Estimating the false-negative test probability of SARS-CoV-2 by RT-PCR

Recent advances in nanomedicine preparative methods and their therapeutic potential for colorectal cancer: a critical review

Colorectal cancer (CRC) is a prevalent malignancy that affects a large percentage of the global population. The conventional treatments for CRC have a number of limitations. Nanoparticles have emerged as a promising cancer treatment method due to their ability to directly target cancer cells and regulate drug release, thereby enhancing therapeutic efficacy and minimizing side effects. This compilation examines the use of nanoparticles as drug delivery systems for CRC treatment. Different nanomaterials can be used to administer anticancer drugs, including polymeric nanoparticles, gold nanoparticles, liposomes, and solid lipid nanoparticles. In addition, we discuss recent developments in nanoparticle preparation techniques, such as solvent evaporation, salting-out, ion gelation, and nanoprecipitation. These methods have demonstrated high efficacy in penetrating epithelial cells, a prerequisite for effective drug delivery. This article focuses on the various targeting mechanisms utilized by CRC-targeted nanoparticles and their recent advancements in this field. In addition, the review offers descriptive information regarding numerous nano-preparative procedures for colorectal cancer treatments. We also discuss the outlook for innovative therapeutic techniques in the management of CRC, including the potential application of nanoparticles for targeted drug delivery. The review concludes with a discussion of current nanotechnology patents and clinical studies used to target and diagnose CRC. The results of this investigation suggest that nanoparticles have great potential as a method of drug delivery for the treatment of colorectal cancer.

Genomic and serological assessment of asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in child labor

Since working children have limited access to testing and monitoring for COVID-19, we decided to measure SARS-CoV-2 prevalence among them and compare it to non-working children. Our objective is to compare the frequency of SARS-CoV-2 genome and anti-SARS-CoV-2 antibody among working and non-working children. Volunteer child labor studying at Defense of Child Labor and Street Children and randomly selected 5-18-year-old (same range as child labor group) unemployed children participated in this study. The groups, respectively, had 65 and 137 members. This is an analytical cross-sectional study that surveys molecular prevalence of SARS-CoV-2 infection by RT-PCR, and seroprevalence of SARS-CoV-2 antibody by ELISA in working and non-working children. The IBM SPSS statistics software version 25 was used for data analysis. The χ2 or Fisher's exact test was used to analyze categorical dependent variables, for calculating odds ratios and 95% confidence intervals. Among the children enrolled in this study, molecular prevalence of SARS-CoV-2 turned out to be 18.5% in working children while it was 5.8% in unemployed children [aOR: 3.00 (CI95%: 1.00-7.00); P value: 0.003] and seroprevalence turned out to be 20% in working children vs 13.9% in non-working children [aOR: 1.000 (CI95%: 0.00-2.00); > P 0.001]. Equal SARS-CoV-2 viral load as adults and no symptoms or mild ones in children, coupled with working children's strong presence in crowded areas and their higher rate of COVID-19 prevalence, make them a probable source for spread of the virus.

da Paixão Melo M, Ferreira da Silva M, de Jesus Gonçalves dos Santos N, de Souza Pessoa N, Silva de Araujo R, de Macedo Godim T, Fraga de Oliveira Tosta S, Brandão Nardy V, Cristina Faria E, Frederico de Carvalho Dominguez Souza B, Laís Almeida dos Santos J, Wikramaratna P, Giovanetti M, Alcântara LCJ, Lourenço J, Leal e Silva de Mello A. Dynamics and Determinants of SARS-CoV-2 RT-PCR Testing on Symptomatic Individuals Attending Healthcare Centers during 2020 in Bahia, Brazil

RT-PCR testing data provides opportunities to explore regional and individual determinants of test positivity and surveillance infrastructure. Using Generalized Additive Models, we explored 222,515 tests of a random sample of individuals with COVID-19 compatible symptoms in the Brazilian state of Bahia during 2020. We found that age and male gender were the most significant determinants of test positivity. There was evidence of an unequal impact among socio-demographic strata, with higher positivity among those living in areas with low education levels during the first epidemic wave, followed by those living in areas with higher education levels in the second wave. Our estimated probability of testing positive after symptom onset corroborates previous reports that the probability decreases with time, more than halving by about two weeks and converging to zero by three weeks. Test positivity rates generally followed state-level reported cases, and while a single laboratory performed ~90% of tests covering ~99% of the state's area, test turn-around time generally remained below four days. This testing effort is a testimony to the Bahian surveillance capacity during public health emergencies, as previously witnessed during the recent Zika and Yellow Fever outbreaks.

Epidemiological, Radiographical, and Laboratorial Characteristics of Chinese Asymptomatic Cases With COVID-19: A Systematic Review and Meta-Analysis

The comprehensive understanding of the characteristics of asymptomatic cases are helpful for the identification and management of patients with asymptomatic COVID-19 infection. Four electronic databases were searched from December 1, 2019 to February 8, 2022 for relevant articles. Data synthesis, subgroup analysis, and sensitivity analysis were performed on the included studies. I² and Q tests were applied to evaluate heterogeneity across studies. The risk of publication bias was assessed and visualized using a funnel plot. A total of 45 studies consisting of 2,655 patients with no symptoms at the screening point were included. Pooled results showed that in China, 65% of initial no-symptoms COVID-19 patients did not present any COVID-19-related symptom during follow-up or by end of disease course (asymptomatic infections). High proportions of initial no-symptoms COVID-19 patients (76%) and patients with asymptomatic infection (55%) had abnormal CT features at the screening point. High proportion of patients with asymptomatic infection had been detected Ig G⁺ (72%) and/or Ig M⁺ (57%) at the screening point. The chest CT scan and SARS-CoV-2-specific antibody testing could serve as effective supplementary methods to identify asymptomatic cases in the early stage of SARS-CoV-2 infection. However, the chest CT scan and the SARS-CoV-2-specific IgM and IgG testing should not replace reverse transcription–polymerase chain reaction (RT-PCR) for screening in asymptomatic patients. The combination of repeated RT-PCR, chest CT scans, and the SARS-CoV-2-specific IgM and IgG testing should be performed for those highly suspected SARS-CoV-2 infections.

Impact of non-pharmaceutical interventions on SARS-CoV-2 outbreaks in English care homes: a modelling study

BACKGROUND

COVID-19 outbreaks still occur in English care homes despite the interventions in place.

METHODS

We developed a stochastic compartmental model to simulate the spread of SARS-CoV-2 within an English care home. We quantified the outbreak risk with baseline non-pharmaceutical interventions (NPIs) already in place, the role of community prevalence in driving outbreaks, and the relative contribution of all importation routes into a fully susceptible care home. We also considered the potential impact of additional control measures in care homes with and without immunity, namely: increasing staff and resident testing frequency, using lateral flow antigen testing (LFD) tests instead of polymerase chain reaction (PCR), enhancing infection prevention and control (IPC), increasing the proportion of residents isolated, shortening the delay to isolation, improving the effectiveness of isolation, restricting visitors and limiting staff to working in one care home. We additionally present a Shiny application for users to apply this model to their facility of interest, specifying care home, outbreak and intervention characteristics.

RESULTS

The model suggests that importation of SARS-CoV-2 by staff, from the community, is the main driver of outbreaks, that importation by visitors or from hospitals is rare, and that the past testing strategy (monthly testing of residents and daily testing of staff by PCR) likely provides negligible benefit in preventing outbreaks. Daily staff testing by LFD was 39% (95% 18-55%) effective in preventing outbreaks at 30 days compared to no testing.

CONCLUSIONS

Increasing the frequency of testing in staff and enhancing IPC are important to preventing importations to the care home. Further work is needed to understand the impact of vaccination in this population, which is likely to be very effective in preventing outbreaks.

Severe Acute Respiratory Syndrome Coronavirus 2 Diagnostic Tests for Border Screening During the Very Early Phase of Coronavirus Disease 2019 Pandemic: A Systematic Review and Meta-Analysis

Diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during border screening among returning residents and prioritized travelers during the early phase of a pandemic can reduce the risk of importation and transmission in the community. This study aimed to compare the accuracy of various SARS-CoV-2 diagnostics and assess their potential utility as border screening for infection and immunity. Systematic literature searches were conducted in six electronic databases for studies reporting SARS-CoV-2 diagnostics (up to April 30, 2020). Meta-analysis and methodological assessment were conducted for all included studies. The performance of the diagnostic tests was evaluated with pooled sensitivity, specificity, and their respective 95% confidence intervals. A total of 5,416 unique studies were identified and 95 studies (at least 29,785 patients/samples) were included. Nucleic acid amplification tests (NAAT) consistently outperformed all other diagnostic methods regardless of the selected viral genes with a pooled sensitivity of 98% and a pooled specificity of 99%. Point-of-care (POC) serology tests had moderately high pooled sensitivity (69%), albeit lower than laboratory-based serology tests (89%), but both had high pooled specificity (96-98%). Serology tests were more sensitive for sampling collected at ≥ 7 days than ≤ 7 days from the disease symptoms onset. POC NAAT and POC serology tests are suitable for detecting infection and immunity against the virus, respectively as border screening. Independent validation in each country is highly encouraged with the preferred choice of diagnostic tool/s.

3D-printed swab with cover for precision diagnosis

The collection capacity of common nasopharyngeal swabs and irregularities of medical personnel limit the accuracy of PCR testing. This study describes a newly designed 3D-printed swab that is combined with a 3D-printed cover to prevent the extraction of undesired nasal secretions. This swab improved the accuracy of PCR test results. The results of a series of experiments showed that, because of the mucus extraction effect, 3D-printed swabs can replace ordinary cotton swabs. The crisis of the worldwide medical supply shortage can be ameliorated to a certain extent by applying 3D printing technology.

Applying the electronic nose for pre-operative SARS-CoV-2 screening

BACKGROUND

Infection with SARS-CoV-2 causes corona virus disease (COVID-19). The most standard diagnostic method is reverse transcription-polymerase chain reaction (RT-PCR) on a nasopharyngeal and/or an oropharyngeal swab. The high occurrence of false-negative results due to the non-presence of SARS-CoV-2 in the oropharyngeal environment renders this sampling method not ideal. Therefore, a new sampling device is desirable. This proof-of-principle study investigated the possibility to train machine-learning classifiers with an electronic nose (Aeonose) to differentiate between COVID-19-positive and negative persons based on volatile organic compounds (VOCs) analysis.

METHODS

Between April and June 2020, participants were invited for breath analysis when a swab for RT-PCR was collected. If the RT-PCR resulted negative, the presence of SARS-CoV-2-specific antibodies was checked to confirm the negative result. All participants breathed through the Aeonose for five minutes. This device contains metal-oxide sensors that change in conductivity upon reaction with VOCs in exhaled breath. These conductivity changes are input data for machine learning and used for pattern recognition. The result is a value between - 1 and + 1, indicating the infection probability.

RESULTS

219 participants were included, 57 of which COVID-19 positive. A sensitivity of 0.86 and a negative predictive value (NPV) of 0.92 were found. Adding clinical variables to machine-learning classifier via multivariate logistic regression analysis, the NPV improved to 0.96.

CONCLUSIONS

The Aeonose can distinguish COVID-19 positive from negative participants based on VOC patterns in exhaled breath with a high NPV. The Aeonose might be a promising, non-invasive, and low-cost triage tool for excluding SARS-CoV-2 infection in patients elected for surgery.

Forecasting of Oxidant/Antioxidant levels of COVID-19 patients by using Expert models with biomarkers used in the Diagnosis/Prognosis of COVID-19

Background

Early detection of oxidant-antioxidant levels and special care in severe patients are important in combating the COVID-19 epidemic. However, this process is costly and time consuming. Therefore, there is a need for faster, reliable and economical methods.

Methods

In this study, antioxidant/oxidant levels of patients were estimated by Expert-models using biomarkers, which are effective in the diagnosis/prognosis of COVID-19 disease. For this purpose, Expert-models were trained and created between the white-blood-cell-count (WBC), lymphocyte-count (LYM), C-reactive-protein (CRP), D-dimer, ferritin values of 35 patients with COVID-19 and antioxidant/oxidant parameter values of the same patients. Error criteria and R² ratio were taken into account for the performance of the models. The validity of the all models was checked by the Box-Jenkis-method.

Results

Antioxidant/Oxidant levels were estimated with 95% confidence-coefficient using the values of WBC, LYM, CRP, D-dimer, ferritin of different 500 patients diagnosed with COVID-19 with the trained models. The error rate of all models was low and the coefficients of determination were sufficient. In the first data set, there was no significant difference between measured antioxidant/oxidant levels and predicted antioxidant/oxidant levels. This result showed that the models are accurate and reliable. In determining antioxidant/oxidant levels, LYM and ferritin biomarkers had the most effect on models, while WBC and CRP biomarkers had the least effect. The antioxidant/oxidant parameter estimated with the highest accuracy was Native-Thiol divided by Total-Thiol.

Conclusions

The results showed that the antioxidant/oxidant levels of infected patients can be estimated accurately and reliably with LYM, ferritin, D-dimer, WBC, CRP biomarkers in the COVID-19 outbreak.

Serological Testing for COVID-19, Immunological Surveillance, and Exploration of Protective Antibodies

Serological testing is a powerful tool in epidemiological studies for understanding viral circulation and assessing the effectiveness of virus control measures, as is the case of SARS-CoV-2, the pathogenic agent of COVID-19. Immunoassays can quantitatively reveal the concentration of antiviral antibodies. The assessment of antiviral antibody titers may provide information on virus exposure, and changes in IgG levels are also indicative of a reduction in viral circulation. In this work, we describe a serological study for the evaluation of antiviral IgG and IgM antibodies and their correlation with antiviral activity. The serological assay for IgG detection used two SARS-CoV-2 proteins as antigens, the nucleocapsid N protein and the 3CL protease. Cross-reactivity tests in animals have shown high selectivity for detection of antiviral antibodies, using both the N and 3CL antigens. Using samples of human serum from individuals previously diagnosed by PCR for COVID-19, we observed high sensitivity of the ELISA assay. Serological results with human samples also suggest that the combination of higher titers of antiviral IgG antibodies to different antigen targets may be associated with greater neutralization activity, which can be enhanced in the presence of antiviral IgM antibodies.

A systematic and meta-analysis review on the diagnostic accuracy of antibodies in the serological diagnosis of COVID-19

BACKGROUND

Serological testing based on different antibody types are an alternative method being used to diagnose SARS-CoV-2 and has the potential of having higher diagnostic accuracy compared to the current gold standard rRT-PCR. Therefore, the objective of this review was to evaluate the diagnostic accuracy of IgG and IgM based point-of-care (POC) lateral flow immunoassay (LFIA), chemiluminescence enzyme immunoassay (CLIA), fluorescence enzyme-linked immunoassay (FIA) and ELISA systems that detect SARS-CoV-2 antigens.

METHOD

A systematic literature search was carried out in PubMed, Medline complete and MedRxiv. Studies evaluating the diagnostic accuracy of serological assays for SARS-CoV-2 were eligible. Study selection and data-extraction were performed by two authors independently. QUADAS-2 checklist tool was used to assess the quality of the studies. The bivariate model and the hierarchical summary receiver operating characteristic curve model were performed to evaluate the diagnostic accuracy of the serological tests. Subgroup meta-analysis was performed to explore the heterogeneity.

RESULTS

The pooled sensitivity for IgG (n = 17), IgM (n = 16) and IgG-IgM (n = 24) based LFIA tests were 0.5856, 0.4637 and 0.6886, respectively compared to rRT-PCR method. The pooled sensitivity for IgG (n = 9) and IgM (n = 10) based CLIA tests were 0.9311 and 0.8516, respectively compared to rRT-PCR. The pooled sensitivity the IgG (n = 10), IgM (n = 11) and IgG-IgM (n = 5) based ELISA tests were 0.8292, 0.8388 and 0.8531 respectively compared to rRT-PCR. All tests displayed high specificities ranging from 0.9693 to 0.9991. Amongst the evaluated tests, IgG based CLIA expressed the highest sensitivity signifying its accurate detection of the largest proportion of infections identified by rRT-PCR. ELISA and CLIA tests performed better in terms of sensitivity compared to LFIA. IgG based tests performed better compared to IgM except for the ELISA.

CONCLUSIONS

We report that IgG-IgM based ELISA tests have the best overall diagnostic test accuracy. Moreover, irrespective of the method, a combined IgG/IgM test seems to be a better choice in terms of sensitivity than measuring either antibody type independently. Given the poor performances of the current LFIA devices, there is a need for more research on the development of highly sensitivity and specific POC LFIA that are adequate for most individual patient applications and attractive for large sero-prevalence studies.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO CRD42020179112.

A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)

The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. In this study we have compiled a list of 639 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639 peptide possibilities to 87 peptides which were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Applying stringent statistical scoring thresholds, combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from a variety of sample types. We also contend that samples taken from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.

How do routine laboratory tests change in coronavirus disease 2019?

How the routine laboratory tests change in terms of coronavirus disease 2019 (COVID-19) was retrospectively analyzed in a large group of patients. Biochemical, hematological and inflammatory variables of a totaly 555 (n = 532 in non-intensive care unit (non-ICU), n = 23 in ICU) patients diagnosed with COVID-19 were analyzed accessing them through the laboratory information system. White blood cell (WBC), neutrophil (NEU), platelet large cell ratio, neutrophil to lymphocyte ratio (NLR), derived NLR (d-NLR), aspartate aminotransferase, urea, creatine kinase (CK) myocardial band (CK-MB), procalcitonin (PCT) values were high whereas lymphocyte (LYM), eosinophil, red blood cells (RBC), hemoglobin, lymphocyte to monocyte ratio, estimated glomerular filtration rate values were low in the ICU group when compared with non-ICU. WBC, NEU, red cell distribution width, alanine transaminase, creatinine, urea, CK-MB, CK, direct bilirubin, lactate dehydrogenase, glucose, C-reactive protein, erythrocyte sedimentation rate, ferritin, D-dimer, PCT and international normalized ratio values increased while RBC, hemoglobin, hematocrit, mean corpuscular volume and total bilirubin values decreased in a significant proportion of patients in both groups based on the normal reference ranges. LYM count was found to be low in a significant number of patients (57.5%) especially in the ICU group and as an important risk factor and diagnostic parameter on admission to ICU (OR: 125, AUC: 0.74). Routine laboratory tests provide important information in terms of both diagnosis and severity of COVID-19. Lymphopenia is a condition that should be monitored which indicates the severity of the disease.

Detection of SARS-CoV-2 from patient fecal samples by whole genome sequencing

BACKGROUND

SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections. Here were sought to identify SARS-CoV-2 by enrichment next-generation sequencing (NGS) from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients.

RESULTS

Study participants underwent testing for SARS-CoV-2 from fecal samples by whole genome enrichment NGS (n = 14), and RT-PCR nasopharyngeal swab analysis (n = 12). The concordance of SARS-CoV-2 detection by enrichment NGS from stools with RT-PCR nasopharyngeal analysis was 100%. Unique variants were identified in four patients, with a total of 33 different mutations among those in which SARS-CoV-2 was detected by whole genome enrichment NGS.

CONCLUSION

These results highlight the potential viability of SARS-CoV-2 in feces, its ongoing mutational accumulation, and its possible role in fecal-oral transmission. This study also elucidates the advantages of SARS-CoV-2 enrichment NGS, which may be a key methodology to document complete viral eradication. Trial registration ClinicalTrials.gov, NCT04359836, Registered 24 April 2020, https://clinicaltrials.gov/ct2/show/NCT04359836?term=NCT04359836&draw=2&rank=1 ).

Leaving no stone unturned in light of the COVID-19 faecal-oral hypothesis? A water, sanitation and hygiene (WASH) perspective targeting low-income countries

The human coronavirus disease (COVID-19) is now a global pandemic. Social distancing, hand hygiene and the use of personal protective equipment dominate the current fight against COVID-19. In developing countries, the need for clean water provision, sanitation and hygiene has only received limited attention. The current perspective examines the latest evidence on the occurrence, persistence and faecal-oral transmission of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the etiological agent causing COVID-19. Evidence shows that SARS-CoV-2 proliferate in the human gastrointestinal system, and is shed via faeces. SARS-CoV-2 can survive and remain viable for up to 6 to 9 days on surfaces. Recent wastewater-based epidemiological studies from several countries also detected SARS-CoV-2 RNA in raw wastewaters. Shell disorder analysis shows that SARS-CoV-2 has a rigid outer shell conferring resilience, and a low shell disorder conferring moderate potential for faecal-oral transmission. Taken together, these findings point to potential faecal-oral transmission of SARS-CoV-2, which may partly explain its rapid transmission. Three potential mechanisms may account for SARS-CoV-2 faecal-oral transmission: (1) untreated contaminated drinking water, (2) raw and poorly cooked marine and aquatic foods from contaminated sources, (3) raw wastewater-based vegetatble production systems (e.g., salads) and aquaculture, and (4) vector-mediated transmission from faecal sources to foods, particularly those from open markets and street vending. SARS-CoV-2 faecal-oral transmission could be particularly high in developing countries due to several risk factors, including; (1) poor drinking water, wastewater and sanitation infrastructure, (2) poor hygiene and food handling practices, (3) unhygienic and rudimentary funeral practices, including home burials close to drinking water sources, and (4) poor social security and health care systems with low capacity to cope with disease outbreaks. Hence, clean drinking water provision, proper sanitation, food safety and hygiene could be critical in the current fight against COVID-19. Future research directions on COVID-19 faecal-oral transmission are highlighted.

On the effectiveness of the search and find method to suppress spread of SARS-CoV-2

Search and find methods*) such as cluster tracing1)-6) or large-scale PCR testing**) of those who exhibit no symptoms or only mild symptoms of COVID-19 is shown by data analysis to be a powerful means to suppress the spread of COVID-19 instead of, or in addition to, lockdown of the entire population. Here we investigate this issue by analyzing the data from some cities and countries and we establish that search and find method is as powerful as lockdown of a city or a country. Moreover, in contrast to lockdown, it neither causes inconvenience to citizens nor does it disrupt the economy. Generally speaking, it is advisable that both social distancing and increased test numbers be employed to suppress spread of the virus. The product of the total test number with the rate of positive cases is the crucial index.

Delayed COVID respiratory failure: what every front line healthcare worker needs to know

The pandemic of COVID-19 has presented several diagnostic challenges in both recognition of acute disease and also the temporal presentation of disease convalescence with return to normal activity. We present a case of delayed clinical progression of COVID-19 associated respiratory failure on day 25 after initial symptom onset and, notably, after initial full resolution of symptoms and negative RT-PCR nasopharyngeal testing. The patient's delayed presentation of exertional dyspnea and the utilization of specific characteristics of chest radiography in confirmation with laboratory cytokine measurement allowed for clinical re-categorization of the patient's status to active COVID-19 clinical disease and changed acute management. COVID-19 positive patients should be advised to continue to monitor for respiratory deterioration for a greatly extended period of time, even if RT-PCR testing is negative and initial clinical symptoms have resolved. Frontline healthcare workers, including first responders and primary care providers, also need to be aware to monitor for and recognize this delayed presentation.

COVID-Net: a tailored deep convolutional neural network design for detection of COVID-19 cases from chest X-ray images

The Coronavirus Disease 2019 (COVID-19) pandemic continues to have a devastating effect on the health and well-being of the global population. A critical step in the fight against COVID-19 is effective screening of infected patients, with one of the key screening approaches being radiology examination using chest radiography. It was found in early studies that patients present abnormalities in chest radiography images that are characteristic of those infected with COVID-19. Motivated by this and inspired by the open source efforts of the research community, in this study we introduce COVID-Net, a deep convolutional neural network design tailored for the detection of COVID-19 cases from chest X-ray (CXR) images that is open source and available to the general public. To the best of the authors' knowledge, COVID-Net is one of the first open source network designs for COVID-19 detection from CXR images at the time of initial release. We also introduce COVIDx, an open access benchmark dataset that we generated comprising of 13,975 CXR images across 13,870 patient patient cases, with the largest number of publicly available COVID-19 positive cases to the best of the authors' knowledge. Furthermore, we investigate how COVID-Net makes predictions using an explainability method in an attempt to not only gain deeper insights into critical factors associated with COVID cases, which can aid clinicians in improved screening, but also audit COVID-Net in a responsible and transparent manner to validate that it is making decisions based on relevant information from the CXR images. By no means a production-ready solution, the hope is that the open access COVID-Net, along with the description on constructing the open source COVIDx dataset, will be leveraged and build upon by both researchers and citizen data scientists alike to accelerate the development of highly accurate yet practical deep learning solutions for detecting COVID-19 cases and accelerate treatment of those who need it the most.

Microfluidic Nano-Scale qPCR Enables Ultra-Sensitive and Quantitative Detection of SARS-CoV-2

A major challenge in controlling the COVID-19 pandemic is the high false-negative rate of the commonly used RT-PCR methods for SARS-CoV-2 detection in clinical samples. Accurate detection is particularly challenging in samples with low viral loads that are below the limit of detection (LoD) of standard one- or two-step RT-PCR methods. In this study, we implemented a three-step approach for SARS-CoV-2 detection and quantification that employs reverse transcription, targeted cDNA preamplification, and nano-scale qPCR based on a commercially available microfluidic chip. Using SARS-CoV-2 synthetic RNA and plasmid controls, we demonstrate that the addition of a preamplification step enhances the LoD of this microfluidic RT-qPCR by 1000-fold, enabling detection below 1 copy/µL. We applied this method to analyze 182 clinical NP swab samples previously diagnosed using a standard RT-qPCR protocol (91 positive, 91 negative) and demonstrate reproducible and quantitative detection of SARS-CoV-2 over five orders of magnitude (<1 to 106 viral copies/µL). Crucially, we detect SARS-CoV-2 with relatively low viral load estimates (<1 to 40 viral copies/µL) in 17 samples with negative clinical diagnosis, indicating a potential false-negative rate of 18.7% by clinical diagnostic procedures. In summary, this three-step nano-scale RT-qPCR method can robustly detect SARS-CoV-2 in samples with relatively low viral loads (<1 viral copy/µL) and has the potential to reduce the false-negative rate of standard RT-PCR-based diagnostic tests for SARS-CoV-2 and other viral infections.

At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR-based tests? A systematic review of individual participant data

BACKGROUND

Tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral ribonucleic acid (RNA) using reverse transcription polymerase chain reaction (RT-PCR) are pivotal to detecting current coronavirus disease (COVID-19) and duration of detectable virus indicating potential for infectivity.

METHODS

We conducted an individual participant data (IPD) systematic review of longitudinal studies of RT-PCR test results in symptomatic SARS-CoV-2. We searched PubMed, LitCOVID, medRxiv, and COVID-19 Living Evidence databases. We assessed risk of bias using a QUADAS-2 adaptation. Outcomes were the percentage of positive test results by time and the duration of detectable virus, by anatomical sampling sites.

RESULTS

Of 5078 studies screened, we included 32 studies with 1023 SARS-CoV-2 infected participants and 1619 test results, from - 6 to 66 days post-symptom onset and hospitalisation. The highest percentage virus detection was from nasopharyngeal sampling between 0 and 4 days post-symptom onset at 89% (95% confidence interval (CI) 83 to 93) dropping to 54% (95% CI 47 to 61) after 10 to 14 days. On average, duration of detectable virus was longer with lower respiratory tract (LRT) sampling than upper respiratory tract (URT). Duration of faecal and respiratory tract virus detection varied greatly within individual participants. In some participants, virus was still detectable at 46 days post-symptom onset.

CONCLUSIONS

RT-PCR misses detection of people with SARS-CoV-2 infection; early sampling minimises false negative diagnoses. Beyond 10 days post-symptom onset, lower RT or faecal testing may be preferred sampling sites. The included studies are open to substantial risk of bias, so the positivity rates are probably overestimated.

Fatal SARS-CoV-2 infection in a renal transplant recipient

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV 2) caused a pandemic that first discovered in Wuhan, China. While 10% of the patients have asymptomatic infection, 15-20% have lung involvement, 5-10% have multiple organ failure, and macrophage activation syndrome. Chronic respiratory diseases, diabetes mellitus, hypertension, and cancer are risk factors for mortality. Prognosis or optimal treatment strategy for renal transplant recipients in SARS-CoV-2 infection is still unknown. Besides fatal cases, there were also milder case reports. In addition, COVID-19 treatment and the maintenance immunosuppression strategy is still under debate. Antiviral therapies and drug interactions are special topics for these patients. To the best of our knowledge, favipiravir and anti-cytokine treatments have not been previously reported in a kidney transplant recipient with SARS-CoV-2 infection before. We report a case of SARS-CoV-2 infection in a kidney transplant recipient with fatal outcomes.

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.

How Reliable are Test Numbers for Revealing the COVID-19 Ground Truth and Applying Interventions?

The number of confirmed cases of COVID-19 is often used as a proxy for the actual number of ground truth COVID-19-infected cases in both public discourse and policy making. However, the number of confirmed cases depends on the testing policy, and it is important to understand how the number of positive cases obtained using different testing policies reveals the unknown ground truth. We develop an agent-based simulation framework in Python that can simulate various testing policies as well as interventions such as lockdown based on them. The interaction between the agents can take into account various communities and mobility patterns. A distinguishing feature of our framework is the presence of another 'flu'-like illness with symptoms similar to COVID-19, that allows us to model the noise in selecting the pool of patients to be tested. We instantiate our model for the city of Bengaluru in India, using census data to distribute agents geographically, and traffic flow mobility data to model long-distance interactions and mixing. We use the simulation framework to compare the performance of three testing policies: Random Symptomatic Testing (RST), Contact Tracing (CT), and a new Location-Based Testing policy (LBT). We observe that if a sufficient fraction of symptomatic patients come out for testing, then RST can capture the ground truth quite closely even with very few daily tests. However, CT consistently captures more positive cases. Interestingly, our new LBT, which is operationally less intensive than CT, gives performance that is comparable with CT. In another direction, we compare the efficacy of these three testing policies in enabling lockdown, and observe that CT flattens the ground truth curve maximally, followed closely by LBT, and significantly better than RST.

DFC, Medina E, Sinche F, Santiago Vispo N, Dahoumane SA, Alexis F. Biomedical Science to Tackle the COVID-19 Pandemic: Current Status and Future Perspectives

The coronavirus infectious disease (COVID-19) pandemic emerged at the end of 2019, and was caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which has resulted in an unprecedented health and economic crisis worldwide. One key aspect, compared to other recent pandemics, is the level of urgency, which has started a race for finding adequate answers. Solutions for efficient prevention approaches, rapid, reliable, and high throughput diagnostics, monitoring, and safe therapies are needed. Research across the world has been directed to fight against COVID-19. Biomedical science has been presented as a possible area for combating the SARS-CoV-2 virus due to the unique challenges raised by the pandemic, as reported by epidemiologists, immunologists, and medical doctors, including COVID-19's survival, symptoms, protein surface composition, and infection mechanisms. While the current knowledge about the SARS-CoV-2 virus is still limited, various (old and new) biomedical approaches have been developed and tested. Here, we review the current status and future perspectives of biomedical science in the context of COVID-19, including nanotechnology, prevention through vaccine engineering, diagnostic, monitoring, and therapy. This review is aimed at discussing the current impact of biomedical science in healthcare for the management of COVID-19, as well as some challenges to be addressed.

Practical Diagnostic Accuracy of Nasopharyngeal Swab Testing for Novel Coronavirus Disease 2019 (COVID-19)

INTRODUCTION

The novel coronavirus (SARS-CoV-2) is the cause of COVID-19, which has had a devastating international impact. Prior reports of testing have reported low sensitivities of nasopharyngeal polymerase chain reaction (PCR), and reports of viral co-infections have varied from 0-20%. Therefore, we sought to determine the accuracy of nasopharyngeal PCR for COVID-19 and rates of viral co-infection.

METHODS

We conducted a retrospective chart review of all patients who received viral testing between March 1, 2020-April 28, 2020. Test results of a complete viral pathogen panel and COVID-19 testing were abstracted. We compared patients with more than one COVID-19 test for diagnostic accuracy against the gold standard of chart review.

RESULTS

We identified 1950 patients, of whom 1024 were tested for COVID-19. There were 221 repeat tests for COVID-19. Among patients with a repeat test, COVID-19 swabs had a sensitivity of 84.6% (95% confidence interval (CI), 69.5-94.4%) and a specificity of 99.5% (95%CI, 97-100%) compared to a clinical and radiographic criterion reference by chart review. We found viral co-infection rates of 2.3% in patients without COVID-19 and 6.1% in patients with COVID-19. Rates of co-infection appeared to be related to base rates of infection in the community and not a specific property of COVID-19.

CONCLUSION

COVID-19 nasopharyngeal PCR specimens are accurate but have imperfect sensitivity. Repeat testing for high-risk patients should be considered, and presence of an alternative virus should not be used to limit testing for COVID-19 for patients where it would affect treatment or isolation.

The Potential Use of Mesenchymal Stem Cells and Their Derived Exosomes as Immunomodulatory Agents for COVID-19 Patients

A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) causing lethal acute respiratory disease emerged in December 2019. The World Health Organization named this disease "COVID-19" and declared it a pandemic on March 11, 2020. Many studies have shown that mesenchymal stem cells (MSCs) and their exosomes (MSCs-Exo), which are isolated from allogenic bone marrow stem cells, significantly lower the risk of alveolar inflammation and other pathological conditions associated with distinct lung injuries. For example, in acute respiratory distress syndrome (ARDS) and pneumonia patients, MSCs-Exo and MSCs provide similar healing properties and some clinical trials have used cell-based inhalation therapy which show great promise. MSCs and MSCs-Exo have shown potential in clinical trials as a therapeutic tool for severely affected COVID-19 patients when compared to other cell-based therapies, which may face challenges like the cells' sticking to the respiratory tract epithelia during administration. However, the use of MSCs or MSCs-Exo for treating COVID-19 should strictly adhere to the appropriate manufacturing practices, quality control measurements, preclinical safety and efficacy data, and the proper ethical regulations. This review highlights the available clinical trials that support the therapeutic potential of MSCs or MSCs-Exo in severely affected COVID-19 patients.

Kawasaki-like disease in children with COVID-19

Children with Coronavirus disease 2019 (COVID-19) are being reported to have manifestations of hyperinflammatory states and/or Kawasaki-like disease. In this study, we investigated children with typical and atypical Kawasaki disease (KD) likely to be associated with COVID-19. We have reported four children with Kawasaki-like disease probably associated with COVID-19. The clinical features were consistent with incomplete KD in three patients. SARS-CoV-2 RT-PCR was positive in one and the serology was positive in one patient with negative RT-PCR. Corticosteroids, anakinra, intravenous immunoglobulin (IVIG), and acetylsalicylic acid were used in the treatment. Three patients recovered after the treatment while one patient died. The literature review revealed 36 articles describing 320 children with Kawasaki-like disease associated with COVID-19. SARS-CoV-2 RT-PCR was negative in 120 (65.5%) of 183 patients while the serology was positive in 130 (83.8%) of 155 patients. The therapeutic options have included IVIG, acetylsalicylic acid, tocilizumab, anakinra, enoxaparin, and methylprednisolone. Pediatric COVID-19 cases may present with atypical/incomplete Kawasaki-like disease. Thus, pediatricians need to be aware of such atypical presentations resembling KD for early diagnosis of COVID-19.

Fighting COVID-19: Integrated Micro- and Nanosystems for Viral Infection Diagnostics

The pandemic of coronavirus disease 2019 (COVID-19) highlights the importance of rapid and sensitive diagnostics of viral infection that enables the efficient tracing of cases and the implementation of public health measures for disease containment. The immediate actions from both academia and industry have led to the development of many COVID-19 diagnostic systems that have secured fast-track regulatory approvals and have been serving our healthcare frontlines since the early stage of the pandemic. On diagnostic technologies, many of these clinically validated systems have significantly benefited from the recent advances in micro- and nanotechnologies in terms of platform design, analytical method, and system integration and miniaturization. The continued development of new diagnostic platforms integrating micro- and nanocomponents will address some of the shortcomings we have witnessed in the existing COVID-19 diagnostic systems. This Perspective reviews the previous and ongoing research efforts on developing integrated micro- and nanosystems for nucleic acid-based virus detection, and highlights promising technologies that could provide better solutions for the diagnosis of COVID-19 and other viral infectious diseases. With the summary and outlook of this rapidly evolving research field, we hope to inspire more research and development activities to better prepare our society for future public health crises.

Direct-RT-qPCR Detection of SARS-CoV-2 without RNA Extraction as Part of a COVID-19 Testing Strategy: From Sample to Result in One Hour

Due to the lack of protective immunity in the general population and the absence of effective antivirals and vaccines, the Coronavirus disease 2019 (COVID-19) pandemic continues in some countries, with local epicentres emerging in others. Due to the great demand for effective COVID-19 testing programmes to control the spread of the disease, we have suggested such a testing programme that includes a rapid RT-qPCR approach without RNA extraction. The Direct-One-Step-RT-qPCR (DIOS-RT-qPCR) assay detects severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in less than one hour while maintaining the high sensitivity and specificity required of diagnostic tools. This optimised protocol allows for the direct use of swab transfer media (14 μL) without the need for RNA extraction, achieving comparable sensitivity to the standard method that requires the time-consuming and costly step of RNA isolation. The limit of detection for DIOS-RT-qPCR was lower than seven copies/reaction, which translates to 550 virus copies/mL of swab. The speed, ease of use and low price of this assay make it suitable for high-throughput screening programmes. The use of fast enzymes allows RT-qPCR to be performed under standard laboratory conditions within one hour, making it a potential point-of-care solution on high-speed cycling instruments. This protocol also implements the heat inactivation of SARS-CoV-2 (75 °C for 10 min), which renders samples non-infectious, enabling testing in BSL-2 facilities. Moreover, we discuss the critical steps involved in developing tests for the rapid detection of COVID-19. Implementing rapid, easy, cost-effective methods can help control the worldwide spread of the COVID-19 infection.

Evaluation of three immunochromatographic tests for rapid detection of antibodies against SARS-CoV-2

Lateral flow immunoassays (LFIA) for rapid detection of specific antibodies (IgM and IgG) against SARS-CoV-2 in different human specimens have been developed in response to the pandemic. The aim of this study is to evaluate three immunocromathographic assays (Sienna®, Wondfo® and Prometheus®) for detection of antibodies against SARS-CoV-2 in serum samples, considering RT-qPCR as a reference. A total of 145 serum samples from 145 patients with clinical suspicion of COVID-19 were collected: all of the samples were tested with Sienna®, 117 with Wondfo® and 89 with Prometheus®. The overall results of sensitivity, specificity, positive predictive value and negative predictive value obtained were as follows: 64.4%, 75%, 85.5% and 47.8% with Sienna®; 45.2%, 81.8%, 80.5% and 47.4% with Wondfo® and 75.5%, 12.5%, 51.4% and 29.4% with Prometheus®. The accuracy of the test for Sienna®, Wondfo® and Prometheus® was 67.6%, 59% and 47.2%, with a prevalence of COVID-19 of 69.7%, 62.4% and 55.1% respectively. Sensitivity of the three tests (Sienna®, Wondfo® and Prometheus® respectively) along the three different stages was 36.6%, 18.8% and 68.6% in the early stage (first week); 81.3%, 74.1% and 90.9% in the intermediate stage (second week) and 100%, 83.3% and 100% in the late stage (third week). The results demonstrate that even though Prometheus® presented a high sensitivity, the specificity was notably lower than the other two tests. Sienna® showed the greatest contrast between sensitivity and specificity, achieving the best accuracy, followed by Wondfo®. The sensitivity of the three ICT assays was higher in late stages of the disease.

Homeless Shelter Characteristics and Prevalence of SARS-CoV-2

INTRODUCTION

The unfolding COVID-19 pandemic has predictably followed the familiar contours of well established socioeconomic health inequities, exposing and often amplifying preexisting disparities. People living in homeless shelters are at higher risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compared to the general population. The purpose of this study was to identify shelter characteristics that may be associated with higher transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

METHODS

We conducted a cross-sectional assessment of five congregate shelters in Rhode Island. Shelter residents 18 years old and older were tested for SARS-CoV-2 from April 19-April 24, 2020. At time of testing, we collected participant characteristics, symptomatology, and vital signs. Shelter characteristics and infection control strategies were collected through a structured phone questionnaire with shelter administrators.

RESULTS

A total of 299 shelter residents (99%, 299/302) participated. Thirty-five (11.7%) tested positive for SARS-CoV-2. Shelter-level prevalence ranged from zero to 35%. Symptom prevalence did not vary by test result. Shelters with positive cases of SARS-CoV-2 were in more densely populated areas, had more transient resident populations, and instituted fewer physical distancing practices compared to shelters with no cases.

CONCLUSION

SARS-CoV-2 prevalence varies with shelter characteristics but not individual symptoms. Policies that promote resident stability and physical distancing may help reduce SARS-CoV-2 transmission. Symptom screening alone is insufficient to prevent SARS-CoV-2 transmission. Frequent universal testing and congregate housing alternatives that promote stability may help reduce spread of infection.

CRISPR Gene Therapy: Applications, Limitations, and Implications for the Future

A series of recent discoveries harnessing the adaptive immune system of prokaryotes to perform targeted genome editing is having a transformative influence across the biological sciences. The discovery of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) proteins has expanded the applications of genetic research in thousands of laboratories across the globe and is redefining our approach to gene therapy. Traditional gene therapy has raised some concerns, as its reliance on viral vector delivery of therapeutic transgenes can cause both insertional oncogenesis and immunogenic toxicity. While viral vectors remain a key delivery vehicle, CRISPR technology provides a relatively simple and efficient alternative for site-specific gene editing, obliviating some concerns raised by traditional gene therapy. Although it has apparent advantages, CRISPR/Cas9 brings its own set of limitations which must be addressed for safe and efficient clinical translation. This review focuses on the evolution of gene therapy and the role of CRISPR in shifting the gene therapy paradigm. We review the emerging data of recent gene therapy trials and consider the best strategy to move forward with this powerful but still relatively new technology.

Anesthesia for oral surgeries during the COVID-19 pandemic

The severe acute respiratory syndrome corona virus 2(SARS-Cov2) virus replicates in the nasal cavity, nasopharynx, and the oropharynx. During oral surgery, the risk of viral transmission is high during instrumentation in these areas, while performing airway management procedures, the oral surgery itself, and related procedures. During the corona virus disease 2019 (COVID-19) pandemic, patients with an oral pathology usually present for emergency procedures. However, patients with oral cancer, being a semi-emergency, may also present for diagnostic and therapeutic procedures. When elective surgeries are resumed, these patients will come to the operating room. In asymptomatic patients, the false-negative rate can be as high as 30%. These patients are a source of infection to the healthcare workers and other patients. This mandates universal precautions to be taken for all patients presenting for surgery. Lesions along the airway, distorted anatomy secondary to cancer therapy, shared airway with the surgeon, surgical handling of the airway and the risk of bleeding, make airway management challenging in these patients, especially while wearing personal protective equipment. Airway management procedures, oral surgery, use of cautery, and other powered surgical instruments in the aero digestive tract, along with constant suctioning are a source of significant aerosol generation, further adding to the risk of viral transmission. Maintaining patient safety, while protecting the healthcare workers from getting infected during oral surgery is paramount. Meticulous advance planning and team preparation are essential. In this review, we discuss the challenges and recommendations for safe anesthesia practice for oral surgery during the COVID-19 pandemic, with special emphasis on risk mitigation.

Rational use of SARS-CoV-2 polymerase chain reaction tests within institutions caring for the vulnerable

Institutions such as hospitals and nursing or long-stay residential homes accommodate individuals at considerable risk of mortality should they acquire SARS-CoV-2 infection. In these settings, polymerase chain reaction tests play a central role in infection prevention and control. Here, we argue that both false negative and false positive tests are possible and that careful consideration of the prior probability of infection and of test characteristics are needed to prevent harm. We outline evidence suggesting that regular systematic testing of asymptomatic and pre-symptomatic individuals could play an important role in reducing transmission of SARS-CoV-2 within institutions. We discuss how such a programme might be organised, arguing that frequent testing and rapid reporting of results are particularly important. We highlight studies demonstrating that polymerase chain reaction testing of pooled samples can be undertaken with acceptable loss of sensitivity, and advocate such an approach where test capacity is limited. We provide an approach to calculating the most efficient pool size. Given the current limitations of tests for SARS-CoV-2 infection, physical distancing and meticulous infection prevention and control will remain essential in institutions caring for vulnerable people.

SARS-CoV-2 antibody testing-questions to be asked

Severe acute respiratory syndrome coronavirus 2 infection and development of coronavirus disease 2019 presents a major health care challenge of global dimensions. Laboratory diagnostics of infected patients, and the assessment of immunity against severe acute respiratory syndrome coronavirus 2, presents a major cornerstone in handling the pandemic. Currently, there is an increase in demand for antibody testing and a large number of tests are already marketed or are in the late stage of development. However, the interpretation of test results depends on many variables and factors, including sensitivity, specificity, potential cross-reactivity and cross-protectivity, the diagnostic value of antibodies of different isotypes, and the use of antibody testing in identification of acutely ill patients or in epidemiological settings. In this article, the recently established COVID-19 Task Force of the German Society for Clinical Chemistry and Laboratory Medicine (DGKL) addresses these issues on the basis of currently available data sets in this rapidly moving field.

Antibody testing for COVID-19: A report from the National COVID Scientific Advisory Panel

Background: The COVID-19 pandemic caused >1 million infections during January-March 2020. There is an urgent need for reliable antibody detection approaches to support diagnosis, vaccine development, safe release of individuals from quarantine, and population lock-down exit strategies. We set out to evaluate the performance of ELISA and lateral flow immunoassay (LFIA) devices. Methods: We tested plasma for COVID (severe acute respiratory syndrome coronavirus 2; SARS-CoV-2) IgM and IgG antibodies by ELISA and using nine different LFIA devices. We used a panel of plasma samples from individuals who have had confirmed COVID infection based on a PCR result (n=40), and pre-pandemic negative control samples banked in the UK prior to December-2019 (n=142). Results: ELISA detected IgM or IgG in 34/40 individuals with a confirmed history of COVID infection (sensitivity 85%, 95%CI 70-94%), vs. 0/50 pre-pandemic controls (specificity 100% [95%CI 93-100%]). IgG levels were detected in 31/31 COVID-positive individuals tested ≥10 days after symptom onset (sensitivity 100%, 95%CI 89-100%). IgG titres rose during the 3 weeks post symptom onset and began to fall by 8 weeks, but remained above the detection threshold. Point estimates for the sensitivity of LFIA devices ranged from 55-70% versus RT-PCR and 65-85% versus ELISA, with specificity 95-100% and 93-100% respectively. Within the limits of the study size, the performance of most LFIA devices was similar. Conclusions: Currently available commercial LFIA devices do not perform sufficiently well for individual patient applications. However, ELISA can be calibrated to be specific for detecting and quantifying SARS-CoV-2 IgM and IgG and is highly sensitive for IgG from 10 days following first symptoms.

Low-Dose Chest CT for the Diagnosis of COVID-19—A Systematic, Prospective Comparison With PCR

BACKGROUND

Only limited evidence has been available to date on the accuracy of systematic low-dose chest computed tomography (LDCT) use in the diagnosis of COVID-19 in patients with non-specific clinical symptoms.

METHODS

The COVID-19 Imaging Registry Study Aachen (COVID-19-Bildgebungs-Register Aachen, COBRA) collects data on imaging in patients with COVID-19. Two of the COBRA partner hospitals (RWTH Aachen University Hospital and Dueren Hospital) systematically perform reverse transcriptase polymerase chain reaction (RT-PCR) from nasopharyngeal swabs as well as LDCT in all patients presenting with manifestations that are compatible with COVID-19. In accordance with the COV-RADS protocol, the LDCT scans were prospectively evaluated before the RT-PCR findings were available in order to categorize the likelihood of COVID-19.

RESULTS

From 18 March to 5 May 2020, 191 patients with COVID-19 manifestations (117 male, age 65 ± 16 years) underwent RT-PCR testing and LDCT. The mean time from the submission of the sample to the availability of the RT-PCR findings was 491 minutes (interquartile range [IQR: 276-1066]), while that from the performance of the CT to the availability of its findings was 9 minutes (IQR: 6-11). A diagnosis of COVID-19 was made in 75/191 patients (39%). The LDCT was positive in 71 of these 75 patients and negative in 106 of the 116 patients without COVID-19, corresponding to 94.7% sensitivity (95% confidence interval [86.9; 98.5]), 91.4% specificity [84.7; 95.8], positive and negative predictive values of 87.7% [78.5; 93.9] and 96.4% [91.1; 98.6], respectively, and an AUC (area under the curve) of 0.959 [0.930; 0.988]. The initial RT-PCR test results were falsely negative in six patients, yielding a sensitivity of 92.0% [83.4; 97.0]; these six patients had positive LDCT findings. 47.4% of the LDCTs that were negative for COVID-19 (55/116) exhibited pathological pulmonary changes, including infiltrates, that were correctly distinguished from SARS-CoV-2 related changes.

CONCLUSION

In patients with symptoms compatible with COVID-19, LDCT can esablish the diagnosis of COVID-19 with comparable sensitivity to RT-PCR testing. In addition, it offers a high specificity for distinguishing COVID-19 from other diseases associated with the same or similar clinical symptoms. We propose the systematic use of LDCT in addition to RT-PCR testing because it helps correct false-negative RT-PCR results, because its results are available much faster than those of RT-PCRtesting, and because it provides additional diagnostic information useful for treatment planning regardless of the type of the infectious agent.

Endoscopic Skull Base Surgery Protocol From the Frontlines: Transnasal Surgery During the COVID-19 Pandemic

Objective

The coronavirus disease 2019 (COVID-19) pandemic disrupted the standard management paradigms for care of patients with sinus and skull base presentations due to concern for patient and health care provider safety, given the high aerosol-generating potential of endonasal procedures.

Data Sources

We reviewed the relevant literature complied from available sources, including PubMed, Google Scholar, and otolaryngology journals providing electronic manuscripts ahead of indexing or publication.

Review Methods

Incorporating available evidence and the projected infection control and resource limitations at our institution, we collectively authored a dynamic set of protocols guiding (1) case stratification, (2) preoperative assessment, (3) operative setup, and (4) postoperative care of patients with sinus or skull base presentations. Due to the rapidly evolving nature of COVID-19 publications, lack of rigorous data, and urgent necessity of standardized protocols, strict inclusion and exclusion criteria were not employed.

Conclusions

As scarce hospital resources are diverted to COVID-19 care and staff are redeployed to forward-facing roles, endonasal procedures have largely ceased, leaving patients with ongoing sinonasal and skull base complaints untreated. Skull base teams now weigh the urgency of surgery in this population with the regional availability of resources.

Implications for Practice

The COVID-19 pandemic will have an enduring and unpredictable impact on hospital operations and surgical skull base practices and will require a dynamic set of management protocols responsive to new evidence and changing resources. In the current resource-limited environment, clinicians may utilize these protocols to assist with stratifying patients by acuity, performing preoperative assessment, and guiding peri- and postoperative care.

Challenges in Laboratory Diagnosis of the Novel Coronavirus SARS-CoV-2

The recent outbreak of the Coronavirus disease 2019 (COVID-19) has quickly spread worldwide since its discovery in Wuhan city, China in December 2019. A comprehensive strategy, including surveillance, diagnostics, research, clinical treatment, and development of vaccines, is urgently needed to win the battle against COVID-19. The past three unprecedented outbreaks of emerging human coronavirus infections at the beginning of the 21st century have highlighted the importance of readily available, accurate, and rapid diagnostic technologies to contain emerging and re-emerging pandemics. Real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) based assays performed on respiratory specimens remain the gold standard for COVID-19 diagnostics. However, point-of-care technologies and serologic immunoassays are rapidly emerging with high sensitivity and specificity as well. Even though excellent techniques are available for the diagnosis of symptomatic patients with COVID-19 in well-equipped laboratories; critical gaps still remain in screening asymptomatic people who are in the incubation phase of the virus, as well as in the accurate determination of live viral shedding during convalescence to inform decisions for ending isolation. This review article aims to discuss the currently available laboratory methods and surveillance technologies available for the detection of COVID-19, their performance characteristics and highlight the gaps in current diagnostic capacity, and finally, propose potential solutions. We also summarize the specifications of the majority of the available commercial kits (PCR, EIA, and POC) for laboratory diagnosis of COVID-19.

Humoral Immune Responses in COVID-19 Patients: A Window on the State of the Art

The novel SARS-CoV-2 is a recently emerging virus causing a human pandemic. A great variety of symptoms associated with COVID-19 disease, ranging from mild to severe symptoms, eventually leading to death. Specific SARS-CoV-2 RT-PCR is the standard method to screen symptomatic people; however, asymptomatic subjects and subjects with undetectable viral load escape from the screening, contributing to viral spread. Currently, the lock down imposed by many governments is an important measure to contain the spread, as there is no specific antiviral therapy or a vaccine and the main treatments are supportive. Therefore, there is urgent need to characterize the virus and the viral-mediated responses, in order to develop specific diagnostic and therapeutic tools to prevent viral transmission and efficiently cure COVID-19 patients. Here, we review the current studies on two viral mediated-responses, specifically the cytokine storm occurring in a subset of patients and the antibody response triggered by the infection. Further studies are needed to explore both the dynamics and the mechanisms of the humoral immune response in COVID-19 patients, in order to guide future vaccine design and antibody-based therapies for the management of the disease.

All India difficult airway association (AIDAA) consensus guidelines for airway management in the operating room during the COVID-19 pandemic

Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) which causes coronavirus disease (COVID-19) is a highly contagious virus. The closed environment of the operation room (OR) with aerosol generating airway management procedures increases the risk of transmission of infection among the anaesthesiologists and other OR personnel. Wearing complete, fluid impermeable personal protective equipment (PPE) for airway related procedures is recommended. Team preparation, clear methods of communication and appropriate donning and doffing of PPEs are essential to prevent spread of the infection. Optimal pre oxygenation, rapid sequence induction and video laryngoscope aided tracheal intubation (TI) are recommended. Supraglottic airways (SGA) and surgical cricothyroidotomy should be preferred for airway rescue. High flow nasal oxygen, face mask ventilation, nebulisation, small bore cannula cricothyroidotomy with jet ventilation should be avoided. Tracheal extubation should be conducted with the same levels of precaution as TI. The All India Difficult Airway Association (AIDAA) aims to provide consensus guidelines for safe airway management in the OR, while attempting to prevent transmission of infection to the OR personnel during the COVID-19 pandemic.

Sensitivity evaluation of 2019 novel coronavirus (SARS-CoV-2) RT-PCR detection kits and strategy to reduce false negative

The early detection and differential diagnosis of respiratory infections increase the chances for successful control of COVID-19 disease. The nucleic acid RT-PCR test is regarded as the current standard for molecular diagnosis. However, the maximal specificity confirmation target ORF1ab gene is considered to be less sensitive than other targets in clinical application. In addition, recent evidence indicated that the initial missed diagnosis of asymptomatic patients with SARS-CoV-2 and discharged patients with "re-examination positive" might be due to low viral load, and the ability of rapid mutation of SARS-CoV-2 also increases the rate of false-negative results. Moreover, the mixed sample nucleic acid detection is helpful in seeking out the early community transmission of SARS-CoV-2 rapidly, but the detection kit needs ultra-high detection sensitivity. Herein, the lowest detection concentration of different nucleic acid detection kits was evaluated and compared to provide direct evidence for the selection of kits for mixed sample detection or make recommendations for the selection of validation kit, which is of great significance for the prevention and control of the current epidemic and the discharge criteria of low viral load patients.

Antibody testing for COVID-19: A report from the National COVID Scientific Advisory Panel

Background: The COVID-19 pandemic caused >1 million infections during January-March 2020. There is an urgent need for reliable antibody detection approaches to support diagnosis, vaccine development, safe release of individuals from quarantine, and population lock-down exit strategies. We set out to evaluate the performance of ELISA and lateral flow immunoassay (LFIA) devices. Methods: We tested plasma for COVID (severe acute respiratory syndrome coronavirus 2; SARS-CoV-2) IgM and IgG antibodies by ELISA and using nine different LFIA devices. We used a panel of plasma samples from individuals who have had confirmed COVID infection based on a PCR result (n=40), and pre-pandemic negative control samples banked in the UK prior to December-2019 (n=142). Results: ELISA detected IgM or IgG in 34/40 individuals with a confirmed history of COVID infection (sensitivity 85%, 95%CI 70-94%), vs. 0/50 pre-pandemic controls (specificity 100% [95%CI 93-100%]). IgG levels were detected in 31/31 COVID-positive individuals tested ≥10 days after symptom onset (sensitivity 100%, 95%CI 89-100%). IgG titres rose during the 3 weeks post symptom onset and began to fall by 8 weeks, but remained above the detection threshold. Point estimates for the sensitivity of LFIA devices ranged from 55-70% versus RT-PCR and 65-85% versus ELISA, with specificity 95-100% and 93-100% respectively. Within the limits of the study size, the performance of most LFIA devices was similar. Conclusions: Currently available commercial LFIA devices do not perform sufficiently well for individual patient applications. However, ELISA can be calibrated to be specific for detecting and quantifying SARS-CoV-2 IgM and IgG and is highly sensitive for IgG from 10 days following first symptoms.