-CoV-2 is a valid strategy to identify COVID-19 patients and decrease turnaround time to definite COVID-19 diagnosis. Also, our data suggest that age at admission possibly with CT value as a combined parameter could be a promising tool for risk assessment of increased length of hospital stay and severity of disease in COVID-19 patients.

Engineering light-initiated afterglow lateral flow immunoassay for infectious disease diagnostics

The pandemic of highly contagious diseases has put forward urgent requirements for high sensitivity and adaptive capacity of point-of-care testing (POCT). Herein, for the first time, we report an aggregation-induced emission (AIE) dye-energized light-initiated afterglow nanoprobes (named LiAGNPs), implemented onto a lateral flow immunoassay (LFIA) test strip, for diagnosis of two highly contagious diseases, human immunodeficiency virus (HIV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as model validation. The primary working mechanism relies on the cyclically generated singlet oxygen (¹O₂)-triggered time-resolved luminescent signals of LiAGNPs in which AIE dyes (TTMN) and chemiluminescent substrates (SO) are loaded. The designed LiAGNPs were found 2-fold and 32-fold sensitive than the currently used Eu(III)-based time-resolved fluorescent nanoparticles and gold nanoparticles in lateral flow immunoassay (LFIA), respectively. In addition, the extra optical behaviors of nude color and fluorescence of LiAGNPs enable the LFIA platform with the capability of the naked eye and fluorescent detection to satisfy the applications under varying scenarios. In short, the versatile LiAGNPs have great potential as a novel time-resolved reporter in enhancing detection sensitivity and application flexibility with LFIA platform for rapid but sensitive infectious disease diagnostics.

Combined RT-PCR and Host Response Point-of-Care Testing in Patients Hospitalised with Suspected COVID-19: A Prospective Diagnostic Accuracy Study

Introduction

RT-PCR has suboptimal sensitivity for the diagnosis of COVID-19. A composite reference standard comprising RT-PCR plus radiological and clinical features has been recommended for diagnostic accuracy studies. The FebriDx finger prick point-of-care test detects an antiviral host response protein (MxA) in 10 min. We evaluated the diagnostic accuracy of FebriDx and RT-PCR compared to a composite reference standard.

Methods

Adults presenting to hospital with suspected COVID-19 were tested by FebriDx and RT-PCR. A composite reference standard was used to classify patients as having COVID-19 based on RT-PCR positivity, or RT-PCR negativity with COVID-19 radiological findings or other clinical criteria. Measures of accuracy were calculated for MxA alone, RT-PCR alone, and both combined. This study is registered with the ISRCTN (ISRCTN14966673) and has completed.

Results

A total of 478 patients were tested, with valid results in 475. Of these 475 patients, 222 (46.7%) were classified as having COVID-19; 192 (40.4%) were RT-PCR positive, and 30 (6.3%) were RT-PCR negative and diagnosed on radiological/clinical criteria. Sensitivity of FebriDx MxA vs the composite reference standard was 186/222 (83.8%, 95% CI 78.3–88.4) and was similar to the sensitivity of RT-PCR (192/222 (86.5%, 95% CI 81.3–90.7), (difference of 2.7%, 95% CI − 3.9 to 9.3, p = 0.42). The sensitivity of combined FebriDx and RT-PCR was 208/222 (93.7%) which was superior to both RT-PCR alone (difference of 9.9, 95% CI 4.1–15.9; p = 0.001) and FebriDx MxA alone (difference of 7.2, 95% CI 1.6–12.9; p = 0.011).

Conclusion

Sensitivity of combined FebriDx and RT-PCR testing was superior to each alone for the detection of COVID-19 in hospital and may improve infection control and treatment decisions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40121-022-00646-4.

Performance of the LumiraDx Microfluidic Immunofluorescence Point-of-Care SARS-CoV-2 Antigen Test in Asymptomatic Adults and Children

OBJECTIVES

The LumiraDx SARS-CoV-2 Ag Test has previously been shown to accurately detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in individuals symptomatic for coronavirus disease 2019 (COVID-19). This evaluation investigated the LumiraDx SARS-CoV-2 Ag Test as an aid in the diagnosis of SARS-CoV-2 infection in asymptomatic adults and children.

METHODS

Asymptomatic individuals at high risk of COVID-19 infection were recruited in 5 point-of-care (POC) settings. Two paired anterior nasal swabs were collected from each participant, tested by using the LumiraDx SARS-CoV-2 Ag Test at the POC, and compared with results from reverse transcription-polymerase chain reaction (RT-PCR) assays (cobas 6800 [Roche Diagnostics] or TaqPath [Thermo Fisher Scientific]). We calculated positive percent agreement (PPA) and negative percent agreement (NPA), then stratified results on the basis of RT-PCR reference platform and cycle threshold.

RESULTS

Of the 222 included study participants confirmed to be symptom-free for at least 2 weeks before testing, the PPA was 82.1% (95% confidence interval [CI], 64.4%-92.1%). The LumiraDx SARS-CoV-2 Ag Test correctly identified 95.8% (95% CI, 79.8%-99.3%) of the samples confirmed positive in fewer than 33 RT-PCR cycles and 100% (95% CI, 85.1%-100%) in fewer than 30 RT-PCR cycles while maintaining 100% NPA.

CONCLUSIONS

This rapid, high-sensitivity test can be used to screen asymptomatic patients for acute SARS-CoV-2 infection in clinic- and community-based settings.

Impact of SARS-CoV-2 transmission-based precautions on inpatient management of general medical patients

This audit reviewed the impact on access to routine medical care and adverse outcomes in patients with suspected SARS‐CoV‐2 infection managed on a ‘COVID‐19’ (CV) ward compared with a general medicine ward at Box Hill Hospital, Victoria. Data were collected at two time points to capture changes associated with onsite testing. We found no healthcare delays from admission to CV wards and observed faster exits from CV wards with improved testing efficiency. This critical finding is relevant as Victoria manages a third wave of infections.

An outlook on microfluidics: the promise and the challenge

This perspective considers ways in which the field of microfluidics can increase its impact by improving existing technologies and enabling new functionalities. We highlight applications where microfluidics has made or can make important contributions, including diagnostics, food safety, and the production of materials. The success of microfluidics assumes several forms, including fundamental innovations in fluid mechanics that enable the precise manipulation of fluids at small scales and the development of portable microfluidic chips for commercial purposes. We identify outstanding technical challenges whose resolution could increase the accessibility of microfluidics to users with both scientific and non-technical backgrounds. They include the simplification of procedures for sample preparation, the identification of materials for the production of microfluidic devices in both laboratory and commercial settings, and the replacement of auxiliary equipment with automated components for the operation of microfluidic devices.

Point of care SARS-CoV-2 nucleic acid testing in schools improves school attendance

Background: National lockdowns have led to significant interruption to children’s education globally. In the Autumn term in 2020, school absence in England and Wales was almost five times higher than the same period in 2019. Transmission of SARS-CoV-2 in schools and ongoing interruption to education remains a concern. However, evaluation of rapid point of care (POC) polymerase chain reaction (PCR) testing in British schools has not been undertaken. Methods: This is a survey of secondary schools in England that implemented PCR-based rapid POC testing. The study aims to measure the prevalence of SARS-CoV-2 infection in schools, to assess the impact of this testing on school attendance and closures, and to describe schools experiences with testing. All schools utilised the SAMBA II SARS-CoV-2 testing platform. Results: 12 fee-paying secondary schools in England were included. Between September 1st 2020 and December 16th 2020, 697 on site rapid POC PCR tests were performed and 6.7% of these were positive for SARS-CoV-2 infection. There were five outbreaks in three schools during this time which were contained. Seven groups of close contacts within the school known as bubbles had to quarantine but there were no school closures. 84% of those tested were absent from school for less than one day whilst awaiting their test result. This potentially saved between 1047 and 1570 days off school in those testing negative compared to the NHS PCR laboratory test. Schools reported a positive impact of having a rapid testing platform as it allowed them to function as fully as possible during this pandemic. Conclusions: Rapid POC PCR testing platforms should be widely available and utilised in school settings. Reliable positive tests will prevent outbreaks and uncontrolled spread of infection within school settings. Reliable negative test results will reassure students, parents and staff and prevent disruption to education.

Analytical performances of the AMPLIQUICK® Respiratory Triplex assay for simultaneous detection and differentiation of SARS-CoV-2, influenza A/B and respiratory syncytial viruses in respiratory specimens

Although patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A, influenza B and respiratory syncytial virus (RSV) show comparable or very similar manifestations, the therapeutic approaches of these respiratory viral infections are different, which requires an accurate diagnosis. Recently, the novel multiplex real-time reverse transcription-polymerase chain reaction assay AMPLIQUICK® Respiratory Triplex (BioSynex SA, Illkirch-Graffenstaden, France) allows simultaneous detection and differentiation of SARS-CoV-2, influenza A, influenza B, and RSV in respiratory tract samples. We herein evaluated the performance of the AMPLIQUICK® Respiratory Triplex for the detection of the four viruses in respiratory specimens, using Allplex™ Respiratory Panel 1 and 2019-nCoV assays (Seegene, Seoul, Korea) as reference comparator assays. A total of 359 archived predetermined respiratory samples, including 83, 145, 19 and 95 positive specimens for SARS-CoV-2, influenza A, influenza B and RSV respectively, were included. The AMPLIQUICK® Respiratory Triplex showed high concordance with the reference assays, with an overall agreement for SARS-CoV-2, influenza A, influenza B, and RSV at 97.6%, 98.8%, 98.3% and 100.0%, respectively, and high κ values ranging from 0.93 to 1.00, indicating an almost perfect agreement between assays. Furthermore, high correlations of cycle threshold (Ct) values were observed for positive samples of the four viruses between the AMPLIQUICK® Respiratory Triplex and comparator assays, with an overall high agreement between Ct values assessed by Bland-Altman analyses. In conclusion, these observations demonstrate that the multiplex AMPLIQUICK® Respiratory Triplex is a reliable assay for the qualitative detection and differentiation of SARS-CoV-2, influenza A, influenza B, and RSV in respiratory specimens, which may prove useful for streamlining diagnostics during the winter influenza-seasons.

Nanobioengineering: A promising approach for early detection of COVID-19

Unique pneumonia due to an unknown source emerged in December 2019 in the city of Wuhan, China. Consequently, the World Health Organization (WHO) declared this condition as a new coronavirus disease-19 also known as COVID-19 on February 11, 2020, which on March 13, 2020 was declared as a pandemic. The virus that causes COVID-19 was found to have a similar genome (80% similarity) with the previously known acute respiratory syndrome also known as SARS-CoV. The novel virus was later named Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 falls in the family of Coronaviridae which is further divided into Nidovirales and another subfamily called Orthocoronavirinae. The four generations of the coronaviruses belongs to the Orthocoronavirinae family that consists of alpha, beta, gamma and delta coronavirus which are denoted as α-CoV, β-CoV, γ-CoV, δ-CoV respectively. The α-CoV and β-CoVs are mainly known to infect mammals whereas γ-CoV and δ-CoV are generally found in birds. The β-CoVs also comprise of SARS-CoV and also include another virus that was found in the Middle East called the Middle East respiratory syndrome virus (MERS-CoV) and the cause of current pandemic SARS-CoV-2. These viruses initially cause the development of pneumonia in the patients and further development of a severe case of acute respiratory distress syndrome (ARDS) and other related symptoms that can be fatal leading to death.

Performance Characteristics and Utility of the Standard Q COVID-19 Antigen Test for Emergency Admissions to Healthcare Facilities

This study evaluated the performance of the COVID-19 Ag-RDT compared to the real-time reverse transcription-polymerase chain reaction (rtRT-PCR) for SARS-CoV-2 detection and its use among patients referred for emergency admission. A total of 120 nasopharyngeal swabs were collected from patients referred for emergency admission and immediately preceded for testing to the Unit of Clinical Microbiology. Out of 60 Ag positive tests, 53 (88.3%) were confirmed by rtRT-PCR, while 7 (11.7%) tested negative (false positives). Out of 60 Ag negative tests, 56 (93.3%) were confirmed negative by rtRT-PCR, and 4 (6.7%) were positive (false negatives). Ct value comparison was performed for 53 samples that were positive by both methods: 8 (15.1%) isolates had Ct value up to 20; 37 (69.8%) 21 to 30 and 8 (15.1%) 31 to 40, respectively. The sensitivity of the analyzed rapid Ag test was 92.9%, and specificity 88.9%. The accuracy of the Ag test was 90.8%. This study has shown that rapid Ag tests can be used in emergency admissions to healthcare facilities. However, rtRT-PCR should be considered after negative antigen test results in symptomatic patients, and after positive antigen test results in asymptomatic persons.

Place des virus respiratoires dans les pneumonies aiguës communautaires de l'adulte : quels changements depuis la Covid-19 ?

L’émergence du SARS-CoV-2 a renforcé l'intérêt pour la place des virus respiratoires, dans les pneumonies aiguës communautaires, en mettant en exergue de nombreux points encore mal connus tels que la part des infections asymptomatiques, les interactions entre virus respiratoires et pathogènes non viraux, leurs périodes d'incubation, leur pathogénicité ou encore la durée d'excrétion variable.

La présentation clinique et radiologique des pneumonies aiguës communautaires ne permet pas toujours de distinguer l'origine virale de l'origine bactérienne.

L'absence de réelle conséquence thérapeutique semble un frein à l'utilisation des PCR multiplex dans la pratique quotidienne. Toutefois, l'amélioration en termes de délai de rendu des résultats et du nombre de pathogènes inclus dans les panels, ainsi que l'accumulation récente de données épidémiologiques et cliniques, devraient aider à rationaliser l'utilisation de ces tests, faciliter l'interprétation de leurs résultats et guider l'utilisation des molécules antivirales en développement.

Reagent Filming for Universal Point-of-Care Diagnostics

Simplifying assays while maintaining the robustness of reagents is a challenge in diagnostics. This problem is exacerbated when translating quality diagnostic assays to developing countries that lack resources and infrastructure such as trained health workers, high-end equipment, and cold-chain systems. To solve this problem, in this study, a simple solution that films assay reagents to simplify the operation of diagnostic assays and preserve the stability of diagnostic reagents without using cold chains is presented. A polyvinyl-alcohol-based water-soluble film is used to encapsulate premeasured and premixed reagents. The reagent film, produced through a simple and scalable cast-drying process, provides a glassy inner matrix with abundant hydroxyl groups that can stabilize various reagents (ranging from chemicals to biological materials) by restricting molecular mobility and generating hydrogen bonds. The reagent film is applied to an enzymatic glucose assay, a high-sensitivity immunoassay for cardiac troponin, and a molecular assay for viral RNA detection, to test its practicability and universal applicability. The film-based assays result in excellent analytical/diagnostic performance and stable long-term reagent storage at elevated temperatures (at 25 or 37 °C, for six months), demonstrating clinical readiness. This technology advances the development and distribution of affordable high-quality diagnostics to resource-limited regions.

Point-of-care COVID-19 testing in the emergency department: current status and future prospects

INTRODUCTION

This expert review outlines current and future point-of-care technologies for the diagnosis of the SARS-CoV-2 virus, which is responsible for causing coronavirus disease COVID-19 in the emergency department. COVID-19 first emerged in late 2019 and is responsible for a range of presentations from minor upper respiratory tract symptoms to severe pneumonia and multisystem organ failure. Among the technologies available include the gold standard of molecular point-of-care tests as well as antigen detection tests.

AREAS COVERED

We discuss point-of-care molecular tests including multiplex, targeted, and single plex panels as well as various antigen testing methodologies in terms of availability and performance characteristics. In addition, we focus on current testing best practices and considerations for point-of-care testing in the emergency department based on a search of the literature available in PubMed to date and a review of FDA and CDC guidance.

EXPERT OPINION

While there have been many advances in SARS-CoV-2 point-of-care testing, there remain challenges to implementation in the emergency department setting. A paradigm shift is needed to improve diagnosis and clinical outcomes.

Point-of-care diagnostics: recent developments in a pandemic age

In this review, we provide an overview of developments in point-of-care (POC) diagnostics during the COVID-19 pandemic. We review these advances within the framework of a holistic POC ecosystem, focusing on points of interest - both technological and non-technological - to POC researchers and test developers. Technologically, we review design choices in assay chemistry, microfluidics, and instrumentation towards nucleic acid and protein detection for severe acute respiratory coronavirus 2 (SARS-CoV-2), and away from the lab bench, developments that supported the unprecedented rapid development, scale up, and deployment of POC devices. We describe common features in the POC technologies that obtained Emergency Use Authorization (EUA) for nucleic acid, antigen, and antibody tests, and how these tests fit into four distinct POC use cases. We conclude with implications for future pandemics, infectious disease monitoring, and digital health.

Cessation and resumption of elective neurointerventional procedures during the coronavirus disease 2019 pandemic and future pandemics

At the time of this writing, the coronavirus disease 2019 pandemic continues to be a global threat, disrupting usual processes, and protocols for delivering health care around the globe. There have been significant regional and national differences in the scope and timing of these disruptions. Many hospitals were forced to temporarily halt elective neurointerventional procedures with the first wave of the pandemic in the spring of 2020, in order to prioritize allocation of resources for acutely ill patients and also to minimize coronavirus disease 2019 transmission risks to non-acute patients, their families, and health care workers. This temporary moratorium on elective neurointerventional procedures is generally credited with helping to “flatten the curve” and direct scarce resources to more acutely ill patients; however, there have been reports of some delaying seeking medical care when it was in fact urgent, and other reports of patients having elective treatment delayed with the result of morbidity and mortality. Many regions have resumed elective neurointerventional procedures, only to now watch coronavirus disease 2019 positivity rates again climbing as winter of 2020 approaches. A new wave is now forecast which may have larger volumes of hospitalized coronavirus disease 2019 patients than the earlier wave(s) and may also coincide with a wave of patients hospitalized with seasonal influenza. This paper discusses relevant and practical elements of cessation and safe resumption of nonemergent neurointerventional services in the setting of a pandemic.

Point of Care Testing for Infectious Disease in Europe: A Scoping Review and Survey Study

Background: Point of care testing (POCT) for infectious diseases is testing conducted near the patient. It allows clinicians to offer the most appropriate treatment more quickly. As POCT devices have increased in accuracy and become more cost-effective, their use has grown, but a systematic assessment of their use for clinical and public health management of infectious diseases in EU/EEA countries has not been previously undertaken.

Methods: A scoping review of the literature on POCT in EU/ EEA countries as at November 2019, and a survey of key stakeholders.

Results: 350 relevant articles were identified and 54 survey responses from 26 EU/EEA countries were analysed. POCT is available for a range of infectious diseases and in all countries responding to the survey (for at least one disease). POCT is commonly available for influenza, HIV/AIDS, Legionnaires' disease and malaria, where it is used in at least half of EU/EEA countries. While POCT has the potential to support many improvements to clinical care of infectious diseases (e.g., faster diagnosis, more appropriate use of antimicrobials), the results suggest POCT is infrequently used to support public health functions (e.g., disease surveillance and reporting).

Conclusion: Although POCT is in use to some extent in all EU/EEA countries, the full benefits of POCT in wider public health functions have yet to be realised. Further research on barriers and facilitators to implementation is warranted.

Point-of-care CRISPR-Cas-assisted SARS-CoV-2 detection in an automated and portable droplet magnetofluidic device

In the fight against COVID-19, there remains an unmet need for point-of-care (POC) diagnostic testing tools that can rapidly and sensitively detect the causative SARS-CoV-2 virus to control disease transmission and improve patient management. Emerging CRISPR-Cas-assisted SARS-CoV-2 detection assays are viewed as transformative solutions for POC diagnostic testing, but their lack of streamlined sample preparation and full integration within an automated and portable device hamper their potential for POC use. We report herein POC-CRISPR - a single-step CRISPR-Cas-assisted assay that incoporates sample preparation with minimal manual operation via facile magnetic-based nucleic acid concentration and transport. Moreover, POC-CRISPR has been adapted into a compact thermoplastic cartridge within a palm-sized yet fully-integrated and automated device. During analytical evaluation, POC-CRISPR was able detect 1 genome equivalent/μL SARS-CoV-2 RNA from a sample volume of 100 μL in < 30 min. When evaluated with 27 unprocessed clinical nasopharyngeal swab eluates that were pre-typed by standard RT-qPCR (Cq values ranged from 18.3 to 30.2 for the positive samples), POC-CRISPR achieved 27 out of 27 concordance and could detect positive samples with high SARS-CoV-2 loads (Cq < 25) in 20 min.

Isolation precautions cause minor delays in diagnostics and treatment of non-COVID patients

Background

Isolation precautions are essential prevent spread of COVID-19 infection but may have a negative impact on inpatient care. The impact of these measures on non-COVID-19 patients remains largely unexplored.

Aim

This study aimed to investigate diagnostic and treatment delays related to isolation precautions, the associated patient outcome, and the predisposing risk factors for delays.

Methods

This observational study was conducted in seven Helsinki region hospitals during the first wave of the COVID-19 pandemic in Finland. The study used data on all non-COVID-19 inpatients, who were initially isolated due to suspected COVID-19, to estimate whether isolation precautions resulted in diagnostic or treatment delays.

Results

Out of 683 non-COVID-19 patients, 33 (4.8%) had delays related to isolation precautions. Clinical condition deteriorated non-fatally in seven (1.0%) patients. The following events were associated with an increased risk of treatment or a diagnostic delay: more than three ward transfers (P = 0.025); referral to an incorrect speciality in the emergency department (P = 0.004); more than three SARS-CoV-2 RT-PCR tests performed (P = 0.022); and where cancer was the final diagnosis (P = 0.018). In contrast, lower respiratory tract symptoms (P = 0.013) decreased the risk.

Conclusions

The use of isolation precautions for patients who did not have COVID-19 had minor negative effects on patient outcomes. The present study underlines the importance of targeting diagnostic efforts to patients with unspecified symptoms and to those with a negative SARS-CoV-2 test result. Thorough investigations to achieve an accurate diagnosis improves the prognosis of patients and facilitates appropriate targeting of hospital resources.

SARS-CoV-2 viral load at presentation to hospital is independently associated with the risk of death

Objectives Previous studies have suggested that SARS-CoV-2 viral load, measured on upper respiratory tract samples at presentation to hospital using PCR Cycle threshold (Ct) value, has prognostic utility. However, these studies have not comprehensively adjusted for factors known to be intimately related to viral load. We aimed to evaluate the association between Ct value at admission and patient outcome whilst adjusting carefully for covariates. Methods We evaluated the association between Ct value at presentation and the outcomes of ICU admission and death, in patients hospitalised during the first wave of the pandemic in Southampton, UK. We adjusted for covariates including age, duration of illness and antibody sero-status, measured by neutralisation assay. Results 185 patients were analysed, with a median [IQR] Ct value of 27.9 [22.6-32.1]. On univariate analysis the Ct value at presentation was associated with the risk of both ICU admission and death. In addition, Ct value significantly differed according to age, the duration of illness at presentation and antibody sero-status. On multivariate analysis, Ct value was independently associated with risk of death (aOR 0.84, 95% CI 0.72-0.96; p = 0.011) but not ICU admission (aOR 1.04, 95% CI 0.93-1.16; p = 0.507). Neutralising antibody status at presentation was not associated with mortality or ICU admission (aOR 10.62, 95% CI 0.47-889; p = 0.199 and aOR 0.46, 95% CI 0.10-2.00; p = 0.302, respectively). Conclusions SARS-CoV-2 Ct value on admission to hospital was independently associated with mortality, when comprehensively adjusting for other factors and could be used for risk stratification.

A comprehensive review of COVID-19 biology, diagnostics, therapeutics, and disease impacting the central nervous system

The ongoing COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a highly transmissible disease. SARS-CoV-2 is estimated to have infected over 153 million people and to have caused over 3.2 million global deaths since its emergence in December 2019. SARS-CoV-2 is the seventh coronavirus known to infect humans, and like other coronaviruses, SARS-CoV-2 infection is characterized by a variety of symptoms including general flu-like symptoms such as a fever, sore throat, fatigue, and shortness of breath. Severe cases often display signs of pneumonia, lymphopenia, acute kidney injury, cardiac injury, cytokine storms, lung damage, acute respiratory distress syndrome (ARDS), multiple organ failure, sepsis, and death. There is evidence that around 30% of COVID-19 cases have central nervous system (CNS) or peripheral nervous system (PNS) symptoms along with or in the absence of the previously mentioned symptoms. In cases of CNS/PNS impairments, patients display dizziness, ataxia, seizure, nerve pain, and loss of taste and/or smell. This review highlights the neurological implications of SARS-CoV-2 and provides a comprehensive summary of the research done on SARS-CoV-2 pathology, diagnosis, therapeutics, and vaccines up to May 5.

A SARS-CoV-2 nucleocapsid ELISA represents a low-cost alternative to lateral flow testing for community screening in LMI countries

Background Controlling the spread of SARS-CoV-2 is problematic because of transmission driven by asymptomatic and pre-symptomatic individuals. Community screening can help identify these individuals but is often too expensive for countries with limited health care resources. Low-cost ELISA assays may address this problem, but their use has not yet been widely reported.

Methods We developed a SARS-CoV-2 nucleocapsid ELISA and assessed its diagnostic performance on nose and throat swab samples from UK hospitalised patients and sputum samples from patients in Ghana.

Results The ELISA had a limit of detection of 8.4 pg/ml antigen and 16 pfu/ml virus. When tested on UK samples (128 positive and 10 negative patients), sensitivity was 58.6% (49.6–67.2) rising to 78.3% (66.7–87.3) if real-time PCR Ct values > 30 were excluded, while specificity was 100% (69.2–100). In a second trial using the Ghanaian samples (121 positive, 96 negative), sensitivity was 52% (42.8–61.2) rising to 72.6% (61.8–81.2) when a > 30 Ct cut-off was applied, while specificity was 100% (96.2–100).

Conclusions: Our data show that nucleocapsid ELISAs can test a variety of patient sample types while achieving levels of sensitivity and specificity required for effective community screening. Further investigations into the opportunities that this provides are warranted.

Syndromic approach to SARS-CoV-2 detection using QIAstat-Dx SARS-CoV-2 panel from clinical samples

The QIAstat-Dx SARS-CoV-2 panel is a multiplex cartridge based assay based on real time PCR which can detect 17 respiratory viruses, including the novel coronavirus SARS-CoV-2. A syndromic approach is the need of the hour for COVID-19 diagnostics among patients presenting with respiratory symptoms. The present study was done to evaluate 120 archived respiratory clinical specimens for SARS-CoV-2 on the SARS-CoV-2 panel. Further, 27 specimens were tested for other respiratory viruses, in comparison with the BioFire RP1.7 platform. The sensitivity and specificity for SARS-CoV-2 on SARS panel was found to be 90.00 % and 100 % respectively, indicating good diagnostic accuracy. The positive predictive value was found to be 100 %, negative predictive value was found to be 99.93 % and accuracy was 99.93 %. Detection of other respiratory viruses observed a concordance of 77.7 %. Despite advantages of speed, minimal expertise and accurate results; significant costs and discrepancies at Ct >35 remain important limitations of the SARS panel.

Syndromic diagnostic testing: a new way to approach patient care in the treatment of infectious diseases

Advanced microbiology technologies such as multiplex molecular assays (i.e. syndromic diagnostic tests) are a novel approach to the rapid diagnosis of common infectious diseases. As the global burden of antimicrobial resistance continues to rise, the judicious use of antimicrobials is of utmost importance. Syndromic panels are now being recognized in some clinical practice guidelines as a 'game-changer' in the diagnosis of infectious diseases. These syndromic panels, if implemented thoughtfully and interpreted carefully, have the potential to improve patient outcomes through improved clinical decision making, optimized laboratory workflow, and enhanced antimicrobial stewardship. This paper reviews the potential benefits of and considerations regarding various infectious diseases syndromic panels, and highlights how to maximize impact through collaboration between clinical microbiology laboratory and antimicrobial stewardship programmes.

Molecular diagnostics in the era of COVID-19

As the COVID-19 pandemic continues to escalate globally and acquires new mutations, accurate diagnostic technologies continue to play a vital role in controlling and understanding the epidemiology of this disease. A plethora of technologies have enabled the diagnosis of individuals, informed clinical management, aided population-wide screening to determine transmission rates and identified cases within the wider community and high-risk settings. This review explores the application of molecular diagnostics technologies in controlling the spread of COVID-19, and the key factors that affect the sensitivity and specificity of the tests used.