The SARS-CoV-2 Spike is a virulence determinant and plays a major role on the attenuated phenotype of Omicron virus in a feline model of infection (preprint)

To assess the role of the Omicron BA.1 Spike (S) protein in the pathogenesis of the severe acute respiratory coronavirus 2 (SARS-CoV-2), we generated recombinant viruses harboring the S D614G mutation (rWA1-D614G) and the Omicron BA.1 S gene (rWA1-Omi-S) in the backbone of the ancestral SARS-CoV-2 WA1 strain genome. The recombinant viruses were characterized in vitro and in vivo. Viral entry, cell-cell fusion, viral plaque size, and viral replication kinetics of the rWA1-Omi-S virus were markedly impaired when compared to the rWA1-D614G virus, demonstrating a lower fusogenicity and ability to spread cell-to-cell of rWA1-Omi-S. To assess the contribution of the Omicron BA.1 S protein to SARS-CoV-2 pathogenesis the pathogenicity of rWA1-D614G and rWA1-Omi-S viruses were compared using a feline model of infection. While the rWA1-D614G-inoculated cats became lethargic and showed increased body temperatures on days 2 and 3 post-infection (pi), rWA1-Omi-S-inoculated cats remained subclinical and gained weight throughout the 14-day experimental period. Animals inoculated with rWA1-D614G presented higher levels of infectious virus shedding in nasal secretions, when compared to rWA1-Omi-S-inoculated animals. In addition, tissue replication of the rWA1-Omi-S was markedly reduced compared to the rWA1-D614G, as evidenced by lower in situ viral RNA and lower viral load in tissues on days 3 and 5 pi. Histologic examination of the nasal turbinate and lungs revealed intense inflammatory infiltration in rWA1-D614G-inoculated animals, whereas rWA1-Omi-S-inoculated cats presented only mild to modest inflammation. Together, these results demonstrate that the S protein is a major virulence determinant for SARS-CoV-2 playing a major role for the attenuated phenotype of the Omicron virus.

Spatial and temporal clustering of anti-SARS-CoV-2 antibodies in Illinois household cats, 2021- 2023 (preprint)

In this study, we evaluated the seroprevalence of SARS-CoV-2 antibodies in Illinois household cats from October 2021 to May 2023. Among 1,715 samples tested by serological assays, 244 samples (14%) tested positive. High-rate temporal, spatial, and space-time clusters of SARS-CoV-2 cases were assessed within 63 counties in Illinois. Three space-time clusters with higher than expected seroprevalence rates were identified in the northeastern, central-east, and southwest regions of Illinois, occurring between June and October 2022. Young cats had a higher rate of seropositivity compared to older cats, and the third quarter of the year had the highest seropositivity rate. This study provides an in-depth analysis of SARS-CoV-2 epidemiology in Illinois household cats, which will aid in COVID-19 control and prevention.

Assessing Tail Risk Via a Generalized Conditional Autoregressive Expectile Model (preprint)

This paper proposes a generalized conditional autoregressive expectile model, including autoregressive components in assessing tail risk, which can be treated as an infinite version of the conditional autoregressive expectile model proposed by Kuan, Yeh and Hsu (2009) and can be implemented as a vehicle for estimating the conditional autoregressive Value-at-Risk by regression quantiles model proposed in Engle and Manganelli (2004) and studied by Xiao and Koenker (2009). Due to the unobservable latent components in the proposed model, the quasi-maximum likelihood estimation method is suggested for estimating the relevant parameters, and a heteroskedasticity and autocorrelation consistent covariance matrix estimator is proposed. Furthermore, a dynamic expectile test is proposed for both in-sample model adequacy evaluation and out-of-sample forecasting for comparison purposes. Finally, Monte Carlo simulations and applications to real data are conducted to illustrate that the proposed methodology is practically useful. Particularly, our empirical study demonstrates that the tail risk characterized by the proposed model achieves a better performance, especially in the period of the Covid-19 epidemic.

Development of monoclonal antibody-based blocking ELISA for detecting SARS-CoV-2 exposure in animals (preprint)

The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a significant threat to public health. Besides humans, SARS-CoV-2 can infect several animal species. Highly sensitive and specific diagnostic reagents and assays are urgently needed for rapid detection and implementation of strategies for prevention and control of the infection in animals. In this study, we initially developed a panel of monoclonal antibodies (mAbs) against SARS-CoV-2 nucleocapsid (N) protein. To detect SARS-CoV-2 antibodies in a broad spectrum of animal species, a mAb-based bELISA was developed. Test validation using a set of animal serum samples with known infection status obtained an optimal percentage of inhibition (PI) cut-off value of 17.6% with diagnostic sensitivity of 97.8% and diagnostic specificity of 98.9%. The assay demonstrates high repeatability as determined by a low coefficient of variation (7.23%, 6.95%, and 5.15%) between-runs, within-run, and within-plate, respectively. Testing of samples collected over time from experimentally infected cats showed that the bELISA was able to detect seroconversion as early as 7 days post-infection. Subsequently, the bELISA was applied for testing pet animals with COVID-19-like symptoms and specific antibody responses were detected in two dogs. The panel of mAbs generated in this study provides a valuable tool for SARS-CoV-2 diagnostics and research. The mAb-based bELISA provides a serological test in aid of COVID-19 surveillance in animals.

Connecting SiO4 in Silicate and Silicate Chain Networks to Compute Kulli Temperature Indices.

A topological index is a numerical parameter that is derived mathematically from a graph structure. In chemical graph theory, these indices are used to quantify the chemical properties of chemical compounds. We compute the first and second temperature, hyper temperature indices, the sum connectivity temperature index, the product connectivity temperature index, the reciprocal product connectivity temperature index and the F temperature index of a molecular graph silicate network and silicate chain network. Furthermore, a QSPR study of the key topological indices is provided, and it is demonstrated that these topological indices are substantially linked with the physicochemical features of COVID-19 medicines. This theoretical method to find the temperature indices may help chemists and others in the pharmaceutical industry forecast the properties of silicate networks and silicate chain networks before trying.

Clinical course of patients with severe SARS-CoV-2 infection co-treatment with Jin Si Herbal Tea in Eastern Taiwan: A retrospective cohort study.

Introduction: Coronavirus disease-2019 (COVID-19) has affected more than 608 million people and has killed 6.5 million people in the world. A few studies showed traditional Chinese medicine can be beneficial for COVID-19 treatment. An herbal preparation Jin Si Herbal Tea (JS) was formulated with herbal extracts known for their potential to decrease spike protein and ACE2 interaction, 3CL, and TRPMSS2 protease activity, and thus aimed to evaluate the clinical course of JS co-treatment along with the usual treatment schedule given for severe COVID-19 patients. Methods: This retrospective cohort study included patients with severe COVID-19 admitted to Hualien Tzu Chi Hospital between June and July 2021. All the patients were co-treated with JS and the primary outcome was death. The secondary outcomes included laboratory exam, Ct value, clinical course, and hospital stays. There were 10 patients recruited in this study and divided into < 70 years and ≧ 70 years groups (n = 5 in each group). Results: Older patients (≧70 years) had a higher Charlson Comorbidity Index, VACO index, and lower hemoglobin levels than < 70 years patients. The trend of lymphocyte count, LDH, D-dimer, and Ct value of non-survivors was not consistent with previous studies. The death rate was 20% and the recovery rate to mild illness in 14 days was 40%. Conclusion: In conclusion, this is the first clinical study of JS co-treatment in severe COVID-19 patients. JS co-treatment might reduce death rate and recovery time. Further large-scale clinical trials would be expected.

The Omicron variant BA.1.1 presents a lower pathogenicity than B.1 D614G and Delta variants in a feline model of SARS-CoV-2 infection (preprint)

Omicron (B.1.1.529) is the most recent SARS-CoV-2 variant of concern (VOC), which emerged in late 2021 and rapidly achieved global predominance in early 2022. In this study, we compared the infection dynamics, tissue tropism and pathogenesis and pathogenicity of SARS-CoV-2 D614G (B.1), Delta (B.1.617.2) and Omicron BA.1.1 sublineage (B.1.1.529) variants in a highly susceptible feline model of infection. While D614G- and Delta-inoculated cats became lethargic, and showed increased body temperatures between days 1 and 3 post-infection (pi), Omicron-inoculated cats remained subclinical and, similar to control animals, gained weight throughout the 14-day experimental period. Intranasal inoculation of cats with D614G- and the Delta variants resulted in high infectious virus shedding in nasal secretions (up to 6.3 log10 TCID50.ml-1), whereas strikingly lower level of viruses shedding (<3.1 log10 TCID50.ml-1) was observed in Omicron-inoculated animals. In addition, tissue distribution of the Omicron variant was markedly reduced in comparison to the D614G and Delta variants, as evidenced by in situ viral RNA detection, in situ immunofluorescence, and quantification of viral loads in tissues on days 3, 5, and 14 pi. Nasal turbinate, trachea, and lung were the main - but not the only - sites of replication for all three viral variants. However, only scarce virus staining and lower viral titers suggest lower levels of viral replication in tissues from Omicron-infected animals. Notably, while D614G- and Delta-inoculated cats had severe pneumonia, histologic examination of the lungs from Omicron-infected cats revealed mild to modest inflammation. Together, these results demonstrate that the Omicron variant BA.1.1 is less pathogenic than D614G and Delta variants in a highly susceptible feline model.

Screening the Hub Genes and Analyzing the Mechanisms in Discharged COVID-19 Patients Retesting Positive through Bioinformatics Analysis (preprint)

Background: With the worldwide spread of COVID-19, people’s health and social order have been exposed to enormous risks. After encountering patients who test positive again after discharge, our study analyzed the pathogenesis to further assess the risk and possibility of virus reactivation. Methods: : A separate microarray was acquired from the Integrated Gene Expression System (GEO), and its samples were divided into two groups: a “convalescent-RTP” group consisting of recovery and “retesting-positive” (RTP) patients (group CR) and a “health-RTP” group consisting of healthy control and RTP patients (group HR). The enrichment analysis was performed with R software, obtaining the gene ontology (GO) and Kyoto pluripotent stem cells (KEGG) of the genes and genomes. Subsequently, the protein–protein interaction (PPI) networks of each group were established and the hub genes were discovered using the cytoHubba plug-in. Results: : In this study, 20 differentially expressed genes were identified, and 6622 genes were identified in the group CR, consisting of 5003 up-regulated and 1619 down-regulated genes. Meanwhile, 7335 genes were screened in the group HR, including 4323 up-regulated and 3012 down-regulated ones. The GO and KEGG analysis of the two groups revealed significant enrichment of these differentially expressed genes in pathways associated with immune response and apoptosis. In the PPI network constructed, 10 hub genes in group CR were identified, including TP53BP1, SNRPD1, SNRPD2, SF3B1, SNRNP200, MRPS16, MRPS9, CALM1, PPP2R1A, YWHAZ. Similarly, TP53BP1, RPS15, EFTUD2, MRPL16, MRPL17, MRPS14, RPL35A, MRPL32, MRPS6, POLR2G were selected as hub genes. Conclusions: : Using the messenger ribonucleic acid (mRNA) expression data from GSE166253, we explore the pathogenesis of retesting positive in COVID-19 from the immune mechanism and molecular level. We found TP53BP1, SNRPD1 and SNRPD2 as hub genes in RTP patients. Hence, their regulatory pathway is vital to the management and prognostic prediction of RTP patients, rendering the further study of these hub genes necessary.

Toward better purchase decision-performance: Linking person-environment fit to explorative and exploitative use of branded applications

Mobile applications (apps) have attracted increasing attention as an unprecedented opportunity for retailers. This study aims to explore how a branded app supports customers’ shopping decision during the COVID-19 (coronavirus) crisis. Integrating person-environment fit theory and the theory of exploitation and exploration, this study links person-app fit and person-brand fit to explorative use and exploitative use of a branded app, which both contribute to customer decision performance. Perceived fluency toward cross-channel integration positively moderates the fit-use linkages. Data obtained from 835 app users verify all of the proposed hypotheses. Results indicate that customers with different fits (person-app fit and person-brand fit) hold different thoughts toward their exploitative use and explorative use, which add equal value to support their decision making. Useful theoretical and practical implications are also provided for researchers and marketers interested in this area.

From people to Panthera: Natural SARS-CoV-2 infection in tigers and lions at the Bronx Zoo (preprint)

We describe the first cases of natural SARS-CoV-2 infection detected in animals in the United States. In March 2020, four tigers and three lions at the Bronx Zoo developed mild respiratory signs. SARS-CoV-2 RNA was detected by rRT-PCR in respiratory secretions and/or feces from all seven affected animals; viral RNA and/or antibodies were detected in their keepers. SARS-CoV-2 was isolated from respiratory secretions or feces from three affected animals; in situ hybridization co-localized viral RNA with cellular damage. Whole genome sequence and haplotype network analyses showed tigers and lions were infected with two different SARS-CoV-2 strains, suggesting independent viral introductions. The source of SARS-CoV-2 infection in the lions is unknown. Epidemiological data and genetic similarities between keeper and tiger viruses indicate human to animal transmission.

The Infectious Nature of Patient-Generated SARS-CoV-2 Aerosol (preprint)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission causing coronavirus disease 2019 (COVID-19) may occur through multiple routes. We collected aerosol samples around six patients admitted into mixed acuity wards in April of 2020 to identify the risk of airborne SARS-CoV-2. Measurements were made to characterize the size distribution of aerosol particles, and size-fractionated, aerosol samples were collected to assess the presence of infectious virus in particles sizes of >4.1 m, 1-4 m, and <1 m in the patient environment. Samples were analyzed by real-time reverse-transcriptase polymerase chain reaction (rRT-PCR), cell culture, western blot, and transmission electron microscopy (TEM). SARS-CoV-2 RNA was detected in all six rooms in all particle size fractions (>4.1 m, 1-4 m, and <1 m). Increases in viral RNA during cell culture of the virus from recovered aerosol samples demonstrated the presence of infectious, replicating virions in three <1 m aerosol samples (P<0.05). Viral replication of aerosol was also observed in the 1-4 m stage but did not reach statistical significance (0.05

Comparative Analysis of Clinical Characteristics in Children and Adults with 2019 Novel Coronavirus Infection: A Descriptive Study (preprint)

Background: Since December 2019, acute respiratory disease (ARD) caused by 2019 novel coronavirus (2019-nCoV) rapidly spread throughout China. Children and adults seemed to differ in the clinical course of the disease. The purpose of the current study is to comparatively analyze the clinical characteristics of children and adult patients with 2019-nCoV infection and to explore the possible causes for the discrepant aspects.Methods: In this retrospective study, the medical records of 32 cases confirmed with 2019-nCoV ARD from Xi'an eighth hospital (Shaanxi, China) from January 31 to February 16, 2020 were reviewed.Results: In all 32 patients contained 7 children and 25 adults. All children were family cluster. For adult patients, local residents of Wuhan, recently travelled to Wuhan, patient contacted with people from Wuhan were 14 (56%), 10 (40%), 1 (4%), respectively. The median incubation period of children and adult was 5 days (range, 3 to 12) and 4 days (range, 2 to 12), respectively. Altogether 10 (40%) adult patients had underlying conditions significantly, but no children had. Fever (Children 71.4% vs. Adult 96%) and cough (Children 71.4% vs. Adult 76%) were the most common symptoms in both groups. The third symptom observed in children was diarrhea and/or vomiting (57.1%), for adult it was myalgia or fatigue (52%). On admission, 5 (71.4%) children patients showed pneumonia roughly the same as adult patients (20, 80%), and that the two group shared a multitude of common imaging characteristics. 20% of adult with leucopoenia, but leukocytosis was significantly more frequently in children (28.6%, P=0.014). More children had elevated creatine kinase isoenzyme (57.1% vs. 4%, P=0.004). All patients were discharged after symptomatic treatment, including oxygen therapy, antiviral treatment, antibiotic treatment. Only one infant was intravenously injected low-dose glucocorticoids.Conclusions: Our results multi-dimensionally demonstrate that children with 2019-nCoV infection present a clinical picture which is often distinct from that of adults. Knowledge of these differences will be helpful for the clinical diagnosis of 2019 novel coronavirus diseases (COVID-19) and for a future discussion on age specific infection case definitions.