COVID-19 paraclinical diagnostic tools: Updates and future trends

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.

Development and Clinical Validation of RT-LAMP-Based Lateral-Flow Devices and Electrochemical Sensor for Detecting Multigene Targets in SARS-CoV-2

Consistently emerging variants and the life-threatening consequences of SARS-CoV-2 have prompted worldwide concern about human health, necessitating rapid and accurate point-of-care diagnostics to limit the spread of COVID-19. Still, However, the availability of such diagnostics for COVID-19 remains a major rate-limiting factor in containing the outbreaks. Apart from the conventional reverse transcription polymerase chain reaction, loop-mediated isothermal amplification-based (LAMP) assays have emerged as rapid and efficient systems to detect COVID-19. The present study aims to develop RT-LAMP-based assay system for detecting multiple targets in N, ORF1ab, E, and S genes of the SARS-CoV-2 genome, where the end-products were quantified using spectrophotometry, paper-based lateral-flow devices, and electrochemical sensors. The spectrophotometric method shows a LOD of 10 agµL−1 for N, ORF1ab, E genes and 100 agµL−1 for S gene in SARS-CoV-2. The developed lateral-flow devices showed an LOD of 10 agµL−1 for all four gene targets in SARS-CoV-2. An electrochemical sensor developed for N-gene showed an LOD and E-strip sensitivity of log 1.79 ± 0.427 pgµL−1 and log 0.067 µA/pg µL−1/mm2, respectively. The developed assay systems were validated with the clinical samples from COVID-19 outbreaks in 2020 and 2021. This multigene target approach can effectively detect emerging COVID-19 variants using combination of various analytical techniques at testing facilities and in point-of-care settings.

SARS-COV-2 - the pandemic of the XXI century, clinical manifestations - neurological implications

In December 2019, in Wuhan, China, the first cases of infection with SARS-CoV 2 responsible for COVID-19 disease were identified. SARS-CoV 2 was declared a pandemic on March 11, 2020, and since then has attracted the medical world's attention. The threat to humans' health that this emerging pandemic could leave raises awareness on the importance of understanding the mechanisms that underlie the developing conditions. The epidemiology, clinical picture, and pathogenesis of COVID-19 show that this virus presents new strategies to overcome the past defensive medicine. While all the current data has focused on the pulmonary and cardiovascular manifestations, little has been written about the neurological implications of the disease. This review updates new clinical aspects that SARS-CoV 2 expresses in humans by focusing primarily on neurological manifestations. The damage to the nervous system became more apparent - anosmia, ageusia, polyneuritis, meningitis, meningoencephalitis, stroke, acute necrotizing encephalopathy. Oxygen therapy is vital for those in critical health situations. Finally, prevention is the most important element in breaking the epidemiological chain.

Protective Measures Practices Among Hospitals' Professionals Working in a Fragile Health System

OBJECTIVE

This study aimed to assess the protective measures among health-care workers (HCWs) in a war-torn area during coronavirus disease 2019 (COVID-19) pandemic.

METHODS

An online cross-sectional questionnaire was administrated to HCWs in Syria between April 1 and May 21, 2020. The questions aimed to assess the HCWs' application of safety, hygiene, and necessary protection considerations while attending to suspected or proven COVID-19 cases. Unpaired t-test and 1-way analysis of variance (ANOVA) were used for statistical analysis.

RESULTS

Of the 290 participants included in the statistical analysis, 250 were medical doctors. Low scores of protective practices were noticed among the participants, as only 12% of doctors had a score above 6/15 points, and only 37.5% of nurses had a score of more than 4/12 points. Medical doctors who were not on the frontlines scored significantly higher than those who were on the frontlines (4.69 vs 3.80 points, respectively; P < 0.001).

CONCLUSIONS

More courses and training sessions should be implemented to improve the practice of protective measures among HCWs (frontliners in particular) in areas with fragile health systems, such as Syria, during the COVID-19 pandemic, especially those on the frontlines. Moreover, specific COVID-19 protection measures guidelines to low-income countries are needed.

SARS-CoV-2 Gene Expression as a Prognosis Predictor for COVID-19

Introduction: Real time quantitative PCR is the gold standard for detection of SARS-CoV-2 which is specific, sensitive, and simple quantitative. The target of RT-qPCR is to assess the expression level of the SARS-CoV-2 gene through cycle threshold values (CT-value). The purpose of this study was to analyze the association of the level of SARS-CoV-2 gene expression and the severity of COVID-19 in patients hospitalized. Method: This research is an analytic observational study with cross sectional method. While the research sample was taken using a consecutive sampling technique from the Medical Records of Sumedang Hospital and Cideres Hospital, West Java, Indonesia from December 2020 to March 2021. Patient parameters include analysis of age, sex, comorbidity, and disease severity. The severity of the patient is classified based on complaints and oxygen saturation. The expression level of the SARS-CoV-2 N gene and E gene were assessed by calculating the relative quantification by comparing the expression of the E and N gene with the expression of the internal control gene by Livak formula (2-ΔΔCT Formula). Result: The Spearman correlation test showed that there was a relationship between the expression of SARS-CoV-2 genes E and N genes with the severity of COVID-19 patients (with r=0.374 and p<0.0001) and (with r=0.452 and p<0.0001). Conclusions:  There is an correlation between the level of expression of genes E and gene N with the severity of patients.  

SARS-CoV2 infection in symptomatic patients: interest of serological tests and predictors of mortality: experience of DR Congo

Background

In symptomatic patients, the diagnostic approach of COVID-19 should be holistic. We aimed to evaluate the concordance between RT-PCR and serological tests (IgM/IgG), and identify the factors that best predict mortality (clinical stages or viral load).

Methods

The study included 242 patients referred to the University hospital of Kinshasa for suspected COVID-19, dyspnea or ARDS between June 1st, 2020 and August 02, 2020. Both antibody-SARS-CoV2 IgM/IgG and RT-PCR method were performed on the day of admission to hospital. The clinical stages were established according to the COVID-19 WHO classification. The viral load was expressed by the CtN2 (cycle threshold value of the nucleoproteins) and the CtE (envelope) genes of SARS- CoV-2 detected using GeneXpert. Kappa test and Cox regression were used as appropriate.

Results

The GeneXpert was positive in 74 patients (30.6%). Seventy two patients (29.8%) had positive IgM and 34 patients (14.0%) had positive IgG. The combination of RT-PCR and serological tests made it possible to treat 104 patients as having COVID-19, which represented an increase in cases of around 41% compared to the result based on GeneXpert alone. The comparison between the two tests has shown that 57 patients (23.5%) had discordant results. The Kappa coefficient was 0.451 (p < 0.001). We recorded 23 deaths (22.1%) among the COVID-19 patients vs 8 deaths (5.8%) among other patients. The severe-critical clinical stage increased the risk of mortality vs. mild-moderate stage (aHR: 26.8, p < 0.001). The values of CtE and CtN2 did not influence mortality significantly.

Conclusion

In symptomatic patients, serological tests are a support which makes it possible to refer patients to the dedicated COVID-19 units and treat a greater number of COVID-19 patients. WHO Clinical classification seems to predict mortality better than SARS-Cov2 viral load.

[How to deal with an unexpected event that could alter the normal activity of cellular therapy? Recommendations of the Francophone Society of Bone Marrow Transplantation and Cellular Therapy (SFGM-TC)]

L’épidémie mondiale de SARS-CoV-2 (COVID-19) a rapidement impacté l’ensemble de l’activité de thérapie cellulaire à travers le monde. Non seulement, cet événement inattendu était une menace pour les patients ayant déjà reçu une greffe de cellules hématopoïétiques ou une autre thérapie cellulaire telle que les cellules CAR-T, mais également, il a été responsable d’une désorganisation des activités de thérapie cellulaire en raison de la dangerosité du virus et du manque de données scientifiques solides quant au mangement des patients et des donneurs. La Société Francophone de Greffe de Moelle et de Thérapie Cellulaire (SFGM-TC) a consacré un atelier pour produire des recommandations utiles en cas de survenu d’un tel événement dans le but d’harmoniser les actions de tous les acteurs impliqués pour que l’on puisse faire face collectivement dans le futur aux défis qui pourraient menacer notre activité. Ce travail n’est pas spécifiquement dédié à l’épidémie de SARS-CoV-2, mais cette dernière a été utilisée comme un exemple concret d’un événement inattendu pour construire nos reflétions et nos recommandations.

Review of Current COVID-19 Diagnostics and Opportunities for Further Development

Diagnostic testing plays a critical role in addressing the coronavirus disease 2019 (COVID-19) pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Rapid and accurate diagnostic tests are imperative for identifying and managing infected individuals, contact tracing, epidemiologic characterization, and public health decision making. Laboratory testing may be performed based on symptomatic presentation or for screening of asymptomatic people. Confirmation of SARS-CoV-2 infection is typically by nucleic acid amplification tests (NAAT), which requires specialized equipment and training and may be particularly challenging in resource-limited settings. NAAT may give false-negative results due to timing of sample collection relative to infection, improper sampling of respiratory specimens, inadequate preservation of samples, and technical limitations; false-positives may occur due to technical errors, particularly contamination during the manual real-time polymerase chain reaction (RT-PCR) process. Thus, clinical presentation, contact history and contemporary phyloepidemiology must be considered when interpreting results. Several sample-to-answer platforms, including high-throughput systems and Point of Care (PoC) assays, have been developed to increase testing capacity and decrease technical errors. Alternatives to RT-PCR assay, such as other RNA detection methods and antigen tests may be appropriate for certain situations, such as resource-limited settings. While sequencing is important to monitor on-going evolution of the SARS-CoV-2 genome, antibody assays are useful for epidemiologic purposes. The ever-expanding assortment of tests, with varying clinical utility, performance requirements, and limitations, merits comparative evaluation. We herein provide a comprehensive review of currently available COVID-19 diagnostics, exploring their pros and cons as well as appropriate indications. Strategies to further optimize safety, speed, and ease of SARS-CoV-2 testing without compromising accuracy are suggested. Access to scalable diagnostic tools and continued technologic advances, including machine learning and smartphone integration, will facilitate control of the current pandemic as well as preparedness for the next one.

Inclusion of Cephalexin in COVID-19 Treatment Combinations May Prevent Lung Involvement in Mild Infections: A Case Report with Pharmacological Genomics Perspective

Novel coronavirus disease 2019 (COVID-19) is caused by a nonsegmented positive sense RNA, enveloped RNA virus that belongs to the family of β-coronaviridae. This virus shall cause acute respiratory distress syndrome (ARDS) which consequently leads to breathing difficulty and need to admit to intensive care units (ICUs). The current conventional treatment combination in most of the hospitals in Iran includes azithromycin 500 + naproxen 500 + vitamin C 1,000 + Zinc + vitamin D3 1,000. In this case reports ( n  = 4), we would like to report significant findings in course of COVID-19 treatment reported to our clinic on August 8 and 9, 2020; patients presented as walk in and were advised house isolation and complete bed rest as there were no signs of lung involvement and their overall condition was stable. By the inclusion of cephalexin 500 in treatment combination, patients who received cephalexin 500 for 5 days along with other medicines did not develop any lung involvement and breathing complications. Cephalexin is the gold standard in upper and lower respiratory tract infections and here also shall play a vital role besides other conventional therapies. Azithromycin is a macrodial antibiotic working via the ABCB1 gene pathway. As of date, there is no clear evidence of pharmacogenomics data in COVID-19 patients. More research needs to be performed in COVID-19 before any sort of pharmacogenomics tests could be advised.