Detection and Diagnosis Technologies for SARS-CoV-2

Detection and diagnosis platforms play key roles in early warning, outbreak control and exit strategy for any pandemic, and they are especially pertinent for the Coronavirus disease 2019 (COVID-19) pandemic. The challenges posed by the speed and extent of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) spread around the globe also offered unprecedented opportunities for the development and deployment of novel strategies and products - not only vaccines and therapeutics, but also diagnostics. This chapter provides a brief summary of the vast array of molecular, serological, cell-based and other diagnostic tools for the specific detection of SARS-CoV-2 infections and immune responses. The focus is on the principles and applications of each platform, while detailed protocols can be found in the cited references. © 2023 by World Scientific Publishing Co. Pte. Ltd.

Time series analysis of the number of tuberculosis cases in tangshan area

Objective The time series analysis model was used to predict and warn the number of tuberculosis (TB) cases in Tangshan area in different time, which provided a reference for scientific prevention and control of TB epidemic in this area. Methods The number of monthly TB cases in Tangshan from January 2005 to December 2021 was collected, and the seasonal autoregressive integrated moving average (SARIMA) model was used to predict the number of TB cases in 2022. Meanwhile, the difference between the predicted number of TB cases and the actual observed number of TB cases in the area was explored during the period of COVID-19 in 2020 by this model and rank test. Results From January 2005 to December 2021, the ARIMA (1, 1, 0) (1, 1, 2)s model was fitted well with the actual observed number of TB cases (AR =-0. 530, ARs =-0.967, MAs = 0. 861, P0. 05;Stationary R2 = 0. 558, R2 = 0. 634, BIC = 7. 887;Ljung-Box Q = 25. 605, P 0. 05), with peaks TB incidence in March, April, and December every year, and the predicted number of TB cases in 2020 was 1 800. From 2005 to 2019, ARIMA (1, 1, 0) (0, 1, 2)s model was fitted well with the actual number of cases (AR =-0. 544, ARs =-0. 840, MAs = 0. 697, P 0. 05;Stationary R2 = 0. 582, R2 = 0. 621, BIC = 7. 939;Ljung-Box Q = 24. 211, P 0. 05), with peaks TB incidence in March, April, and December every year, and the predicted number of TB cases in 2020 was 1 985. The observed and predicted number of TB cases from January 2020 to May 2020 were statistically significant (Z =-2. 023, P0. 05). Conclusion It is necessary to increase the intensity of early warning of TB in March, April, and December every year in Tangshan to prevent the epidemic of TB. At the same time, the coordination of the staff of TB prevention institutions and the emergency system should be strengthened during the epidemic situation of COVID-19, and effectively ensure the registration and medical treatment of TB patients during the epidemic situation. © 2023, Editorial Department of Medical Pest Control. All rights reserved.

Clinical characteristics and serum IgG, IgM antibody manifestations of patients infected with SARS-CoV-2 B.1.1.529 (Omicron) variant strain

Objective To analyze the clinical characteristics and changes of serum IgG, IgM antibodies in patients infected with the SARS-CoV-2 B.1.1.529 (Omicron) variant. Methods The clinical data of 82 patients with SARS-CoV-2 B.1.1.529 variant was analyzed retrospectively. Based on the presence of pneumonia on chest CT, the patients were divided into pneumonia group and non-pneumonia group. Serum IgG, IgM antibodies were observed at 5 time points T1 (1~<4 d), T2 (4~<8 d), T3 (8~<15 d), T4 (15~<22 d) and T5 (22~<30 d) after admission. Results Among the 82 patients infected with the SARSCoV-2 B.1.1.529 variant strain, there were 62 cases of cough, 31 cases of fever, 33 cases of throat discomfort, 5 cases of muscle soreness and 3 cases of diarrhea. The serum IgG antibody levels at 5 time points were 50.22 (142.20) AU/mL, 326.50 (220.63) AU / mL, 368.23 (76.21) AU / mL, 368.65 (79) AU / mL, and 385.26 (113.10) AU / mL, respectively. The level of serum IgG antibody in the pneumonia group was lower than that of the non-pneumonia group at T1 and T4 time points, and the differences were statistically significant (P<0.05), the positive rate of serum IgG antibody in the pneumonia group was lower than that of the non-pneumonia group at the T1 time point, and the difference was statistically significant (P<0.05) . The serum IgM antibody levels at 5 time points were 0.41 (0.81) AU/mL, 0.95 (1.62) AU/mL, 1.09 (2.42) AU/mL, 0.74 (3) AU/mL, and 0.81 (3.10) AU / mL respectively, and there was no significant difference between the two groups. Conclusion The clinical symptoms of patients infected with the SARS-CoV-2 B.1.1.529 variant strain are mild. Serum IgG antibodies increased after infection, but there are some differences between the pneumonia group and the non-pneumonia group, whether serum IgG has a protective effect needs further research;the serum IgM antibodies do not increase highly after infection, there are some differences between individuals. © 2022 Editorial Office of Chinese Journal of Schistosomiasis Control. All rights reserved.

Human Nasal Epithelial Cells Sustain Persistent SARS-CoV-2 Infection In Vitro, despite Eliciting a Prolonged Antiviral Response

The dynamics of SARS-CoV-2 infection in COVID-19 patients are highly variable, with a subset of patients demonstrating prolonged virus shedding, which poses a significant challenge for disease management and transmission control. In this study, the long-term dynamics of SARS-CoV-2 infection were investigated using a human well-differentiated nasal epithelial cell (NEC) model of infection. NECs were observed to release SARS-CoV-2 virus onto the apical surface for up to 28 days post-infection (dpi), further corroborated by viral antigen staining. Single-cell transcriptome sequencing (sc-seq) was utilized to explore the host response from infected NECs after short-term (3-dpi) and long-term (28-dpi) infection. We identified a unique population of cells harboring high viral loads present at both 3 and 28 dpi, characterized by expression of cell stress-related genes DDIT3 and ATF3 and enriched for genes involved in tumor necrosis factor alpha (TNF-alpha) signaling and apoptosis. Remarkably, this sc-seq analysis revealed an antiviral gene signature within all NEC cell types even at 28 dpi. We demonstrate increased replication of basal cells, absence of widespread cell death within the epithelial monolayer, and the ability of SARS-CoV-2 to replicate despite a continuous interferon response as factors likely contributing to SARS-CoV-2 persistence. This study provides a model system for development of therapeutics aimed at improving viral clearance in immunocompromised patients and implies a crucial role for immune cells in mediating viral clearance from infected epithelia. IMPORTANCE Increasing medical attention has been drawn to the persistence of symptoms (long-COVID syndrome) or live virus shedding from subsets of COVID-19 patients weeks to months after the initial onset of symptoms. In vitro approaches to model viral or symptom persistence are needed to fully dissect the complex and likely varied mechanisms underlying these clinical observations. We show that in vitro differentiated human NECs are persistently infected with SARS-CoV-2 for up to 28 dpi. This viral replication occurred despite the presence of an antiviral gene signature across all NEC cell types even at 28 dpi. This indicates that epithelial cell intrinsic antiviral responses are insufficient for the clearance of SARS-CoV-Z implying an essential role for tissue-resident and infiltrating immune cells for eventual viral clearance from infected airway tissue in COVID-19 patients.

[Analysis of CT features of 15 children with 2019 novel coronavirus infection].

Objective: To explore imaging characteristics of children with 2019 novel coronavirus (2019-nCoV) infection. Methods: A retrospective analysis was performed on clinical data and chest CT images of 15 children diagnosed with 2019-nCoV infection. They were admitted to the Third People's Hospital of Shenzhen from January 16 to February 6, 2020. The distribution and morphology of pulmonary lesions on chest CT images were analyzed. Results: Among the 15 children, 5 were males and 10 females, aged from 4 to 14 years. Five of the 15 children were febrile and 10 were asymptomatic on the first visit. The first nasal or pharyngeal swab samples in all the 15 cases were positive for 2019-nCoV nucleic acid. For their first chest CT images, 6 patients had no lesions, while 9 patients had pulmonary inflammatory lesions. Seven cases had small nodular ground glass opacities and 2 cases had speckled ground glass opacities. After 3 to 5 days of treatment, 2019-nCoV nucleic acid in a second respiratory sample turned negative in 6 cases. Among them, chest CT images showed less lesions in 2 cases, no lesion in 3 cases, and no improvement in 1 case. The remaining 9 cases were still positive in a second nucleic acid test. Six patients showed similar chest CT inflammation, while 3 patients had new lesions, which were all small nodular ground glass opacities. Conclusions: The early chest CT images of children with 2019-nCoV infection are mostly small nodular ground glass opacities. The clinical symptoms of children with 2019-nCoV infection are nonspecific. Dynamic reexamination of chest CT and nucleic acid are important.

Evolution of SARS Coronavirus and the Relevance of Modern Molecular Epidemiology

This chapter discusses the evolution of severe acute respiratory syndrome (SARS) coronavirus and the relevance of modern molecular epidemiology. The first case was reported in China in November 2002 and led to a disastrous worldwide pandemic. An international SARS network was established by WHO to rapidly identify the causative agent. In March 2003, the SARS coronavirus was identified. The majority of the early cases were limited to the Guangdong province of China, which have a unique dietary tradition favoring freshly slaughtered game meat;therefore, studies were conducted in those markets for evidence of SARS-CoV. Antibodies against SARS-CoV were detected in masked palm civets. By using serological and PCR surveillance, it was discovered that SARS-like CoV or SL-CoVs were present in different horseshoe bats in the genus Rhinolophus and that they are the likely natural reservoir hosts of bat SL-CoVs. There are more than 60 different horseshoe species around the world, and one or more of them may serve as the natural reservoir of SARS-CoV and/or its progenitor virus(es). It is therefore likely that another outbreak could occur on a similar scale as that of the SARS-CoV outbreaks but our response to a future outbreak caused by any bat-borne coronavirus will be much more effective. SARS is an example demonstrating the evolution of an animal virus into a human pathogen responsible for one of the most severe global pandemic. It is paramount that from now we include active surveillance of wild animals as part of an integrated infectious disease prevention and control strategy. FAU - Shi, Zhengli

Neuroimaging in Zoonotic Outbreaks Affecting the Central Nervous System: Are We Fighting the Last War?

When preparing for the coronavirus disease 2019 pandemic and its effects on the CNS, radiologists should be familiar with neuroimaging appearances in past zoonotic infectious disease outbreaks. Organisms that have crossed the species barrier from animals to humans include viruses such as Hendra, Nipah, Severe Acute Respiratory Syndrome, and influenza, as well as bacteria and others. Brain CT and MR imaging findings have included cortical abnormalities, microinfarction in the white matter, large-vessel occlusion, and features of meningitis. In particular, the high sensitivity of diffusion-weighted MR imaging in detecting intracranial abnormalities has been helpful in outbreaks. Although the coronaviruses causing the previous Severe Acute Respiratory Syndrome outbreak and the current coronavirus disease 19 pandemic are related, it is important to be aware of their similarities as well as potential differences. This review describes the neuroimaging appearances of selected zoonotic outbreaks so that neuroradiologists can better understand the current pandemic and potential future outbreaks.

Study on mechanism of Shengmai Injection against novel coronavirus pneumonia based on network pharmacology and molecular docking technology

Objective: To explore the potential material basis of Shengmai Injection for the treatment of coronavirus disease 2019 (COVID-19) through network pharmacology and molecular docking technology. Methods : The active compounds of Shengmai Injection were screened by TCMSP and BATMAN-TCM database. The action target was predicted by TCMSP and Targetnet online database, and the active component-action target network diagram was constructed by Cytoscape 3.7.1;Taking "coronavirus pneumonia" as the keyword, coronavirus-related disease targets were searched in GeneCards database and OMIM database. The common target was selected by intersection with the target of Shengmai Injection as the research target. The common target was imported into STRING database to obtain data, and then the protein-protein interaction network map was constructed in Cytoscape 3.7.1 software;The enrichment analysis of GO function and KEGG pathway was carried out by using R language to predict its action mechanism and construct the "component-target-pathway" network diagram;Molecular docking analysis of key targets was carried out by DiscoveryStudio 2.5 software. Results: A total of 22 active compounds were obtained from Shengmai Injection. They were DNOP, β-sitosterol, angeloylgomisin O, gomisin A, gomisin R, wuweizisu C, interiotherin B, changnanic acid, kadsulactone, kadsulignan B, neokadsuranic acid A, neokadsuranic acid B, neokadsuranic acid C, neokadsuranin, schisanlactone A, schisanlactone E, schizandronic acid, uridine, diosgenin, guanosine, N-trans-feruloyltyramine and stigmasterol. There were 224 corresponding targets and 16 common targets with COVID-19, namely CASP3, CASP8, PTGS2, BCL2, BAX, PRKCA, PTGS1, PIK3CG, F10, NOS3, DPP4, NOS2, TLR9, ACE, ICAM1 and PRKCE. The key targets were CASP3, PTGS2, NOS2, NOS3 and ICAM1. GO functional enrichment analysis showed that there were 771 entries for biological processes, 11 entries for cell composition and 79 items for molecular function. A total of 67 signal pathways were screened by KEGG pathway enrichment analysis, which were mainly related to AGE-RAGE signaling pathway in diabetic complications, apoptosis-multiple species, p53 signaling pathway, small cell lung cancer, and so on. The results of molecular docking showed that the components with better docking with the key targets were schisanlactone E, stigmasterol and N-trans-feruloyltyramine. Conclusion: The active compounds in Shengmai Injection, such as schisanlactone E, stigmasterol, N-trans-feruloyltyramine, can act on CASP3, PTGS2, NOS2, NOS3 and other targets to regulate multiple signaling pathways for anti-inflammatory, immune regulation, anti-shock and increasing blood oxygen saturation. This may play a role in the treatment of COVID-19.

[Analysis of CT features of 15 Children with 2019 novel coronavirus infection].

Objective: To explore imaging characteristics of children with 2019 novel coronavirus (2019-nCoV) infection. Methods: A retrospective analysis was performed on clinical data and chest CT images of 15 children diagnosed with 2019-nCoV. They were admitted to the third people's Hospital of Shenzhen from January 16 to February 6, 2020. The distribution and morphology of pulmonary lesions on chest CT images were analyzed. Results: Among the 15 children, there were 5 males and 10 females, aged from 4 to 14 years old. Five of the 15 children were febrile and 10 were asymptomatic on first visit. The first nasal or pharyngeal swab samples in all the 15 cases were positive for 2019-nCoV nucleic acid. For their first chest CT images, 6 patients had no lesions, while 9 patients had pulmonary inflammation lesions. Seven cases of small nodular ground glass opacities and 2 cases of speckled ground glass opacities were found. After 3 to 5 days of treatment, 2019-nCoV nucleic acid in a second respiratory sample turned negative in 6 cases. Among them, chest CT images showed less lesions in 2 cases, no lesion in 3 cases, and no improvement in 1 case. Other 9 cases were still positive in a second nucleic acid test. Six patients showed similar chest CT inflammation, while 3 patients had new lesions, which were all small nodular ground glass opacities. Conclusions: The early chest CT images of children with 2019-nCoV infection are mostly small nodular ground glass opacities. The clinical symptoms of children with 2019-nCoV infection are nonspecific. Dynamic reexamination of chest CT and nucleic acid are important.