Laboratory Diagnosis of SARS-CoV-2 Pneumonia

Persisting Shadows: Unraveling the Impact of Long COVID-19 on Respiratory, Cardiovascular, and Nervous Systems

The coronavirus disease 2019 (COVID-19), instigated by the zoonotic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), rapidly transformed from an outbreak in Wuhan, China, into a widespread global pandemic. A significant post-infection condition, known as 'long- COVID-19' (or simply 'long- COVID'), emerges in a substantial subset of patients, manifesting with a constellation of over 200 reported symptoms that span multiple organ systems. This condition, also known as 'post-acute sequelae of SARS-CoV-2 infection' (PASC), presents a perplexing clinical picture with far-reaching implications, often persisting long after the acute phase. While initial research focused on the immediate pulmonary impact of the virus, the recognition of COVID-19 as a multiorgan disruptor has unveiled a gamut of protracted and severe health issues. This review summarizes the primary effects of long COVID on the respiratory, cardiovascular, and nervous systems. It also delves into the mechanisms underlying these impacts and underscores the critical need for a comprehensive understanding of long COVID's pathogenesis.

Bioanalytical sensors using the heat-transfer method HTM and related techniques

This review provides an overview on bio- and chemosensors based on a thermal transducer platform that monitors the thermal interface resistance R th between a solid chip and the supernatant liquid. The R th parameter responds in a surprisingly strong way to molecular-scale changes at the solid-liquid interface, which can be measured thermometrically, using for instance thermocouples in combination with a controllable heat source. In 2012, the effect was first observed during on-chip denaturation experiments on complementary and mismatched DNA duplexes that differ in their melting temperature. Since then, the concept is addressed as heat-transfer method, in short HTM, and numerous applications of the basic sensing principle were identified. Functionalizing the chip with bioreceptors such as molecularly imprinted polymers makes it possible to detect neurotransmitters, inflammation markers, viruses, and environmental pollutants. In combination with aptamer-type receptors, it is also possible to detect proteins at low concentrations. Changing the receptors to surface-imprinted polymers has opened up new possibilities for quantitative bacterial detection and identification in complex matrices. In receptor-free variants, HTM was successfully used to characterize lipid vesicles and eukaryotic cells (yeast strains, cancer cell lines), the latter showing spontaneous detachment under influence of the temperature gradient inherent to HTM. We will also address modifications to the original HTM technique such as M-HTM, inverted HTM, thermal wave transport analysis TWTA, and the hot-wire principle. The article concludes with an assessment of the possibilities and current limitations of the method, together with a technological forecast.

Evaluation of the Cytotoxic and Antiviral Effects of Small Molecules Selected by In Silico Studies as Inhibitors of SARS-CoV-2 Cell Entry

The spike protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) relies on host cell surface glycans to facilitate interaction with the angiotensin-converting enzyme 2 (ACE-2) receptor. This interaction between ACE2 and the spike protein is a gateway for the virus to enter host cells and may be targeted by antiviral drugs to inhibit viral infection. Therefore, targeting the interaction between these two proteins is an interesting strategy to prevent SARS-CoV-2 infection. A library of glycan mimetics and derivatives was selected for a virtual screening performed against both ACE2 and spike proteins. Subsequently, in vitro assays were performed on eleven of the most promising in silico compounds to evaluate: (i) their efficacy in inhibiting cell infection by SARS-CoV-2 (using the Vero CCL-81 cell line as a model), (ii) their impact on ACE2 expression (in the Vero CCL-81 and MDA-MB-231 cell lines), and (iii) their cytotoxicity in a human lung cell line (A549). We identified five synthetic compounds with the potential to block SARS-CoV-2 infection, three of them without relevant toxicity in human lung cells. Xanthene 1 stood out as the most promising anti-SARS-CoV-2 agent, inhibiting viral infection and viral replication in Vero CCL-81 cells, without causing cytotoxicity to human lung cells.

Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives

The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.

Performance evaluation of an electrostatic precipitator with a copper plate using an aerosolized SARS-CoV-2 surrogate (bacteriophage phi 6)

The global spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has reminded us of the importance of developing technologies to reduce and control bioaerosols in built environments. For bioaerosol control, the interaction between researchers and biomaterials is essential, and considering the characteristics of target pathogens is strongly required. Herein, we used enveloped viral aerosols, bacteriophage phi 6, for evaluating the performance of an electrostatic precipitator (ESP) with a copper-collecting plate (Cu-plate). In particular, bacteriophage phi 6 is an accessible enveloped virus that can be operated in biosafety level (BSL)-1 as a promising surrogate for SARS-CoV-2 with structural and morphological similarities. ESP with Cu-plate showed >91% of particle removal efficiency for viral aerosols at 77 cm/s of airflow face velocity. Moreover, the Cu-plate presented a potent antiviral performance of 5.4-relative log reduction within <15 min of contact. We believe that the evaluation of ESP performance using an aerosolized enveloped virus and plaque assay is invaluable. Our results provide essential information for the development of bioaerosol control technologies that will lead the post-corona era.

Comparative analysis of chest radiography and lung ultrasound to predict intra-hospital prognosis of patients admitted for acute SARS-CoV-2 pneumonia (COVID-19)

Background

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.

Patients and methods

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.

Results

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).

Conclusions

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.

Evaluation of the diagnostic performance of PanbioTM Abbott SARS-CoV-2 rapid antigen test for the detection of COVID-19 from suspects attending ALERT center

BACKGROUND

The emergence and rapid spread of coronavirus disease 2019 (COVID-19), a potentially lethal disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is causing public health issues around the world. In resource-constrained nations, rapid Abbott SARS-CoV-2 antigen test kits are critical for addressing diagnostic gaps in health institutions and community screening. However, there is no evidence or proof of diagnostic performance in Ethiopia. The aim of this study was to compare the performance of PanbioTM Abbott SARS-CoV-2antigen rapid test kit to the gold standard, RT-PCR, in COVID-19 patients with clinical symptoms suggestive of COVID-19.

METHOD

A prospective, cross-sectional study was conducted between November 2021 and April 2022, on 120 suspected patients recruited from outpatient, emergency, and intensive care units in one of the tertiary hospitals in Ethiopia. Nasopharyngeal swabs were collected from suspected cases and were tested using the Abbott SARS-CoV-2 kit, a rapid diagnostic test (RDT) and compared to the reference standard RT-PCR.

RESULT

The sensitivity and specificity of the RDT were 74.2% and 100%, respectively. A total of 62 samples (51.6%) were RT-PCR positive. Of these, 46 were Ag-RDT positive. Sensitivity among symptomatic patients was 79.4% (95% CI 68.3-90). The Abbot RDT and RT-PCR had a Kappa value of agreement of 0.735 (p < 0.001). These values were acceptable when compared to the WHO's suggested thresholds.

CONCLUSION

The finding from this study support the use of the Abbot RDT as a diagnostic tool in COVID-19 suspects, mainly in those with higher viral loads.

Clinical Added Value of SARS-CoV-2 Antigen Detection in Blood Samples

This study evaluated the performances of immunoassays (LFIA and ELISA) designed for SARS-CoV-2 Antigen (Ag)-detection in nasopharyngeal (NP) and serum samples in comparison to RT-PCR. NP samples from patients with respiratory symptoms (183 RT-PCR-positive and 74 RT-PCR-negative samples) were collected from March to April and November to December 2020. Seroconversion and antigen dynamics were assessed by symptom onset and day of RT-PCR diagnosis. Serum samples from 87 COVID-19 patients were used to investigate the added value of Ag quantification, at diagnosis and during follow-up. The sensitivity of COVID-VIRO-LFIA on samples with Ct ≤ 33, considered as the contagious threshold, was 86% on NPs (CI 95%: 79–90.5) and 76% on serum samples (CI 95%: 59.4–88), with a specificity of 100%. Serum N-Ag was detected during active infection as early as day two from symptom onset, with a diagnostic sensitivity of 81.5%. Within one week of symptom onset, diagnostic sensitivity and specificity reached 90.9% (95% CI, 85.1%–94.6%) and 98.3% (95% CI, 91.1%–99.9%), respectively. Serum N-Ag concentration closely correlated with disease severity. Longitudinal analysis revealed the simultaneous increase of antibodies and decrease of N-Ag. Sensitivities of COVID-VIRO-LFIA and COV-QUANTO-ELISA tests on NP and serum samples were close to 80%. They are suitable COVID-19-laboratory diagnostic tests, particularly when blood samples are available, thus reducing the requirement for NP sampling, and subsequent PCR analysis. ELISA titers may help to identify patients at risk of poor outcomes.

Understanding and combating COVID-19 using the biology and chemistry of SARS-CoV-2

The coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Symptoms of COVID-19 can range from asymptomatic to severe, which could lead to fatality. Like other pathogenic viruses, the infection of SARS-CoV-2 relies on binding its spike glycoprotein to the host receptor angiotensin-converting enzyme 2 (ACE 2). Molecular studies suggested that there is a high affinity between the spike glycoprotein and ACE 2 that might arise due to their hydrophobic interaction. This property is mainly responsible for making this virus highly infectious. Apart from this, the transmissibility of the virus, prolonged viability in certain circumstances, and rapid mutations also contributed to the current pandemic situation. Nanotechnology provides potential alternative solutions to combat COVID-19 with the development of i. nanomaterial-based COVID-19 detection technology, ii. nanomaterial-based disinfectants, iii. nanoparticle-based vaccines, and iv. nanoparticle-based drug delivery. Hence, this review provides diverse insight into understanding COVID-19.

Absence of Mortality Differences Between the First and Second COVID-19 Waves in Kidney Transplant Recipients

Introduction

SARS-CoV-2 pandemic evolved in 2 consecutive waves during 2020. Improvements in the management of COVID-19 led to a reduction in mortality rates among hospitalized patients during the second wave. Whether this progress benefited kidney transplant recipients (KTRs), a population particularly vulnerable to severe COVID-19, remained unclear.

Methods

In France, 957 KTRs were hospitalized for COVID-19 in 2020 and their data were prospectively collected into the French Solid Organ Transplant (SOT) COVID registry. The presentation, management, and outcomes of the 359 KTRs diagnosed during the first wave were compared to those of the 598 of the second wave.

Results

Baseline comorbidities were similar between KTRs of the 2 waves. Maintenance immunosuppression was reduced in most patients but withdrawal of antimetabolite (73.7% vs. 58.4%, P < 0.001) or calcineurin inhibitor (32.1% vs. 16.6%, P < 0.001) was less frequent during the second wave. Hydroxychloroquine and azithromycin that were commonly used during the first wave (21.7% and 30.9%, respectively) but were almost abandoned during the second wave. In contrast, the use of high dose corticosteroids doubled (19.5% vs. 41.6%, P < 0.001). Despite these changing trends in COVID-19 management, 60-day mortality was not statistically different between the 2 waves (25.3% vs. 23.9%; Log Rank, P = 0.48) and COVID-19 hospitalization period was not associated with death due to COVID-19 in multivariate analysis (Hazard ratio 0.89, 95% confidence interval 0.67–1.17, P = 0.4).

Conclusion

We conclude that changing of therapeutic trends during 2020 did not reduce COVID-19 related mortality among KTRs. Our data indirectly support the importance of vaccination and neutralizing monoclonal anti-SARS-CoV-2 antibodies to protect KTRS from severe COVID-19.

Probing the mutation independent interaction of DNA probes with SARS-CoV-2 variants through a combination of surface-enhanced Raman scattering and machine learning

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution has been characterized by the emergence of sets of mutations impacting the virus characteristics, such as transmissibility and antigenicity, presumably in response to the changing immune profile of the human population. The presence of mutations in the SARS-CoV-2 virus can potentially impact therapeutic and diagnostic test performances. We design and develop here a unique set of DNA probes i.e., antisense oligonucleotides (ASOs) which can interact with genetic sequences of the virus irrespective of its ongoing mutations. The probes, developed herein, target a specific segment of the nucleocapsid phosphoprotein (N) gene of SARS-CoV-2 with high binding efficiency which do not mutate among the known variants. Further probing into the interaction profile of the ASOs reveals that the ASO-RNA hybridization remains unaltered even for a hypothetical single point mutation at the target RNA site and diminished only in case of the hypothetical double or triple point mutations. The mechanism of interaction among the ASOs and SARS-CoV-2 RNA is then explored with a combination of surface-enhanced Raman scattering (SERS) and machine learning techniques. It has been observed that the technique, described herein, could efficiently discriminate between clinically positive and negative samples with ∼100% sensitivity and ∼90% specificity up to 63 copies/mL of SARS-CoV-2 RNA concentration. Thus, this study establishes N gene targeted ASOs as the fundamental machinery to efficiently detect all the current SARS-CoV-2 variants regardless of their mutations.

Peptide Binder with High-Affinity for the SARS-CoV-2 Spike Receptor-Binding Domain

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.

Análisis comparativo de la radiografía de tórax y la ecografía pulmonar para predecir el pronóstico intra-hospitalario de pacientes ingresados por neumonía secundaria a SARS-COV2 (COVID-19)

Antecedentes

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.

Pacientes y métodos

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.

Resultados

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).

Conclusiones

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.

A Novel Rapid Test to Detect Anti-SARS-CoV-2 N Protein IgG Based on Shear Horizontal Surface Acoustic Wave (SH-SAW)

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.