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Journal ArticleDOI

Laboratory Diagnosis of SARS-CoV-2 Pneumonia.

TL;DR: In this paper, the authors delineate the categories of testing measures developed to date, analyze the efficacy of collecting patient specimens from diverse regions of the respiratory tract, and present the up and coming technologies which have made pathogen identification easier and more accessible to the public.
Abstract: The emergence and rapid proliferation of Coronavirus Disease-2019, throughout the past year, has put an unprecedented strain on the global schema of health infrastructure and health economy. The time-sensitive agenda of identifying the virus in humans and delivering a vaccine to the public constituted an effort to flatten the statistical curve of viral spread as it grew exponentially. At the forefront of this effort was an exigency of developing rapid and accurate diagnostic strategies. These have emerged in various forms over the past year-each with strengths and weaknesses. To date, they fall into three categories: (1) those isolating and replicating viral RNA in patient samples from the respiratory tract (Nucleic Acid Amplification Tests; NAATs), (2) those detecting the presence of viral proteins (Rapid Antigen Tests; RATs) and serology-based exams identifying antibodies to the virus in whole blood and serum. The latter vary in their detection of immunoglobulins of known prevalence in early-stage and late-stage infection. With this review, we delineate the categories of testing measures developed to date, analyze the efficacy of collecting patient specimens from diverse regions of the respiratory tract, and present the up and coming technologies which have made pathogen identification easier and more accessible to the public.
Citations
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Journal ArticleDOI
TL;DR: In this article , a set of DNA probes targeting a specific segment of the nucleocapsid phosphoprotein (N) gene of SARS-CoV-2 with high binding efficiency was developed.

19 citations

Journal ArticleDOI
05 Oct 2021
TL;DR: In this article, a shear-horizontal surface acoustic wave (SH-SAW) biosensor was developed to detect the anti-SARS-CoV-2 nucleocapsid antibody.
Abstract: Since the Coronavirus disease 2019 (COVID-19) pandemic outbreak, many methods have been used to detect antigens or antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), including viral culture, nucleic acid test, and immunoassay. The shear-horizontal surface acoustic wave (SH-SAW) biosensor is a novel pathogen detection platform with the advantages of high sensitivity and short detection time. The objective of this study is to develop a SH-SAW biosensor to detect the anti-SARS-CoV-2 nucleocapsid antibody. The rabbit sera collected from rabbits on different days after SARS-CoV-2 N protein injection were evaluated by SH-SAW biosensor and enzyme-linked immunosorbent assay (ELISA). The results showed that the SH-SAW biosensor achieved a high correlation coefficient (R = 0.9997) with different concentrations (34.375–1100 ng/mL) of the “spike-in” anti-N protein antibodies. Compared to ELISA, the SH-SAW biosensor has better sensitivity and can detect anti-N protein IgG signals earlier than ELISA on day 6 (p < 0.05). Overall, in this study, we demonstrated that the SH-SAW biosensor is a promising platform for rapid in vitro diagnostic (IVD) testing, especially for antigen or antibody testing.

9 citations

Journal ArticleDOI
TL;DR: The optimal diagnostic test for SARS-CoV-2 infection should be selected based on a patient's clinical syndrome and presentation in relation to symptom onset as mentioned in this paper , and the optimal test should be chosen based on the patient's symptoms and presentation.

4 citations

Journal ArticleDOI
TL;DR: In this paper , a comparison between the Schalekamp radiological lung scale and LUZ-score ultrasound scale was performed in stable COVID-19 patients, and the results showed that the LUZ scale failed to identify patients at higher risk at admission for the primary end-point.
Abstract: Point of care lung ultrasound (POCUS) has been recently used to assess prognosis in COVID-19 patients. However, there are no data comparing POCUS and chest-X ray, a technique widely used.Retrospective analysis in stable COVID-19 patients. Schalekamp radiological lung scale and LUZ-Score ultrasound scale were compared. Primary end-point was in-hospital death and/or need for Intensive Care Unit admission.A total of 138 patients were included. Median Schalekamp scale was 2 (2) and median LUZ-Score scale was 21 (10). No significant correlation was observed between both techniques. Patients with a LUZ-Score ≥ 21 points at admission had worse lung function and higher concentrations of LDH, CRP and Interleuquine-6. Schalekamp scale failed to identify patients at a higher risk at admission for the primary end-point. Addition of POCUS to a previous clinical model, improved risk prediction (AUC 0.805 [95% CI: 0.662-0.948]; P = <0.001).Chest X-ray and POCUS showed no correlation at admission in this analysis. Only POCUS identified a group of patients with greater clinical and analytical involvement. POCUS improved, previous clinical model, while chest X-ray did not add relevant predictive information for the primary endpoint.La ecografía torácica es una técnica novedosa para estratificar el riesgo de los pacientes COVID-19. Sin embargo, no existen datos que comparen dicha técnica con la radiografía de tórax, una técnica ampliamente utilizada en esta enfermedad.Análisis retrospectivo en pacientes estables COVID-19. Se compararon la escala de daño pulmonar radiológica de Schalekamp y ecográfica de LUZ-Score. El objetivo primario fue la muerte intrahospitalaria o la necesidad de ingreso en la UCI para tratamiento con ventilación mecánica.Se reclutaron 138 pacientes. La mediana de la escala de Schalekamp fue de 2 (2) y la del LUZ-Score de 21 (10). No se objetivó una correlación significativa entre ambas escalas. Los pacientes con un LUZ-Score ≥ 21 puntos al ingreso presentaron peor función pulmonar y mayores concentraciones de LDH, PCR e interleucina-6. La escala radiológica de Schalekamp no logró identificar a una población de mayor riesgo. Únicamente la adición de la ecografía pulmonar a un modelo de valoración clínica mejoró de manera significativa el área bajo la curva para el objetivo primario (ABC 0,805 [IC 95%: 0,662−0,948]; p ≤ 0,001).No se objetivó una correlación entre la afectación radiológica y la ecográfica. Únicamente la ecografía pulmonar identificó un subgrupo de pacientes con una mayor afectación clínico-analítica. La ecografía pulmonar mejoró el modelo de predicción clínico, mientras que la radiografía de tórax no añadió información relevante.

3 citations

Journal ArticleDOI
TL;DR: The R1 peptide exhibited high-affinity for specific binding with the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with a dissociation constant KD of (7.5 ± 1.9) × 10–10 M, which maintained high binding affinity with the RBD derived from Gamma, Lambda, Delta, and Omicron variants.
Abstract: Rapid antigen detection tests are urgently needed for the early diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The discovery of a binder with high affinity and selectivity for the biomarkers presented by SARS-CoV-2 is crucial to the development of the rapid antigen detection method. We utilized the surface biopanning to identify a peptide binder R1 from a phage-displayed peptide library consisting of 109 independent phage recombinants. The R1 peptide exhibited high-affinity for specific binding with the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with a dissociation constant KD of (7.5 ± 1.9) × 10–10 M, which maintained high binding affinity with the RBD derived from Gamma, Lambda, Delta, and Omicron variants. The composition and sequence dependence of binding characteristics in R1–RBD interactions was revealed by the binding affinity fluctuations between RBD and the scrambled sequences or single-site mutants of R1. The R1-functionalized gold nanoparticles possessed concentration-dependent response to RBD and selectivity over bovine serum albumin and human serum albumin. The peptide binder R1 shows the potential to be used for constructing a rapid detection method for the early-stage diagnostics for SARS-CoV-2.

3 citations

References
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Journal ArticleDOI
TL;DR: Wang et al. as discussed by the authors used univariable and multivariable logistic regression methods to explore the risk factors associated with in-hospital death, including older age, high SOFA score and d-dimer greater than 1 μg/mL.

20,189 citations

Journal ArticleDOI
13 Mar 2020-Science
TL;DR: The authors show that this protein binds at least 10 times more tightly than the corresponding spike protein of severe acute respiratory syndrome (SARS)–CoV to their common host cell receptor, and test several published SARS-CoV RBD-specific monoclonal antibodies found that they do not have appreciable binding to 2019-nCoV S, suggesting that antibody cross-reactivity may be limited between the two RBDs.
Abstract: The outbreak of a novel coronavirus (2019-nCoV) represents a pandemic threat that has been declared a public health emergency of international concern. The CoV spike (S) glycoprotein is a key target for vaccines, therapeutic antibodies, and diagnostics. To facilitate medical countermeasure development, we determined a 3.5-angstrom-resolution cryo-electron microscopy structure of the 2019-nCoV S trimer in the prefusion conformation. The predominant state of the trimer has one of the three receptor-binding domains (RBDs) rotated up in a receptor-accessible conformation. We also provide biophysical and structural evidence that the 2019-nCoV S protein binds angiotensin-converting enzyme 2 (ACE2) with higher affinity than does severe acute respiratory syndrome (SARS)-CoV S. Additionally, we tested several published SARS-CoV RBD-specific monoclonal antibodies and found that they do not have appreciable binding to 2019-nCoV S, suggesting that antibody cross-reactivity may be limited between the two RBDs. The structure of 2019-nCoV S should enable the rapid development and evaluation of medical countermeasures to address the ongoing public health crisis.

7,324 citations

Journal ArticleDOI
TL;DR: A validated diagnostic workflow for 2019-nCoV is presented, its design relying on close genetic relatedness of 2019- nCoV with SARS coronavirus, making use of synthetic nucleic acid technology.
Abstract: Background The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur. Aim We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available. Methods Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology. Results The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive – Global (EVAg), a European Union infrastructure project. Conclusion The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.

6,229 citations

Journal ArticleDOI
04 Mar 2020-Science
TL;DR: Cryo–electron microscopy structures of full-length human ACE2 in the presence of the neutral amino acid transporter B0AT1 with or without the receptor binding domain (RBD) of the surface spike glycoprotein of SARS-CoV-2 are presented, providing important insights into the molecular basis for coronavirus recognition and infection.
Abstract: Angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for severe acute respiratory syndrome-coronavirus (SARS-CoV) and the new coronavirus (SARS-CoV-2) that is causing the serious coronavirus disease 2019 (COVID-19) epidemic. Here, we present cryo-electron microscopy structures of full-length human ACE2 in the presence of the neutral amino acid transporter B0AT1 with or without the receptor binding domain (RBD) of the surface spike glycoprotein (S protein) of SARS-CoV-2, both at an overall resolution of 2.9 angstroms, with a local resolution of 3.5 angstroms at the ACE2-RBD interface. The ACE2-B0AT1 complex is assembled as a dimer of heterodimers, with the collectrin-like domain of ACE2 mediating homodimerization. The RBD is recognized by the extracellular peptidase domain of ACE2 mainly through polar residues. These findings provide important insights into the molecular basis for coronavirus recognition and infection.

4,109 citations

Journal ArticleDOI
TL;DR: It is estimated that 44% (95% confidence interval, 25–69%) of secondary cases were infected during the index cases’ presymptomatic stage, in settings with substantial household clustering, active case finding and quarantine outside the home.
Abstract: We report temporal patterns of viral shedding in 94 patients with laboratory-confirmed COVID-19 and modeled COVID-19 infectiousness profiles from a separate sample of 77 infector–infectee transmission pairs. We observed the highest viral load in throat swabs at the time of symptom onset, and inferred that infectiousness peaked on or before symptom onset. We estimated that 44% (95% confidence interval, 30–57%) of secondary cases were infected during the index cases’ presymptomatic stage, in settings with substantial household clustering, active case finding and quarantine outside the home. Disease control measures should be adjusted to account for probable substantial presymptomatic transmission. Presymptomatic transmission of SARS-CoV-2 is estimated to account for a substantial proportion of COVID-19 cases.

3,943 citations