Comparative Performance of SARS-CoV-2 Detection Assays Using Seven Different Primer-Probe Sets and One Assay Kit

A systematic review on recent trends in transmission, diagnosis, prevention and imaging features of COVID-19

As the new cases of COVID-19 are growing every daysince January 2020, the major way to control the spread wasthrough early diagnosis. Prevention and early diagnosis are the key strategies followed by most countries. This study presents the perspective of different modes of transmission of coronavirus,especially during clinical practices and among the pediatrics. Further, the diagnostic methods and the advancement of the computerized tomography have been discussed. Droplets, aerosol, and close contact are thesignificantfactors to transfer the infection to the suspect. This study predicts the possible transmission of the virus through medical practices such as ophthalmology, dental, and endoscopy procedures. With regard to pediatric transmission, as of now, only afew child fatalities had been reported. Childrenusually respond to the respiratory virus; however, COVID-19 response ison the contrary. The possibility of getting infected is minimal for the newborn. There has been no asymptomatic spread in children until now. Moreover, breastfeedingwould not transmit COVID-19, which is encouraging hygiene news for the pediatric. In addition, the current diagnostic methods for COVID-19 including Immunoglobulin M (IgM) and Immunoglobulin G (IgG)and chest computed topography(CT) scan, reverse transcription-polymerase chain reaction (RT-PCR) andimmunochromatographic fluorescence assay, are also discussed in detail. The introduction of artificial intelligence and deep learning algorithmhas the ability to diagnose COVID-19 in precise. However, the developments of a potential technology for the identification of the infection, such as a drone with thermal screening without human intervention, need to be encouraged.

Review of guidelines and recommendations from 17 countries highlights the challenges that clinicians face caring for neonates born to mothers with COVID-19

AIM

This review examined how applicable national and regional clinical practice guidelines and recommendations for managing neonates born to mothers with COVID-19 mothers were to the evolving pandemic.

METHODS

A systematic search and review identified 20 guidelines and recommendations that had been published by May 25, 2020. We analysed documents from 17 countries: Australia, Brazil, Canada, China, France, India, Italy, Japan, Saudi Arabia, Singapore, South Africa, South Korea, Spain, Sweden, Switzerland, the UK and the United States.

RESULTS

The documents were based on expert consensus with limited evidence and were of variable, low methodological rigour. Most did not provide recommendations for delivery methods or managing symptomatic infants. None provided recommendations for post-discharge assimilation of potentially infected infants into the community. The majority encouraged keeping mothers and infants together, subject to infection control measures, but one-third recommended separation. Although breastfeeding or using breastmilk was widely encouraged, two countries specifically prohibited this.

CONCLUSION

The guidelines and recommendations for managing infants affected by COVID-19 were of low, variable quality and may be unsustainable. It is important that transmission risks are not increased when new information is incorporated into clinical recommendations. Practice guidelines should emphasise the extent of uncertainty and clearly define gaps in the evidence.

Molecular diagnostic technologies for COVID-19: Limitations and challenges

BACKGROUND

To curb the spread of the COVID-19 (coronavirus disease 2019) pandemic, the world needs diagnostic systems capable of rapid detection and quantification of the novel coronavirus (SARS-CoV-2). Many biomedical companies are rising to the challenge and developing COVID-19 diagnostics. In the last few months, some of these diagnostics have become commercially available for healthcare workers and clinical laboratories. However, the diagnostic technologies have specific limitations and reported several false-positive and false-negative cases, especially during the early stages of infection.

AIM

This article aims to review recent developments in the field of COVID-19 diagnostics based on molecular technologies and analyze their clinical performance data.

KEY CONCEPTS

The literature survey and performance-based analysis of the commercial and pre-commercial molecular diagnostics address several questions and issues related to the limitations of current technologies and highlight future research and development challenges to enable timely, rapid, low-cost, and accurate diagnosis of emerging infectious diseases.

Expedited SARS-CoV-2 screening of donors and recipients supports continued solid organ transplantation

Universal screening of potential organ donors and recipients for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is now recommended prior to transplantation in the United States during the coronavirus disease 19 (COVID-19) pandemic. Challenges have included limited testing capacity, short windows of organ viability, brief lead time for notification of potential organ recipients, and the need to test lower respiratory donor specimens to optimize sensitivity. In an early U.S. epicenter of the outbreak, we designed and implemented a system to expedite this testing and the results here from the first 3 weeks. The process included a Laboratory Medicine designee for communication with organ recovery and transplant clinical staff, specialized sample labeling and handoff, and priority processing. Thirty-two organs recovered from 14 of 17 screened donors were transplanted vs 70 recovered from 23 donors during the same period in 2019. No pretransplant or organ donors tested positive for SARS-CoV-2. Median turnaround time from specimen receipt was 6.8 hours (donors), 6.5 hours (recipients): 4.5 hours faster than daily inpatient median. No organ recoveries or transplantations were disrupted by a lack of SARS-CoV-2 testing. Waitlist inactivations for COVID-19 precautions were reduced in our region. Systems that include specialized ordering pathways and adequate testing capacity can support continued organ transplantation, even in a SARS-CoV-2 hyperendemic area.

Epidemiologic and Clinical Characteristics of COVID-19 Patients from a Quarantine Center in a Developing Community: A Retrospective Study

Purpose

Coronavirus disease 2019 (COVID-19) is an ongoing infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) agent, and is generally known as novel coronavirus. The impact of the disease has had apparent effects on health, social, and economic levels. This study aimed to investigate the epidemiologic features, clinical presentations, laboratory examination, and outcomes of COVID-19 patients in Jordan.

Patients and Methods

This retrospective study included all COVID-19 patients admitted to the quarantine center at King Abdullah University Hospital in Jordan between March 16 and May 21, 2020. Patient information was abstracted from hospital electronic records and included patient demographics, symptoms, comorbidities, laboratory tests, infection period, and outcome.

Results

Approximately 42% of the quarantined individuals were asymptomatic. The majority of symptomatic patients had mild to moderate symptoms of the disease. Only ten patients (9.3%) had severe symptoms, with one of them progressed to a critical stage and died 15 days after admission. Erythrocyte sedimentation rate (ESR), lactate dehydrogenase (LDH), and D-dimer levels were significantly elevated in many patients. More than two-thirds (69.8%) of the symptomatic patients were females. Elevated ESR and LDH levels, along with longer periods of infection, were significantly associated with symptomatic patients.

Conclusion

A large proportion of Jordanian patients were asymptomatic carriers of the virus. This finding emphasizes the importance of a continuous surveillance process to discover these contagious carriers to control the disease spread. Additionally, we suggest that future analyses should investigate for sexual variation in the inflammatory response to this viral infection since most of our symptomatic patients were females. Finally, the role of ESR and LDH biomarkers should be investigated further for the possibility of earlier identification of patients with greater risk.

Analytical sensitivity and clinical performance of a triplex RT-qPCR assay using CDC N1, N2, and RP targets for SARS-CoV-2 diagnosis

Background

Several RT-qPCR kits are available for SARS-CoV-2 diagnosis and some have emergency use authorization from the US Food and Drug Administration. In particular, the nCoV19 CDC kit includes two targets for detecting SARS-CoV-2 (N1 and N2) and an RNaseP (RP) target for RNA extraction quality control, all of which are labeled with FAM, and thus three PCR reactions are required per sample.

Methods

We designed a triplex RT-qPCR assay based on nCoV19 primers and probes where N1, N2, and RP are labeled with FAM, HEX, and Cy5, respectively, so only a single PCR reaction is required for each sample for SARS-CoV-2 diagnosis.

Results

In total, 172 samples were analyzed in both singleplex and triplex assays, where 86 samples tested SARS-CoV-2 negative with both assays, so the triplex assay specificity was 100%. In addition, 86 samples tested SARS-Co-V 2 positive with the singleplex assay and 84 with the triplex assay, so the sensitivity was 97.7%. The limit of detection for the triplex assay was determined as 1000 copies/mL.

Conclusions

This new triplex RT-qPCR assay based on primers and probes from the CDC protocol is highly reliable for SARS-CoV-2 diagnosis, and it could speed up detection and save reagents during the current SARS-CoV-2 testing supplies shortage.

Cell-based culture of SARS-CoV-2 informs infectivity and safe de-isolation assessments during COVID-19

Background

The detection of SARS-CoV-2 RNA by real-time polymerase chain reaction (PCR) in respiratory samples collected from persons recovered from COVID-19 does not necessarily indicate shedding of infective virions. By contrast, the isolation of SARS-CoV-2 using cell-based culture likely indicates infectivity, but there are limited data on the correlation between SARS-CoV-2 culture and PCR.

Methods

One hundred and ninety-five patients with varying severity of COVID-19 were tested (outpatients [n=178]), inpatients [n=12] and critically unwell patients admitted to the intensive care unit [ICU; n=5]). SARS-CoV-2 PCR positive samples were cultured in Vero C1008 cells and inspected daily for cytopathic effect (CPE). SARS-CoV-2-induced CPE was confirmed by PCR of culture supernatant. Where no CPE was observed, PCR was performed on day four to confirm absence of virus replication. Cycle threshold (Ct) of the day four PCR (Ct_culture) and the PCR of the original clinical sample (Ct_sample) were compared, and positive cultures were defined where Ct_sample - Ct_culture was ≥3.

Findings

Of 234 samples collected, 228 (97%) were from the upper respiratory tract. SARS-CoV-2 was only successfully isolated from samples with Ct_sample ≤32, including in 28/181 (15%), 19/42 (45%) and 9/11 samples (82%) collected from outpatients, inpatients, and ICU patients, respectively. The mean duration from symptom onset to culture positivity was 4.5 days (range 0-18). SARS-CoV-2 was significantly more likely to be isolated from samples collected from inpatients (p<0∙001) and ICU patients (p<0∙0001) compared with outpatients respectively, and in samples with lower Ct_sample.

Conclusion

SARS-CoV-2 culture may be used as a surrogate marker for infectivity and inform de-isolation protocols.

Nucleic Acid and Immunological Diagnostics for SARS-CoV-2: Processes, Platforms and Pitfalls

Accurate diagnosis at an early stage of infection is essential for the successful management of any contagious disease. The coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus is a pandemic that has affected 214 countries affecting more than 37.4 million people causing 1.07 million deaths as of the second week of October 2020. The primary diagnosis of the infection is done either by the molecular technique of RT-qPCR by detecting portions of the RNA of the viral genome or through immunodiagnostic tests by detecting the viral proteins or the antibodies produced by the host. As the demand for the test increased rapidly many naive manufacturers entered the market with novel kits and more and more laboratories also entered the diagnostic arena making the test result more error-prone. There are serious debates globally and regionally on the sensitivity and specificity of these tests and about the overall accuracy and reliability of the tests for decision making on control strategies. The significance of the test is also complexed by the presence of asymptomatic carriers, re-occurrence of infection in cured patients as well as by the varied incubation periods of the infection and shifting of the viral location in the host tissues. In this paper, we review the techniques available for SARS-CoV-2 diagnosis and probable factors that can reduce the sensitivity and specificity of the different test methods currently in vogue. We also provide a checklist of factors to be considered to avoid fallacious practices to reduce false positive and false negative results by the clinical laboratories.

Neutralizing Antibodies Correlate with Protection from SARS-CoV-2 in Humans during a Fishery Vessel Outbreak with a High Attack Rate

The development of vaccines against SARS-CoV-2 would be greatly facilitated by the identification of immunological correlates of protection in humans. However, to date, studies on protective immunity have been performed only in animal models and correlates of protection have not been established in humans. Here, we describe an outbreak of SARS-CoV-2 on a fishing vessel associated with a high attack rate. Predeparture serological and viral reverse transcription-PCR (RT-PCR) testing along with repeat testing after return to shore was available for 120 of the 122 persons on board over a median follow-up of 32.5 days (range, 18.8 to 50.5 days). A total of 104 individuals had an RT-PCR-positive viral test with a cycle threshold (CT ) of <35 or seroconverted during the follow-up period, yielding an attack rate on board of 85.2% (104/122 individuals). Metagenomic sequencing of 39 viral genomes suggested that the outbreak originated largely from a single viral clade. Only three crew members tested seropositive prior to the boat's departure in initial serological screening and also had neutralizing and spike-reactive antibodies in follow-up assays. None of the crew members with neutralizing antibody titers showed evidence of bona fide viral infection or experienced any symptoms during the viral outbreak. Therefore, the presence of neutralizing antibodies from prior infection was significantly associated with protection against reinfection (Fisher's exact test, P = 0.002).

Challenges and Controversies to Testing for COVID-19

The coronavirus disease (COVID-19) pandemic has placed the clinical laboratory and testing for SARS-CoV-2 front and center in the worldwide discussion of how to end the outbreak. Clinical laboratories have responded by developing, validating, and implementing a variety of molecular and serologic assays to test for SARS-CoV-2 infection. This has played an essential role in identifying cases, informing isolation decisions, and helping to curb the spread of disease. However, as the demand for COVID-19 testing has increased, laboratory professionals have faced a growing list of challenges, uncertainties, and, in some situations, controversy, as they have attempted to balance the need for increasing test capacity with maintaining a high-quality laboratory operation. The emergence of this new viral pathogen has raised unique diagnostic questions for which there have not always been straightforward answers. In this commentary, the author addresses several areas of current debate, including (i) the role of molecular assays in defining the duration of isolation/quarantine, (ii) whether the PCR cycle threshold value should be included on patient reports, (iii) if specimen pooling and testing by research staff represent acceptable solutions to expand screening, and (iv) whether testing a large percentage of the population is feasible and represents a viable strategy to end the pandemic.

"One health" inspired SARS-CoV-2 surveillance: The Galapagos Islands experience

The COVID-19 pandemic has spread worldwide since the outbreak in Wuhan (China) in December 2019, currently infecting over 25 million people and causing more than 800.000 deaths. In Ecuador, up to the 30th of August 2020, overall 113.648 confirmed cases and 6.555 deaths have been declared. Besides overloading of hospital, capacity for molecular diagnosis of SARS-CoV-2 by the Ministry of Public Health was quickly overwhelmed. In this context, emergency authorization for SARS-CoV-2 RT-qPCR diagnosis was granted to other institutions, like the “Agencia de Regulación y Control para la Bioseguridad y Cuarentena de Galápagos” (ABG), that implemented “LabGal” with support of One Health Research Group from “Universidad de Las Américas” (UDLA). The previous experience of ABG and the One Health Research Group in conducting massive surveillance of zoonotic diseases on livestock was crucial to the success on the control of COVID-19 outbreak at Galapagos Islands by the end of May 2020, when Latin American countries were leading the spread of the pandemic.

COVID-19 in a patient with a flare of systemic lupus erythematosus: A rare case-report

This is a rare case-report of a young female with systemic lupus erythematosus and end-stage kidney disease (on maintenance hemodialysis) who was admitted to our intensive care unit due to life-threatening COVID-19. The patient was diagnosed with a flare of lupus; while being on maintenance hydroxychloroquine therapy. However, after the administration of steroids she made an uneventful recovery and was discharged home. In this report, the diagnostic dilemmas and the therapeutic challenges due to the overlapping clinical, imaging, and laboratory findings between lupus and COVID-19 pneumonitis are outlined. In conclusion, patients with lupus may be affected by COVID-19 despite the administration of hydroxychloroquine. The administration of steroids may have a beneficial effect on mitigating both the flare of SLE and the COVID-19 associated hyperinflammation.

Detection of COVID-19: A review of the current literature and future perspectives

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the coronavirus disease 2019 (COVID-19) worldwide pandemic. This unprecedented situation has garnered worldwide attention. An effective strategy for controlling the COVID-19 pandemic is to develop highly accurate methods for the rapid identification and isolation of SARS-CoV-2 infected patients. Many companies and institutes are therefore striving to develop effective methods for the rapid detection of SARS-CoV-2 ribonucleic acid (RNA), antibodies, antigens, and the virus. In this review, we summarize the structure of the SARS-CoV-2 virus, its genome and gene expression characteristics, and the current progression of SARS-CoV-2 RNA, antibodies, antigens, and virus detection. Further, we discuss the reasons for the observed false-negative and false-positive RNA and antibody detection results in practical clinical applications. Finally, we provide a review of the biosensors which hold promising potential for point-of-care detection of COVID-19 patients. This review thereby provides general guidelines for both scientists in the biosensing research community and for those in the biosensor industry to develop a highly sensitive and accurate point-of-care COVID-19 detection system, which would be of enormous benefit for controlling the current COVID-19 pandemic.

SARS-CoV-2 in wastewater: State of the knowledge and research needs

The ongoing global pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a Public Health Emergency of International Concern, which was officially declared by the World Health Organization. SARS-CoV-2 is a member of the family Coronaviridae that consists of a group of enveloped viruses with single-stranded RNA genome, which cause diseases ranging from common colds to acute respiratory distress syndrome. Although the major transmission routes of SARS-CoV-2 are inhalation of aerosol/droplet and person-to-person contact, currently available evidence indicates that the viral RNA is present in wastewater, suggesting the need to better understand wastewater as potential sources of epidemiological data and human health risks. Here, we review the current knowledge related to the potential of wastewater surveillance to understand the epidemiology of COVID-19, methodologies for the detection and quantification of SARS-CoV-2 in wastewater, and information relevant for human health risk assessment of SARS-CoV-2. There has been growing evidence of gastrointestinal symptoms caused by SARS-CoV-2 infections and the presence of viral RNA not only in feces of infected individuals but also in wastewater. One of the major challenges in SARS-CoV-2 detection/quantification in wastewater samples is the lack of an optimized and standardized protocol. Currently available data are also limited for conducting a quantitative microbial risk assessment (QMRA) for SARS-CoV-2 exposure pathways. However, modeling-based approaches have a potential role to play in reducing the impact of the ongoing COVID-19 outbreak. Furthermore, QMRA parameters obtained from previous studies on relevant respiratory viruses help to inform risk assessments of SARS-CoV-2. Our understanding on the potential role of wastewater in SARS-CoV-2 transmission is largely limited by knowledge gaps in its occurrence, persistence, and removal in wastewater. There is an urgent need for further research to establish methodologies for wastewater surveillance and understand the implications of the presence of SARS-CoV-2 in wastewater.

Wastewater and public health: the potential of wastewater surveillance for monitoring COVID-19

Pathogenic viruses represent one of the greatest threats to human well-being. As evidenced by the COVID-19 global pandemic, however, halting the spread of highly contagious diseases is notoriously difficult. Successful control strategies therefore have to rely on effective surveillance. Here, we describe how monitoring wastewater from urban areas can be used to detect the arrival and subsequent decline of pathogens, such as SARS-CoV-2. As the amount of virus shed in faeces and urine varies largely from person to person, it is very difficult to quantitatively determine the number of people who are infected in the population. More research on the surveillance of viruses in wastewater using accurate and validated methods, as well as subsequent risk analysis and modelling is paramount in understanding the dynamics of viral outbreaks.

Sensitivity of different RT-qPCR solutions for SARS-CoV-2 detection

OBJECTIVES

The ongoing COVID-19 pandemic continues to impose demands on diagnostic screening. In anticipation that the recurrence of outbreaks and the measures for lifting the lockdown worldwide may cause supply chain issues over the coming months, this study assessed the sensitivity of a number of one-step retrotranscription and quantitative polymerase chain reaction (RT-qPCR) solutions to detect SARS-CoV-2.

METHODS

Six different RT-qPCR alternatives were evaluated for SARS-CoV-2/COVID-19 diagnosis based on standard RNA extractions. The one with best sensitivity was also assessed with direct nasopharyngeal swab viral transmission medium (VTM) heating; thus overcoming the RNA extraction step.

RESULTS

A wide variability in the sensitivity of RT-qPCR solutions was found that was associated with a range of false negatives from 2% (0.3-7.9%) to 39.8% (30.2-50.2%). Direct preheating of VTM combined with the best solution provided a sensitivity of 72.5% (62.5-81.0%), in the range of some of the solutions based on standard RNA extractions.

CONCLUSIONS

Sensitivity limitations of currently used RT-qPCR solutions were found. These results will help to calibrate the impact of false negative diagnoses of COVID-19, and to detect and control new SARS-CoV-2 outbreaks and community transmissions.

A Characteristic Chest Radiographic Pattern in the Setting of the COVID-19 Pandemic

PURPOSE

To determine the utility of chest radiography in aiding clinical diagnosis of coronavirus disease 2019 (COVID-19) utilizing reverse-transcription polymerase chain reaction (RT-PCR) as the standard of comparison.

MATERIALS AND METHODS

A retrospective study was performed of persons under investigation for COVID-19 presenting to this institution during the exponential growth phase of the COVID-19 outbreak in New Orleans (March 13-25, 2020). Three hundred seventy-six in-hospital chest radiographic examinations for 366 individual patients were reviewed along with concurrent RT-PCR tests. Two experienced radiologists categorized each chest radiograph as characteristic, nonspecific, or negative in appearance for COVID-19, utilizing well-documented COVID-19 imaging patterns. Chest radiograph categorization was compared against RT-PCR results to determine the utility of chest radiography in diagnosing COVID-19.

RESULTS

Of the 366 patients, the study consisted of 178 male (49%) and 188 female (51%) patients with a mean age of 52.7 years (range, 17 to 98 years). Of the 376 chest radiographic examinations, 37 (10%) exhibited the characteristic COVID-19 appearance; 215 (57%) exhibited the nonspecific appearance; and 124 (33%) were considered negative for a pulmonary abnormality. Of the 376 RT-PCR tests evaluated, 200 (53%) were positive and 176 (47%) were negative. RT-PCR tests took an average of 2.5 days ± 0.7 to provide results. Sensitivity and specificity for correctly identifying COVID-19 with a characteristic chest radiographic pattern was 15.5% (31/200) and 96.6% (170/176), with a positive predictive value and negative predictive value of 83.8% (31/37) and 50.1% (170/339), respectively.

CONCLUSION

The presence of patchy and/or confluent, bandlike ground-glass opacity or consolidation in a peripheral and mid to lower lung zone distribution on a chest radiograph obtained in the setting of pandemic COVID-19 was highly suggestive of severe acute respiratory syndrome coronavirus 2 infection and should be used in conjunction with clinical judgment to make a diagnosis.© RSNA, 2020.

Pooling of SARS-CoV-2 samples to increase molecular testing throughput

BACKGROUND

SARS-CoV-2 testing demand has outpaced its supply. Pooling samples for lower risk populations has the potential to accommodate increased demand for SARS-CoV-2 molecular testing.

OBJECTIVE

To evaluate the sensitivity, specificity, and reproducibility of 4-way pooling of SARS-CoV-2 specimens for high-throughput RT-PCR.

STUDY DESIGN

Individual samples were pooled 1:4 through automated liquid handling, extracted, and assayed by our emergency use authorized CDC-based RT-PCR laboratory developed test. Positive samples were serially diluted and theoretical and empirical PCR cycle thresholds were evaluated. Thirty-two distinct positive samples were pooled into negative specimens and individual CTs were compared to pooled CTs. Low positive samples were repeated for reproducibility and 32 four-way pools of negative specimens were assayed to determine specificity.

RESULTS

Four-way pooling was associated with a loss of sensitivity of 1.7 and 2.0 CTs for our N1 and N2 targets, respectively. Pooling correctly identified SARS-CoV-2 in 94 % (n = 30/32) of samples tested. The two low positive specimens (neat CT > 35) not detected by pooling were individually repeated and detected 75 % (n=6/8) and 37.5 % (n = 3/8) of the time, respectively. All specimens individually determined negative were also negative by pooling.

CONCLUSION

We report that 1:4 pooling of samples is specific and associated with an expected 2 CT loss in analytical sensitivity. Instead of running each sample individually, pooling of four samples will allow for a greater throughput and conserve scarce reagents.

Molecular diagnosis of COVID-19 in different biologic matrix, their diagnostic validity and clinical relevance: A systematic review

Due to COVID 19 outbreak many studies are being conducted for therapeutic strategies and vaccines but detection methods play an important role in the containment of the disease. Hence, this systematic review aims to evaluate the effectiveness of the molecular detection techniques in COVID-19. For framing the systematic review 6 literature databases (PubMed, EMBASE, OVID, Web of Science, Scopus and Google Scholar) were searched for relevant studies and articles were screened for relevant content till 25th April 2020. Observations from this systematic review reveal the utility of RT-PCR with serological testing as one such method cannot correlate with accurate results. Availability of point of care devices do not conform to sensitivity and specificity in comparison to the conventional methods due to lack of clinical investigations. Pivotal aim of molecular and serological research is the development of detection methods that can support the clinical decision making of patients suspected with SARS-CoV-2. However, none of the methods were 100% sensitive and specific; hence additional studies are required to overcome the challenges addressed here. We hope that the present article with its observations and suggestions will assist the researchers to realize this vision in future.

Demonstration and Mitigation of Aerosol and Particle Dispersion During Mastoidectomy Relevant to the COVID-19 Era

BACKGROUND

COVID-19 has become a global pandemic with a dramatic impact on healthcare systems. Concern for viral transmission necessitates the investigation of otologic procedures that use high-speed drilling instruments, including mastoidectomy, which we hypothesized to be an aerosol-generating procedure.

METHODS

Mastoidectomy with a high-speed drill was simulated using fresh-frozen cadaveric heads with fluorescein solution injected into the mastoid air cells. Specimens were drilled for 1-minute durations in test conditions with and without a microscope. A barrier drape was fashioned from a commercially available drape (the OtoTent). Dispersed particulate matter was quantified in segments of an octagonal test grid measuring 60 cm in radius.

RESULTS

Drilling without a microscope dispersed fluorescent particles 360 degrees, with the areas of highest density in quadrants near the surgeon and close to the surgical site. Using a microscope or varying irrigation rates did not significantly reduce particle density or percent surface area with particulate. Using the OtoTent significantly reduced particle density and percent surface area with particulate across the segments of the test grid beyond 30 cm (which marked the boundary of the OtoTent) compared with the microscope only and no microscope test conditions (Kruskall-Wallis test, p = 0.0066).

CONCLUSIONS

Mastoidectomy with a high-speed drill is an aerosol-generating procedure, a designation that connotes the potential high risk of viral transmission and need for higher levels of personal protective equipment. A simple barrier drape significantly reduced particulate dispersion in this study and could be an effective mitigation strategy in addition to appropriate personal protective equipment.

Comparison of the diagnostic efficacy between two PCR test kits for SARS-CoV-2 nucleic acid detection

BACKGROUND

To compare the diagnostic efficacy between two different real-time reverse transcription polymerase chain reaction (RT-PCR) test kits for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid detection and provide references for laboratories.

METHODS

Throat swab samples from 18 hospitalized patients were clinically diagnosed with coronavirus disease 2019 (COVID-19) and 100 hospitalized patients without COVID-19 were collected. SARS-CoV-2 nucleic acid was detected in throat swab samples with RT-PCR test kits from Sansure Biotech Inc (Hunan, China) and Shanghai BioGerm Medical Biotechnology Co., Ltd.(Shanghai, China). The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and kappa value were analyzed, and three parallel tests were performed with three weakly positive samples.

RESULTS

The sensitivity, specificity, PPV, NPV, and kappa value of the Sansure PCR kit were 0.833, 1.000, 1.000, 0.971, and 0.894, respectively, and the sensitivity, specificity, PPV, NPV, and kappa value of the BioGerm PCR kit were 0.944, 1.000, 1.000, 0.990, and 0.966, respectively. For the three parallel tests, the coefficient of variation value of the BioGerm PCR kit in all three samples was the smallest for both the ORF1ab and N gene.

CONCLUSION

The detection efficacy of the BioGerm PCR kit for SARS-CoV-2 nucleic acid detection was relatively higher than that of the Sansure PCR kit.

A compendium answering 150 questions on COVID-19 and SARS-CoV-2

In December 2019, China reported the first cases of the coronavirus disease 2019 (COVID-19). This disease, caused by the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), has developed into a pandemic. To date, it has resulted in ~9 million confirmed cases and caused almost 500 000 related deaths worldwide. Unequivocally, the COVID-19 pandemic is the gravest health and socioeconomic crisis of our time. In this context, numerous questions have emerged in demand of basic scientific information and evidence-based medical advice on SARS-CoV-2 and COVID-19. Although the majority of the patients show a very mild, self-limiting viral respiratory disease, many clinical manifestations in severe patients are unique to COVID-19, such as severe lymphopenia and eosinopenia, extensive pneumonia, a "cytokine storm" leading to acute respiratory distress syndrome, endothelitis, thromboembolic complications, and multiorgan failure. The epidemiologic features of COVID-19 are distinctive and have changed throughout the pandemic. Vaccine and drug development studies and clinical trials are rapidly growing at an unprecedented speed. However, basic and clinical research on COVID-19-related topics should be based on more coordinated high-quality studies. This paper answers pressing questions, formulated by young clinicians and scientists, on SARS-CoV-2, COVID-19, and allergy, focusing on the following topics: virology, immunology, diagnosis, management of patients with allergic disease and asthma, treatment, clinical trials, drug discovery, vaccine development, and epidemiology. A total of 150 questions were answered by experts in the field providing a comprehensive and practical overview of COVID-19 and allergic disease.

Direct RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step

The ongoing COVID-19 pandemic has created an unprecedented need for rapid diagnostic testing. The World Health Organization (WHO) recommends a standard assay that includes an RNA extraction step from a nasopharyngeal (NP) swab followed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect the purified SARS-CoV-2 RNA. The current global shortage of RNA extraction kits has caused a severe bottleneck to COVID-19 testing. The goal of this study was to determine whether SARS-CoV-2 RNA could be detected from NP samples via a direct RT-qPCR assay that omits the RNA extraction step altogether. The direct RT-qPCR approach correctly identified 92% of a reference set of blinded NP samples (n = 155) demonstrated to be positive for SARS-CoV-2 RNA by traditional clinical diagnostic RT-qPCR that included an RNA extraction. Importantly, the direct method had sufficient sensitivity to reliably detect those patients with viral loads that correlate with the presence of infectious virus. Thus, this strategy has the potential to ease supply choke points to substantially expand COVID-19 testing and screening capacity and should be applicable throughout the world.

SARS-CoV-2-triggered neutrophil extracellular traps mediate COVID-19 pathology

Severe COVID-19 patients develop acute respiratory distress syndrome that may progress to cytokine storm syndrome, organ dysfunction, and death. Considering that neutrophil extracellular traps (NETs) have been described as important mediators of tissue damage in inflammatory diseases, we investigated whether NETs would be involved in COVID-19 pathophysiology. A cohort of 32 hospitalized patients with a confirmed diagnosis of COVID-19 and healthy controls were enrolled. The concentration of NETs was augmented in plasma, tracheal aspirate, and lung autopsies tissues from COVID-19 patients, and their neutrophils released higher levels of NETs. Notably, we found that viable SARS-CoV-2 can directly induce the release of NETs by healthy neutrophils. Mechanistically, NETs triggered by SARS-CoV-2 depend on angiotensin-converting enzyme 2, serine protease, virus replication, and PAD-4. Finally, NETs released by SARS-CoV-2–activated neutrophils promote lung epithelial cell death in vitro. These results unravel a possible detrimental role of NETs in the pathophysiology of COVID-19. Therefore, the inhibition of NETs represents a potential therapeutic target for COVID-19.

Comparison of Primer-Probe Sets among Different Master Mixes for Laboratory Screening of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Background

There is a shortage of chemical reagents for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis and a surge of SARS-CoV-2 cases, especially in limited-resource settings. Therefore, the combination of an optimal assay kit is necessary.

Methods

We compared the ability to screen SARS-CoV-2 among three primer-probe sets in two different master mixes, Invitrogen™ SuperScript™ III One-Step RT-PCR and LightCycler Multiplex RNA Virus Master.

Results

The assay with TIB-Molbiol, IDT, and Phu Sa sets for LightCycler Multiplex RNA Virus Master or Invitrogen™ SuperScript™ III One-Step RT-PCR showed positive results from a single reaction of triplicate in the three days of 4.8 copies per reaction. R squared and amplification efficiency were 0.97 and ranged from 107 to 108%, respectively.

Conclusions

Our findings indicated that TIB-Molbiol, IDT, and Phu Sa primer-probe sets could be beneficial for the laboratory screening of SARS-CoV-2 by RT-qPCR assay of E gene. There is a need to consider the combination of these reagent sets as a new strategy to increase the testing capacity of screening programs for COVID-19.

A Rapid SARS-CoV-2 RT-PCR Assay for Low Resource Settings

Quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is the gold standard recommended to test for acute SARS-CoV-2 infection. However, it generally requires expensive equipment such as RNA isolation instruments and real-time PCR thermal cyclers. As a pandemic, COVID-19 has spread indiscriminately, and many low resource settings and developing countries do not have the means for fast and accurate COVID-19 detection to control the outbreak. Additionally, long assay times, in part caused by slow sample preparation steps, have created a large backlog when testing patient samples suspected of COVID-19. With many PCR-based molecular assays including an extraction step, this can take a significant amount of time and labor, especially if the extraction is performed manually. Using COVID-19 clinical specimens, we have collected evidence that the RT-qPCR assay can feasibly be performed directly on patient sample material in virus transport medium (VTM) without an RNA extraction step, while still producing sensitive test results. If RNA extraction steps can be omitted without significantly affecting clinical sensitivity, the turn-around time of COVID-19 tests, and the backlog we currently experience can be reduced drastically. Furthermore, our data suggest that rapid RT-PCR can be implemented for sensitive and specific molecular diagnosis of COVID-19 in locations where sophisticated laboratory instruments are not available. Our USD 300 set up achieved rapid RT-PCR using thin-walled PCR tubes and a water bath setup using sous vide immersion heaters, a Raspberry Pi computer, and a single servo motor that can process up to 96 samples at a time. Using COVID-19 positive clinical specimens, we demonstrated that RT-PCR assays can be performed in as little as 12 min using untreated samples, heat-inactivated samples, or extracted RNA templates with our low-cost water bath setup. These findings can help rapid COVID-19 testing to become more accessible and attainable across the globe.

Saliva Sampling and Its Direct Lysis, an Excellent Option To Increase the Number of SARS-CoV-2 Diagnostic Tests in Settings with Supply Shortages

As part of any plan to lift or ease the confinement restrictions that are in place in many different countries, there is an urgent need to increase the capacity of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Detection of the viral genome through reverse transcription-quantitative PCR (RT-qPCR) is the gold standard for this virus; however, the high demand of the materials and reagents needed to sample individuals, purify the viral RNA, and perform the RT-qPCR has resulted in a worldwide shortage of several of these supplies. Here, we show that directly lysed saliva samples can serve as a suitable source for viral RNA detection that is less expensive and can be as efficient as the classical protocol, which involves column purification of the viral RNA. In addition, it bypasses the need for swab sampling, decreases the risk of the health care personnel involved in the testing process, and accelerates the diagnostic procedure.

Mutations on COVID-19 diagnostic targets

Effective, sensitive, and reliable diagnostic reagents are of paramount importance for combating the ongoing coronavirus disease 2019 (COVID-19) pandemic when there is neither a preventive vaccine nor a specific drug available for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It will cause a large number of false-positive and false-negative tests if currently used diagnostic reagents are undermined. Based on genotyping of 31,421 SARS-CoV-2 genome samples collected up to July 23, 2020, we reveal that essentially all of the current COVID-19 diagnostic targets have undergone mutations. We further show that SARS-CoV-2 has the most mutations on the targets of various nucleocapsid (N) gene primers and probes, which have been widely used around the world to diagnose COVID-19. To understand whether SARS-CoV-2 genes have mutated unevenly, we have computed the mutation rate and mutation h-index of all SARS-CoV-2 genes, indicating that the N gene is one of the most non-conservative genes in the SARS-CoV-2 genome. We show that due to human immune response induced APOBEC mRNA (C > T) editing, diagnostic targets should also be selected to avoid cytidines. Our findings might enable optimally selecting the conservative SARS-CoV-2 genes and proteins for the design and development of COVID-19 diagnostic reagents, prophylactic vaccines, and therapeutic medicines.

Availability

Interactive real-time online Mutation Tracker.

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Essentially all of the current COVID-19 diagnostic targets have undergone mutations.

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SARS-CoV-2 nucleocapsid (N) gene primers and probes have the most mutations.

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It would be better to select diagnostic targets avoiding cytidines.

First detection of SARS-CoV-2 in untreated wastewaters in Italy

Several studies have demonstrated the advantages of environmental surveillance through the monitoring of sewage for the assessment of viruses circulating in a given community (wastewater-based epidemiology, WBE). During the COVID-19 public health emergency, many reports have described the presence of SARS-CoV-2 RNA in stools from COVID-19 patients, and a few studies reported the occurrence of SARS-CoV-2 in wastewaters worldwide. Italy is among the world's worst-affected countries in the COVID-19 pandemic, but so far there are no studies assessing the presence of SARS-CoV-2 in Italian wastewaters. To this aim, twelve influent sewage samples, collected between February and April 2020 from Wastewater Treatment Plants in Milan and Rome, were tested adapting, for concentration, the standard WHO procedure for Poliovirus surveillance. Molecular analysis was undertaken with three nested protocols, including a newly designed SARS-CoV-2 specific primer set. SARS-CoV-2 RNA detection was accomplished in volumes of 250 ml of wastewaters collected in areas of high (Milan) and low (Rome) epidemic circulation, according to clinical data. Overall, 6 out of 12 samples were positive. One of the positive results was obtained in a Milan wastewater sample collected a few days after the first notified Italian case of autochthonous SARS-CoV-2. The study confirms that WBE has the potential to be applied to SARS-CoV-2 as a sensitive tool to study spatial and temporal trends of virus circulation in the population.

First detection of SARS-CoV-2 in untreated wastewaters in Italy

Several studies have demonstrated the advantages of environmental surveillance through the monitoring of sewage for the assessment of viruses circulating in a given community (wastewater-based epidemiology, WBE). During the COVID-19 public health emergency, many reports have described the presence of SARS-CoV-2 RNA in stools from COVID-19 patients, and a few studies reported the occurrence of SARS-CoV-2 in wastewaters worldwide. Italy is among the world's worst-affected countries in the COVID-19 pandemic, but so far there are no studies assessing the presence of SARS-CoV-2 in Italian wastewaters. To this aim, twelve influent sewage samples, collected between February and April 2020 from Wastewater Treatment Plants in Milan and Rome, were tested adapting, for concentration, the standard WHO procedure for Poliovirus surveillance. Molecular analysis was undertaken with three nested protocols, including a newly designed SARS-CoV-2 specific primer set. SARS-CoV-2 RNA detection was accomplished in volumes of 250 ml of wastewaters collected in areas of high (Milan) and low (Rome) epidemic circulation, according to clinical data. Overall, 6 out of 12 samples were positive. One of the positive results was obtained in a Milan wastewater sample collected a few days after the first notified Italian case of autochthonous SARS-CoV-2. The study confirms that WBE has the potential to be applied to SARS-CoV-2 as a sensitive tool to study spatial and temporal trends of virus circulation in the population.

First detection of SARS-CoV-2 in untreated wastewaters in Italy

Several studies have demonstrated the advantages of environmental surveillance through the monitoring of sewage for the assessment of viruses circulating in a given community (wastewater-based epidemiology, WBE). During the COVID-19 public health emergency, many reports have described the presence of SARS-CoV-2 RNA in stools from COVID-19 patients, and a few studies reported the occurrence of SARS-CoV-2 in wastewaters worldwide. Italy is among the world's worst-affected countries in the COVID-19 pandemic, but so far there are no studies assessing the presence of SARS-CoV-2 in Italian wastewaters. To this aim, twelve influent sewage samples, collected between February and April 2020 from Wastewater Treatment Plants in Milan and Rome, were tested adapting, for concentration, the standard WHO procedure for Poliovirus surveillance. Molecular analysis was undertaken with three nested protocols, including a newly designed SARS-CoV-2 specific primer set. SARS-CoV-2 RNA detection was accomplished in volumes of 250 ml of wastewaters collected in areas of high (Milan) and low (Rome) epidemic circulation, according to clinical data. Overall, 6 out of 12 samples were positive. One of the positive results was obtained in a Milan wastewater sample collected a few days after the first notified Italian case of autochthonous SARS-CoV-2. The study confirms that WBE has the potential to be applied to SARS-CoV-2 as a sensitive tool to study spatial and temporal trends of virus circulation in the population.

Serodiagnostics for Severe Acute Respiratory Syndrome-Related Coronavirus 2 : A Narrative Review

Accurate serologic tests to detect host antibodies to severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) will be critical for the public health response to the coronavirus disease 2019 pandemic. Many use cases are envisaged, including complementing molecular methods for diagnosis of active disease and estimating immunity for individuals. At the population level, carefully designed seroepidemiologic studies will aid in the characterization of transmission dynamics and refinement of disease burden estimates and will provide insight into the kinetics of humoral immunity. Yet, despite an explosion in the number and availability of serologic assays to test for antibodies against SARS-CoV-2, most have undergone minimal external validation to date. This hinders assay selection and implementation, as well as interpretation of study results. In addition, critical knowledge gaps remain regarding serologic correlates of protection from infection or disease, and the degree to which these assays cross-react with antibodies against related coronaviruses. This article discusses key use cases for SARS-CoV-2 antibody detection tests and their application to serologic studies, reviews currently available assays, highlights key areas of ongoing research, and proposes potential strategies for test implementation.

COVID-19 Clinical Diagnostics and Testing Technology

Given the global nature of the coronavirus disease 2019 (COVID-19) pandemic, the need for disease detection and expanding testing capacity remains critical priorities. This review discusses the technological advances in testing capability and methodology that are currently used or in development for detecting the novel coronavirus. We describe the current clinical diagnostics and technology, including molecular and serological testing approaches, for severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) testing as well as address their advantages and limitations. Nucleic acid amplification technology for molecular diagnostics remains the gold standard for virus detection. We highlight alternative molecular detection techniques used for developing novel COVID-19 diagnostics on the horizon. Antibody response against SARS-CoV-2 remains poorly understood and proper validation of serology tests is necessary to demonstrate their accuracy and clinical utility. In order to bring the pandemic under control, we must speed up the development of rapid and widespread testing through improvements in clinical diagnostics and testing technology as well as access to these tools.

Clinical and Laboratory Diagnosis of SARS-CoV-2, the Virus Causing COVID-19

In December 2019, a novel beta (β) coronavirus eventually named SARS-CoV-2 emerged in Wuhan, Hubei province, China, causing an outbreak of severe and even fatal pneumonia in humans. The virus has spread very rapidly to many countries across the world, resulting in the World Health Organization (WHO) to declare a pandemic on March 11, 2020. Clinically, the diagnosis of this unprecedented illness, called coronavirus disease-2019 (COVID-19), becomes difficult because it shares many symptoms with other respiratory pathogens, including influenza and parainfluenza viruses. Therefore, laboratory diagnosis is crucial for the clinical management of patients and the implementation of disease control strategies to contain SARS-CoV-2 at clinical and population level. Here, we summarize the main clinical and imaging findings of COVID-19 patients and discuss the advances, features, advantages, and limitations of different laboratory methods used for SARS-CoV-2 diagnosis.

Comparative Analysis of Primer-Probe Sets for RT-qPCR of COVID-19 Causative Virus (SARS-CoV-2)

Coronavirus disease 2019 (COVID-19) is a newly emerging human infectious disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2, also previously known as 2019-nCoV). Within 8 months of the outbreak, more than 10,000,000 cases of COVID-19 have been confirmed worldwide. Since human-to-human transmission occurs easily and the rate of human infection is rapidly increasing, sensitive and early diagnosis is essential to prevent a global outbreak. Recently, the World Health Organization (WHO) announced various primer-probe sets for SARS-CoV-2 developed at different institutions: China Center for Disease Control and Prevention (China CDC, China), Charité (Germany), The University of Hong Kong (HKU, Hong Kong), National Institute of Infectious Diseases in Japan (Japan NIID, Japan), National Institute of Health in Thailand (Thailand NIH, Thailand), and US CDC (USA). In this study, we compared the ability to detect SARS-CoV-2 RNA among seven primer-probe sets for the N gene and three primer-probe sets for the Orf1 gene. The results revealed that "NIID_2019-nCOV_N" from the Japan NIID and "ORF1ab" from China CDC represent a recommendable performance of RT-qPCR analysis for SARS-CoV-2 molecular diagnostics without nonspecific amplification and cross-reactivity for hCoV-229E, hCoV-OC43, and MERS-CoV RNA. Therefore, the appropriate combination of NIID_2019-nCOV_N (Japan NIID) and ORF1ab (China CDC) sets should be selected for sensitive and reliable SARS-CoV-2 molecular diagnostics.

Comparative Analysis of Primer-Probe Sets for RT-qPCR of COVID-19 Causative Virus (SARS-CoV-2)

Coronavirus disease 2019 (COVID-19) is a newly emerging human infectious disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2, also previously known as 2019-nCoV). Within 8 months of the outbreak, more than 10,000,000 cases of COVID-19 have been confirmed worldwide. Since human-to-human transmission occurs easily and the rate of human infection is rapidly increasing, sensitive and early diagnosis is essential to prevent a global outbreak. Recently, the World Health Organization (WHO) announced various primer-probe sets for SARS-CoV-2 developed at different institutions: China Center for Disease Control and Prevention (China CDC, China), Charité (Germany), The University of Hong Kong (HKU, Hong Kong), National Institute of Infectious Diseases in Japan (Japan NIID, Japan), National Institute of Health in Thailand (Thailand NIH, Thailand), and US CDC (USA). In this study, we compared the ability to detect SARS-CoV-2 RNA among seven primer-probe sets for the N gene and three primer-probe sets for the Orf1 gene. The results revealed that "NIID_2019-nCOV_N" from the Japan NIID and "ORF1ab" from China CDC represent a recommendable performance of RT-qPCR analysis for SARS-CoV-2 molecular diagnostics without nonspecific amplification and cross-reactivity for hCoV-229E, hCoV-OC43, and MERS-CoV RNA. Therefore, the appropriate combination of NIID_2019-nCOV_N (Japan NIID) and ORF1ab (China CDC) sets should be selected for sensitive and reliable SARS-CoV-2 molecular diagnostics.

Comparison of SARS-CoV-2 detection from combined nasopharyngeal/oropharyngeal swab samples by a laboratory-developed real-time RT-PCR test and the Roche SARS-CoV-2 assay on a cobas 8800 instrument

OBJECTIVE

Although several assays have been developed to detect SARS-CoV-2 RNA in clinical specimens, their relative performance is unknown.

METHODS

The concordance between the cobas 8800 SARS-CoV-2 and a laboratory developed (LD) reverse transcriptase-polymerase chain reaction (RT-PCR) assay was assessed on 377 combined nasopharyngeal/oropharyngeal swabs in Hanks medium.

RESULTS

The positive and negative agreement between these assays were 99.3 % (95 % CI, 97.3-99.9) and 77.1 % (95 % CI, 67.7-84.4), respectively, for an overall agreement of 93.6 % (95 % CI, 90.7-95.7) beyond random chance (kappa of 0.82, 95 % CI, 0.75-0.85). Of the 22 samples positive by cobas SARS-CoV-2 only, 9 were positive only for ORF-1 gene and had Cycle thresholds (Ct) > 35.1, 8 were positive only for the E gene with Ct > 35.5 and 5 were positive for both targets with Ct > 33.9. Samples positive only with the cobas assay were more often positive with only one gene target (77.3 %) than samples positive in both assays (16.9 %, p < 0.0001). Ct values in the cobas SARS-CoV-2 assay were significantly higher in the 279 samples testing positive in both assays (32.9 %, 95 % CI 32.3-33.6) compared to the 22 samples with discordant results (36.6 %, 95 % CI 36.2-37.1; p = 0.0009). An excellent correlation (r² = 0.98) was obtained between Ct values of the ORF-1 and E targets in the cobas assays and a good correlation was obtained between LD RT-PCR test and cobas SARS CoV-2 ORF-1 target (r² = 0.82).

CONCLUSION

Our study demonstrated an excellent concordance between a LD RT-PCR and the cobas SARS-CoV-2 tests on the 8800 platform.

Sensitivity, Specificity and Predictive Values of Molecular and Serological Tests for COVID-19: A Longitudinal Study in Emergency Room

BACKGROUND

We assessed the sensitivity, specificity and positive and negative predictive value (PPV and NPV) of molecular and serological tests for the diagnosis of SARS-CoV-2 infection.

METHODS

A total of 346 patients were enrolled in the emergency room. We evaluated three Reverse Transcriptase-real time PCRs (RT-PCRs) including six different gene targets, five serologic rapid diagnostic tests (RDT) and one ELISA. The final classification of infected/non-infected patients was performed using Latent Class Analysis combined with clinical re-assessment of incongruous cases.

RESULTS

Out of these, 24.6% of patients were classified as infected. The molecular test RQ-SARS-nCoV-2 showed the highest performance with 91.8% sensitivity, 100% specificity, 100.0% PPV and 97.4% NPV respectively. Considering the single gene targets, S and RdRp of RQ-SARS-nCoV-2 had the highest sensitivity (94.1%). The in-house RdRp presented the lowest sensitivity (62.4%). The specificity ranged from 99.2% for in-house RdRp and N2 to 95.0% for E. The PPV ranged from 97.1% of N2 to 85.4% of E and the NPV from 98.1% of S to 89.0% of in-house RdRp. All serological tests had < 50% sensitivity and low PPV and NPV. VivaDiag IgM (RDT) had 98.5% specificity, with 84.0% PPV, but 24.7% sensitivity.

CONCLUSION

Molecular tests for SARS-CoV-2 infection showed excellent specificity, but significant differences in sensitivity. Serological tests have limited utility in a clinical context.

Automated SARS-COV-2 RNA extraction from patient nasopharyngeal samples using a modified DNA extraction kit for high throughput testing

BACKGROUND

The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) has prompted a need for mass testing to identify patients with viral infection. The high demand has created a global bottleneck in testing capacity, which prompted us to modify available resources to extract viral RNA and perform reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to detect SARS-COV-2.

OBJECTIVES

Report on the use of a DNA extraction kit, after modifications, to extract viral RNA that could then be detected using an FDA-approved SARS-COV-2 RT-qPCR assay.

MATERIALS AND METHODS

Initially, automated RNA extraction was performed using a modified DNA kit on samples from control subjects, a bacteriophage, and an RNA virus. We then verified the automated extraction using the modified kit to detect in-lab propagated SARSCOV-2 titrations using an FDA approved commercial kit (S, N, and ORF1b genes) and an in-house primer-probe based assay (E, RdRp2 and RdRp4 genes).

RESULTS

Automated RNA extraction on serial dilutions SARS-COV-2 achieved successful one-step RT-qPCR detection down to 60 copies using the commercial kit assay and less than 30 copies using the in-house primer-probe assay. Moreover, RT-qPCR detection was successful after automated RNA extraction using this modified protocol on 12 patient samples of SARS-COV-2 collected by nasopharyngeal swabs and stored in viral transport media.

CONCLUSIONS

We demonstrated the capacity of a modified DNA extraction kit for automated viral RNA extraction and detection using a platform that is suitable for mass testing.

LIMITATIONS

Small patient sample size.

CONFLICT OF INTEREST

None.

Metropolitan wastewater analysis for COVID-19 epidemiological surveillance

The COVID-19 disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a rapidly emerging pandemic which has enforced extreme containment measures worldwide. In the absence of a vaccine or efficient treatment, cost-effective epidemiological surveillance strategies are urgently needed. Here, we have used RT-qPCR for SARS-CoV-2 detection in a series of longitudinal metropolitan wastewaters samples collected from February to April 2020, during the earliest stages of the epidemic in the Region of Valencia, Spain. We were able to consistently detect SARS-CoV-2 RNA in samples taken in late February, when communicated cases in that region were only incipient. We also find that the wastewater viral RNA context increased rapidly and anticipated the subsequent ascent in the number of declared cases. Our results strongly suggest that the virus was undergoing community transmission earlier than previously believed, and suggest that wastewater analysis could be sensitive and cost-effective strategy for COVID-19 epidemiological surveillance. Routine implementation of this surveillance tool would significantly improve our preparedness against new or re-occurring viral outbreaks.

Metropolitan wastewater analysis for COVID-19 epidemiological surveillance

The COVID-19 disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a rapidly emerging pandemic which has enforced extreme containment measures worldwide. In the absence of a vaccine or efficient treatment, cost-effective epidemiological surveillance strategies are urgently needed. Here, we have used RT-qPCR for SARS-CoV-2 detection in a series of longitudinal metropolitan wastewaters samples collected from February to April 2020, during the earliest stages of the epidemic in the Region of Valencia, Spain. We were able to consistently detect SARS-CoV-2 RNA in samples taken in late February, when communicated cases in that region were only incipient. We also find that the wastewater viral RNA context increased rapidly and anticipated the subsequent ascent in the number of declared cases. Our results strongly suggest that the virus was undergoing community transmission earlier than previously believed, and suggest that wastewater analysis could be sensitive and cost-effective strategy for COVID-19 epidemiological surveillance. Routine implementation of this surveillance tool would significantly improve our preparedness against new or re-occurring viral outbreaks.

Assessment of Disparities in COVID-19 Testing and Infection Across Language Groups in Seattle, Washington

This cross-sectional study evaluates the proportion of patients tested for coronavirus disease 2019 (COVID-19) and the proportion of positive cases, using language as a surrogate for immigrant status.

Comparison of the analytical sensitivity of seven commonly used commercial SARS-CoV-2 automated molecular assays

The SARS-CoV-2 pandemic has challenged molecular microbiology laboratories to quickly implement and validate diagnostic assays and to expand testing capacity in a short timeframe. Multiple molecular diagnostic methods received FDA emergency use authorization (EUA) and were promptly validated for use nationwide. Several studies reported the analytical and/ or clinical evaluation of these molecular assays, however differences in the viral materials used for these evaluations complicated direct comparison of their analytical performance. In this study, we compared the analytical sensitivity (lower limit of detection, LOD) of seven commonly used qualitative SARS-CoV-2 molecular assays: the Abbott Molecular RealTime SARS-CoV-2 assay, the NeuMoDx™ SARS-CoV-2 assay, the Roche Cobas®SARS-CoV-2 assay, the BD SARS-CoV-2 reagents for BD MAX™ system, the Hologic Aptima® SARS-CoV-2 assay, the Xpert Xpress SARS-CoV-2 test, and the GenMark ePlex SARS-CoV-2 test. The comparison was performed utilizing a single positive clinical specimen that was serially diluted in viral transport media and quantified by the EUA approved SARS-CoV-2 droplet digital PCR (ddPCR) assay. Replicate samples were prepared and evaluated for reproducibility across different molecular assays with multiple replicates per assay. Our data demonstrated that the seven assays could detect 100 % of replicates at a nucleocapsid gene concentration of (N1 = 1,267 and N2 = 1,392) copies/mL. At a one log less concentration, the Abbott, the Roche, and the Xpert Xpress assays detected 100 % of the tested replicates.

In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age

Despite limited genomic diversity, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown a wide range of clinical manifestations in different patient populations. The mechanisms behind these host differences are still unclear. Here, we examined host response gene expression across infection status, viral load, age, and sex among shotgun RNA sequencing profiles of nasopharyngeal (NP) swabs from 430 individuals with PCR-confirmed SARS-CoV-2 and 54 negative controls. SARS-CoV-2 induced a strong antiviral response with up-regulation of antiviral factors such as OAS1-3 and IFIT1-3 and T helper type 1 (Th1) chemokines CXCL9/10/11, as well as a reduction in transcription of ribosomal proteins. SARS-CoV-2 culture in human airway epithelial (HAE) cultures replicated the in vivo antiviral host response 7 days post infection, with no induction of interferon-stimulated genes after 3 days. Patient-matched longitudinal specimens (mean elapsed time = 6.3 days) demonstrated reduction in interferon-induced transcription, recovery of transcription of ribosomal proteins, and initiation of wound healing and humoral immune responses. Expression of interferon-responsive genes, including ACE2, increased as a function of viral load, while transcripts for B cell-specific proteins and neutrophil chemokines were elevated in patients with lower viral load. Older individuals had reduced expression of the Th1 chemokines CXCL9/10/11 and their cognate receptor CXCR3, as well as CD8A and granzyme B, suggesting deficiencies in trafficking and/or function of cytotoxic T cells and natural killer (NK) cells. Relative to females, males had reduced B cell-specific and NK cell-specific transcripts and an increase in inhibitors of nuclear factor kappa-B (NF-κB) signaling, possibly inappropriately throttling antiviral responses. Collectively, our data demonstrate that host responses to SARS-CoV-2 are dependent on viral load and infection time course, with observed differences due to age and sex that may contribute to disease severity.

COVID-19 outbreak in Jordan: Epidemiological features, clinical characteristics, and laboratory findings

BACKGROUND

In March 2020, an outbreak of coronavirus 19 (COVID-19) was detected in the North of Jordan. This retrospective study is the first from Jordan to report the epidemiologic, clinical, laboratory, and radiologic characteristics of COVID-19 infected patients.

METHODS

All patients with laboratory-confirmed COVID-19 infection by RT-PCR in the North of Jordan admitted between March 15 and April 2, 2020 were included. The clinical features, radiological, and laboratory findings were reviewed.

RESULTS

Of 81 patients affected, 79 (97.5%) shared a common exposure to four recent travelers from endemic areas. The mean age was 40 years. Although about half (44 [54.3%]) were females, symptomatic patients were mostly females (75%). The most common presenting symptoms were nasal congestion, sore throat and dry cough. Less than one-third (31%) had chronic diseases. Although 84% of patients reported receiving Bacille Calmette-Guérin (BCG) vaccination, more asymptomatic patients had BCG than symptomatic (p = 0.017). Almost all patients (97.5%) had an elevated D-dimer level. Erythrocyte sedimentation rate (ESR) and c-reactive protein were elevated in 50% and 42.7% of patients, respectively. High ESR found to be the predictor of abnormal chest radiograph observed in 13 (16%) patients with OR of 14.26 (95% CI 1.37-147.97, p = 0.026).

CONCLUSIONS

An outbreak of COVID-19 infection in northern Jordan affected more females and relatively young individuals and caused mainly mild illnesses. The strict outbreak response measures applied at early stages probably contributed to the lenient nature of this outbreak, but the contribution of other factors to such variability in COVID-19 presentation is yet to be explained.

SARS-CoV-2 and cancer: Are they really partners in crime?

The outbreak of the SARS-CoV-2 pandemic has overwhelmed health care systems in many countries. The clinical presentation of the SARS-CoV-2 varies between a subclinical or flu-like syndrome to that of severe pneumonia with multi-organ failure and death. Initial reports have suggested that cancer patients may have a higher susceptibility to get infected by the SARS-CoV-2 virus but current evidence remains poor as it is biased by important confounders. Patients with ongoing or recent cancer treatment for advanced active disease, metastatic solid tumors and hematological malignancies are at higher risk of developing severe COVID-19 respiratory disease that requires hospitalization and have a poorer disease outcome compared to individuals without cancer. However it is not clear whether these are independent risk factors, or mainly driven by male gender, age, obesity, performance status, uncontrolled diabetes, cardiovascular disease and various other medical conditions. These often have a greater influence on the probability to die due to SARS-CoV-2 then cancer. Delayed diagnosis and suboptimal cancer management due to the pandemic results in disease upstaging and has considerable impact cancer on specific death rates. Surgery during the peak of the pandemic seems to increase mortality, but there is no convincing evidence that adjuvant systemic cancer therapy and radiotherapy are contraindicated, implicating that cancer treatment can be provided safely after individual risk/benefit assessment and some adaptive measures. Underlying immunosuppression, elevated cytokine levels, altered expression of the angiotensin converting enzyme (ACE-2) and TMPRSS2, and a prothrombotic status may fuel the effects of a SARS-CoV-2 in some cancer patients, but have the potential to be used as biomarkers for severe disease and therapeutic targets. The rapidly expanding literature on COVID-19 should be interpreted with care as it is often hampered by methodological and statistical flaws.

Co-infection of SARS-CoV-2 and Bordetella bronchiseptica in a young man with idiopathic non-cystic bronchiectasis and vitamin D3 deficiency

This is the first reported case, to our knowledge, of co-infection of Bordetella bronchiseptica and SARS-CoV-2 in a young patient with underlying idiopathic bronchiectasis and vitamin D3 deficiency that was treated successfully with a combination therapeutic regime integrating doxycycline, empiric therapies for COVID-19, vitamin D supplementation, and supportive ICU care. Large prospective studies are required to investigate further the role of co-infections in COVID-19 patients with bronchiectasis. Randomized control trials should examine the putative beneficial role of vitamin D supplementation in patients with COVID-19.

A Comprehensive Overview of the COVID-19 Literature: Machine Learning–Based Bibliometric Analysis (Preprint).. [DOI: 10.2196/preprints.23703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

BACKGROUND

Shortly after the emergence of COVID-19, researchers rapidly mobilized to study numerous aspects of the disease such as its evolution, clinical manifestations, effects, treatments, and vaccinations. This led to a rapid increase in the number of COVID-19–related publications. Identifying trends and areas of interest using traditional review methods (eg, scoping and systematic reviews) for such a large domain area is challenging.

OBJECTIVE

We aimed to conduct an extensive bibliometric analysis to provide a comprehensive overview of the COVID-19 literature.

METHODS

We used the COVID-19 Open Research Dataset (CORD-19) that consists of a large number of research articles related to all coronaviruses. We used a machine learning–based method to analyze the most relevant COVID-19–related articles and extracted the most prominent topics. Specifically, we used a clustering algorithm to group published articles based on the similarity of their abstracts to identify research hotspots and current research directions. We have made our software accessible to the community via GitHub.

RESULTS

Of the 196,630 publications retrieved from the database, we included 28,904 in our analysis. The mean number of weekly publications was 990 (SD 789.3). The country that published the highest number of COVID-19–related articles was China (2950/17,270, 17.08%). The highest number of articles were published in bioRxiv. Lei Liu affiliated with the Southern University of Science and Technology in China published the highest number of articles (n=46). Based on titles and abstracts alone, we were able to identify 1515 surveys, 733 systematic reviews, 512 cohort studies, 480 meta-analyses, and 362 randomized control trials. We identified 19 different topics covered among the publications reviewed. The most dominant topic was public health response, followed by clinical care practices during the COVID-19 pandemic, clinical characteristics and risk factors, and epidemic models for its spread.

CONCLUSIONS

We provide an overview of the COVID-19 literature and have identified current hotspots and research directions. Our findings can be useful for the research community to help prioritize research needs and recognize leading COVID-19 researchers, institutes, countries, and publishers. Our study shows that an AI-based bibliometric analysis has the potential to rapidly explore a large corpus of academic publications during a public health crisis. We believe that this work can be used to analyze other eHealth-related literature to help clinicians, administrators, and policy makers to obtain a holistic view of the literature and be able to categorize different topics of the existing research for further analyses. It can be further scaled (for instance, in time) to clinical summary documentation. Publishers should avoid noise in the data by developing a way to trace the evolution of individual publications and unique authors.

Detection of SARS-CoV-2 RNA in commercial passenger aircraft and cruise ship wastewater: a surveillance tool for assessing the presence of COVID-19 infected travellers

BACKGROUND

Wastewater-based epidemiology (WBE) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be an important source of information for coronavirus disease 2019 (COVID-19) management during and after the pandemic. Currently, governments and transportation industries around the world are developing strategies to minimize SARS-CoV-2 transmission associated with resuming activity. This study investigated the possible use of SARS-CoV-2 RNA wastewater surveillance from airline and cruise ship sanitation systems and its potential use as a COVID-19 public health management tool.

METHODS

Aircraft and cruise ship wastewater samples (n = 21) were tested for SARS-CoV-2 using two virus concentration methods, adsorption-extraction by electronegative membrane (n = 13) and ultrafiltration by Amicon (n = 8), and five assays using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) and RT-droplet digital PCR (RT-ddPCR). Representative qPCR amplicons from positive samples were sequenced to confirm assay specificity.

RESULTS

SARS-CoV-2 RNA was detected in samples from both aircraft and cruise ship wastewater; however concentrations were near the assay limit of detection. The analysis of multiple replicate samples and use of multiple RT-qPCR and/or RT-ddPCR assays increased detection sensitivity and minimized false-negative results. Representative qPCR amplicons were confirmed for the correct PCR product by sequencing. However, differences in sensitivity were observed among molecular assays and concentration methods.

CONCLUSIONS

The study indicates that surveillance of wastewater from large transport vessels with their own sanitation systems has potential as a complementary data source to prioritize clinical testing and contact tracing among disembarking passengers. Importantly, sampling methods and molecular assays must be further optimized to maximize detection sensitivity. The potential for false negatives by both wastewater testing and clinical swab testing suggests that the two strategies could be employed together to maximize the probability of detecting SARS-CoV-2 infections amongst passengers.