SARS-CoV-2 infection causes fibrotic pathogenesis through deregulating mitochondrial beta-oxidation (preprint)

The global high prevalence of COVID-19 is a major challenge for health professionals and patients. SARS-CoV-2 virus mutate predominantly in the spike proteins, whilst the other key viral components remain stable. Previous studies have shown that the human oral cavity can potentially act as reservoir of the SARS-CoV-2 virus. COVID-19 can cause severe oral mucosa lesions and is likely to be connected with poor periodontal conditions. However, the consequence of SARS-CoV-2 viral infection on human oral health has not been systematically examined. In this research, we aimed to study the pathogenicity of SARS-CoV-2 viral components on human periodontal tissues and cells. We found that by exposing to SARS-CoV-2, especially to the viral envelope and membrane proteins, the human periodontal fibroblasts could develop fibrotic pathogenic phenotypes, including hyperproliferation that was concomitant induced together with increased apoptosis and senescence. The fibrotic degeneration was mediated by a down-regulation of mitochondrial β-oxidation in the fibroblasts. Fatty acid β-oxidation inhibitor, etomoxir treatment could mirror the same pathological consequence on the cells, similar to SARS-CoV-2 infection. Our results therefore provide novel mechanistic insights into how SARS-CoV-2 infection can affect human periodontal health at the cell and molecular level with potential new therapeutic targets for COVID-19 induced fibrosis.

SARS-CoV-2 causes periodontal fibrosis by deregulating mitochondrial beta-oxidation (preprint)

The global high prevalence of COVID-19 is a major challenge for health professionals and patients. SARS-CoV-2 virus mutate predominantly in the spike proteins, whilst the other key viral components remain stable. Previous studies have shown that the human oral cavity can potentially act as reservoir of the SARS-CoV-2 virus and COVID-19 is likely to be connected with poor periodontal health. However, the consequence of SARS-CoV-2 viral infection on human oral health has not been systematically examined. In this research, we aimed to study the pathogenicity of SARS-CoV-2 viral components on human periodontal health. We found that human periodontal tissues, particularly the fibroblasts highly expressed ACE2 and TMPRSS2. Exposure to SARS-CoV-2, especially by the viral envelope and membrane proteins induced fibrotic pathogenic phenotypes, including periodontal fibroblast hyperproliferation, concomitant with increased apoptosis and senescence. The fibrotic degeneration was mediated by a down-regulation of mitochondrial {beta}-oxidation. Fatty acid beta-oxidation inhibitor, etomoxir treatment could mirror the same pathological consequence on the fibroblasts, similar to SARS-CoV-2 infection. Our results therefore provide novel mechanistic insights into how SARS-CoV-2 infection can affect human periodontal health at the cell and molecular level.

The impact of COVID-19 on pediatric adenoid hypertrophy in Beijing (preprint)

Objective: Since the outbreak of COVID-19, wearing masks and frequent hand washing have become common phenomena. The purpose of this study was to explore the impact of such lifestyle changes on adenoid hypertrophy in children in Beijing. Methods: Baidu Index platform was used to search with adenoid hypertrophy as the keyword, and the search volume of terms from 2017 to 2021 was recorded weekly. Meanwhile, the visits to adenoid hypertrophy in the otolaryngology department of Children’s Hospital, Capital Institute of Pediatrics in the same period were collected and compared, and analyzed. Results: (1) Baidu index indicated that the following group of adenoid hypertrophy was mainly parents of childbearing age, and female parents paid more attention;  (2) From 2017 to 2019, the online attention and outpatient visits to adenoid hypertrophy increased year by year. After the COVID-19 outbreak, the increasing trend declined and stagnated. Conclusions: After the outbreak of COVID-19, epidemic prevention policies (wearing masks, hand hygiene, reducing movement of people, etc.) have a certain inhibitory effect on adenoid hypertrophy.  Keywords: adenoid hypertrophy, COVID-19, Baidu Index platform, masks, hand hygiene Key points: Adenoid hypertrophy may be associated with recurrent respiratory infections in childhood. After the onset of COVID-19, China enacted many epidemic prevention policies. Wearing masks and hand hygiene may reduce the incidence of respiratory infections. Web data provides insight into the real needs of the population. After the onset of COVID, there was a stagnation in network attention and outpatient visit rates for adenoid hypertrophy.

Role of tannic acid against SARS-cov-2 cell entry by targeting the interface region between S-protein-RBD and human ACE2

Coronavirus disease 2019 (COVID-19) was caused by a new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 utilizes human angiotensin converting enzyme 2 (hACE2) as the cellular receptor of its spike glycoprotein (SP) to gain entry into cells. Consequently, we focused on the potential of repurposing clinically available drugs to block the binding of SARS-CoV-2 to hACE2 by utilizing a novel artificial-intelligence drug screening approach. Based on the structure of S-RBD and hACE2, the pharmacophore of SARS-CoV-2-receptor-binding-domain (S-RBD) -hACE2 interface was generated and used to screen a library of FDA-approved drugs. A total of 20 drugs were retrieved as S-RBD-hACE2 inhibitors, of which 16 drugs were identified to bind to S-RBD or hACE2. Notably, tannic acid was validated to interfere with the binding of S-RBD to hACE2, thereby inhibited pseudotyped SARS-CoV-2 entry. Experiments involving competitive inhibition revealed that tannic acid competes with S-RBD and hACE2, whereas molecular docking proved that tannic acid interacts with the essential residues of S-RBD and hACE2. Based on the known antiviral activity and our findings, tannic acid might serve as a promising candidate for preventing and treating SARS-CoV-2 infection.

Oridonin Inhibits SARS‐CoV‐2 by Targeting Its 3C‐Like Protease

Oridonin Inhibits SARS‐CoV‐2 Oridonin, a natural product extracted from Rabdosia rubescens, possesses a wide range of pharmacological properties, including anti‐inflammatory, anti‐cancer, anti‐microbial, neuroprotection, immunoregulation, etc. In article number 2100124, Baisen Zhong, Litao Sun, and co‐workers demonstrate that Oridonin targets the SARS‐CoV‐2 3CL protease by covalently binding to cysteine145 in its active pocket to exert an anti‐SARS‐CoV‐2 effect, which provides a novel candidate for the treatment of COVID‐19. © 2022 WILEY‐VCH GmbH

Proteomic and Metabolomic Characterization of SARS-CoV-2-Infected Cynomolgus Macaque at Early Stage

Although tremendous effort has been exerted to elucidate the pathogenesis of severe COVID-19 cases, the detailed mechanism of moderate cases, which accounts for 90% of all patients, remains unclear yet, partly limited by lacking the biopsy tissues. Here, we established the COVID-19 infection model in cynomolgus macaques (CMs), monitored the clinical and pathological features, and analyzed underlying pathogenic mechanisms at early infection stage by performing proteomic and metabolomic profiling of lung tissues and sera samples from COVID-19 CMs models. Our data demonstrated that innate immune response, neutrophile and platelet activation were mainly dysregulated in COVID-19 CMs. The symptom of neutrophilia, lymphopenia and massive “cytokines storm”, main features of severe COVID-19 patients, were greatly weakened in most of the challenged CMs, which are more semblable as moderate patients. Thus, COVID-19 model in CMs is rational to understand the pathogenesis of moderate COVID-19 and may be a candidate model to assess the safety and efficacy of therapeutics and vaccines against SARS-CoV-2 infection.

A cocktail containing two synergetic antibodies broadly neutralizes SARS-CoV-2 and its variants including Omicron BA.1 and BA.2 (preprint)

Neutralizing antibodies (NAbs) can prevent and treat infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, continuously emerging variants, such as Omicron, have significantly reduced the potency of most known NAbs. The selection of NAbs with broad neutralizing activities and the identification of conserved critical epitopes are still urgently needed. Here, we identified an extremely potent antibody (55A8) by single B-cell sorting from convalescent SARS-CoV-2-infected patients that recognized the receptor-binding domain (RBD) in the SARS-CoV-2 spike (S) protein. 55A8 could bind to wild-type SARS-CoV-2, Omicron BA.1 and Omicron BA.2 simultaneously with 58G6, a NAb previously identified by our group. Importantly, an antibody cocktail containing 55A8 and 58G6 (2-cocktail) showed synergetic neutralizing activity with a half-maximal inhibitory concentration (IC50) in the picomolar range in vitro and prophylactic efficacy in hamsters challenged with Omicron (BA.1) through intranasal delivery at an extraordinarily low dosage (25 g of each antibody daily) at 3 days post-infection. Structural analysis by cryo-electron microscopy (cryo-EM) revealed that 55A8 is a Class III NAb that recognizes a highly conserved epitope. It could block angiotensin-converting enzyme 2 (ACE2) binding to the RBD in the S protein trimer via steric hindrance. The epitopes in the RBD recognized by 55A8 and 58G6 were found to be different and complementary, which could explain the synergetic mechanism of these two NAbs. Our findings not only provide a potential antibody cocktail for clinical use against infection with current SARS-CoV-2 strains and future variants but also identify critical epitope information for the development of better antiviral agents.

Investigating dynamic relations between factual information and misinformation: Empirical studies of tweets related to prevention measures during COVID‐19

During COVID‐19, misinformation on social media has affected people's adoption of appropriate prevention behaviors. Although an array of approaches have been proposed to suppress misinformation, few have investigated the role of disseminating factual information during crises. None has examined its effect on suppressing misinformation quantitatively using longitudinal social media data. Therefore, this study investigates the temporal correlations between factual information and misinformation, and intends to answer whether previously predominant factual information can suppress misinformation. It focuses on two prevention measures, that is, wearing masks and social distancing, using tweets collected from April 3 to June 30, 2020, in the United States. We trained support vector machine classifiers to retrieve relevant tweets and classify tweets containing factual information and misinformation for each topic concerning the prevention measures’ effects. Based on cross‐correlation analyses of factual and misinformation time series for both topics, we find that the previously predominant factual information leads the decrease of misinformation (i.e., suppression) with a time lag. The research findings provide empirical understandings of dynamic relations between misinformation and factual information in complex online environments and suggest practical strategies for future misinformation management during crises and emergencies.

Empirical studies of tweets related to prevention measures during COVID-19

Abstract During COVID-19, misinformation on social media has affected people's adoption of appropriate prevention behaviors. Although an array of approaches have been proposed to suppress misinformation, few have investigated the role of disseminating factual information during crises. None has examined its effect on suppressing misinformation quantitatively using longitudinal social media data. Therefore, this study investigates the temporal correlations between factual information and misinformation, and intends to answer whether previously predominant factual information can suppress misinformation. It focuses on two prevention measures, that is, wearing masks and social distancing, using tweets collected from April 3 to June 30, 2020, in the United States. We trained support vector machine classifiers to retrieve relevant tweets and classify tweets containing factual information and misinformation for each topic concerning the prevention measures? effects. Based on cross-correlation analyses of factual and misinformation time series for both topics, we find that the previously predominant factual information leads the decrease of misinformation (i.e., suppression) with a time lag. The research findings provide empirical understandings of dynamic relations between misinformation and factual information in complex online environments and suggest practical strategies for future misinformation management during crises and emergencies.

Continuous Renal Replacement Therapy with oXiris Filter May Not Be an Effective Resolution to Alleviate Cytokine Release Syndrome in non-AKI Patients with Severe and Critical COVID-19 (preprint)

Background: In this study, we aimed to determine whether continuous renal replacement therapy (CRRT) with oXiris filter may alleviate cytokine release syndrome (CRS) in non-AKI patients with severe and critical coronavirus disease 2019 (COVID-19). Methods: Non-AKI patients with severe and critical COVID-19 treated between February 14 and March 26, 2020 were included and randomly divided into intervention group and control group according to the random number table. Patients in the intervention group received CRRT with oXiris filter plus conventional treatment, while those in the control group only received conventional treatment. Demographic data were collected and collated at admission. During ICU hospitalization, the serum levels of cytokine and inflammatory chemokines, including IL-2, IL-4, IL-6, IL-10, TNF-α, and IFN-γ, were measured daily to reflect the degree of CRS induced by SARS-CoV-2 infection. Clinical data, including white blood cell count (WBC), neutrophil proportion (NEUT%), lymphocyte count (LYMPH), lymphocyte percentage (LYM%), platelet (PLT), C-reaction protein (CRP), high sensitivity C-reactive protein (hs-CRP), alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bilirubin (TB), albumin (ALB), serum creatinine (SCr), D-Dimer, fibrinogen (FIB), IL-2, IL-4, IL-6, IL-10, TNF-α, IFN-γ, number of hospital days and sequential organ failure assessment (SOFA) score were obtained and collated from medical records during hospitalization, and then compared between the two groups. Results: Age, and SCr significantly differed between the two groups. Besides the IL-2 level that was significantly lower on day 2 than that on day 1 in the intervention group, and the IL-6 levels that were significantly higher on day 1, and day 2 in the intervention group compared to the control group, similar to the IL-10 level on day 5, there were no significant differences between the groups. Conclusion: CRRT with oXiris filter may not effectively alleviate CRS in non-AKI patients with severe and critical COVID-19. Thus, its application in these patients should be considered with caution to avoid increasing the unnecessary burden on society and individuals and making the already overwhelmed medical system even more strained (IRB number: IRB-AF/SC-04).

Ultrapotent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants (preprint)

Accumulating mutations in the SARS-CoV-2 Spike (S) protein can increase the possibility of immune escape, challenging the present COVID-19 prophylaxis and clinical interventions. Here, 3 receptor binding domain (RBD) specific monoclonal antibodies (mAbs), 58G6, 510A5 and 13G9, with high neutralizing potency blocking authentic SARS-CoV-2 virus displayed remarkable efficacy against authentic B.1.351 virus. Each of these 3 mAbs in combination with one neutralizing Ab recognizing non-competing epitope exhibited synergistic effect against authentic SARS-CoV-2 virus. Surprisingly, structural analysis revealed that 58G6 and 13G9, encoded by the IGHV1-58 and the IGKV3-20 germline genes, both recognized the steric region S470-495 on the RBD, overlapping the E484K mutation presented in B.1.351. Also, 58G6 directly bound to another region S450-458 in the RBD. Significantly, 58G6 and 510A5 both demonstrated prophylactic efficacy against authentic SARS-CoV-2 and B.1.351 viruses in the transgenic mice expressing human ACE2 (hACE2), protecting weight loss and reducing virus loads. These 2 ultrapotent neutralizing Abs can be promising candidates to fulfill the urgent needs for the prolonged COVID-19 pandemic.

Ultrapotent SARS-CoV-2 neutralizing antibodies effectively block new-emerging mutational variants (preprint)

Accumulating mutations on SARS-CoV-2 Spike (S) protein may increase the possibility of immune escape, challenging the present COVID-19 prophylaxis and clinical interventions. Here, in a panel of receptor binding domain (S-RBD) specific monoclonal antibodies (mAbs) with high neutralizing potency against authentic SARS-CoV-2, at least 6 of them were found to efficiently block the pseudovirus of 501Y.V2, a highly transmissible SARS-CoV-2 variant with escape mutations. The top 3 neutralizing Abs (13G9, 58G6 and 510A5) exhibited comparative ultrapotency as those being actively pursued for clinical development. Interestingly, the antigenic sites for the majority of our neutralizing Abs overlapped with a single epitope (13G9e) on S-RBD. Further, the 3-dimensional structures of 2 ultrapotent neutralizing Abs 13G9 or 58G6 in complex with SARS-CoV-2 S trimer demonstrated that both Abs bound to a steric region within S472–490. Moreover, a specific linear region (S450–457) was identified as an additional target for 58G6. Importantly, our cryo-electron microscopy (cryo-EM) analysis revealed a unique phenomenon that the S-RBDs interacting with the fragments of antigen binding (Fabs) of 13G9 or 58G6 encoded by the IGHV1-58 and the IGKV3-20 gene segments were universally in the ‘up’ conformation in all observed particles. The potent neutralizing Abs presented in the current study may be promising candidates to fulfill the urgent needs for the current pandemic of SARS-CoV-2, and may of fundamental value for the next-generation vaccine development.

High resolution computed tomography for the diagnosis of 2019 novel coronavirus (2019-nCoV) pneumonia: a study from multiple medical centers in western China.

BACKGROUND: To evaluate the role of high-resolution computed tomography (HRCT) in the diagnosis of 2019 novel coronavirus (2019-nCoV) pneumonia and to provide experience in the early detection and diagnosis of 2019-nCoV pneumonia. METHODS: Seventy-two patients confirmed to be infected with 2019-nCoV from multiple medical centers in western China were retrospectively analyzed, including epidemiologic characteristics, clinical manifestations, laboratory findings and HRCT chest features. RESULTS: All patients had lung parenchymal abnormalities on HRCT scans, which were mostly multifocal in both lungs and asymmetric in all patients, and were mostly in the peripheral or subpleural lung regions in 52 patients (72.22%), in the central lung regions in 16 patients (22.22%), and in both lungs with "white lung" manifestations in 4 patients (5.56%). Subpleural multifocal consolidation was a predominant abnormality in 38 patients (52.78%). Ground-glass opacity was seen in 34 patients (47.22%). Interlobular septal thickening was found in 18 patients, 8 of whom had only generally mild thickening with no zonal predominance. Reticulation was seen in 8 patients (11.11%), and was mild and randomly distributed. In addition, both lungs of 28 patients had 2 or 3 CT imaging features. Out of these 72 patients, 36 were diagnosed as early stage, 32 patients as progressive stage, and 4 patient as severe stage pneumonia. Moreover, the diagnostic accuracy of HRCT features combined with epidemiological history was not significantly different from the detection of viral nucleic acid (all P >0.05). CONCLUSIONS: The HRCT features of 2019-nCoV pneumonia are characteristic to a certain degree, which when combined with epidemiological history yield high clinical value in the early detection and diagnosis of 2019-nCoV pneumonia.

Clinical features and imaging findings in six coronavirus disease 2019 patients

Objective To summarize the clinical features and imaging findings of six coronavirus disease 2019 (COVID-19) patients, so as to provide evidences for early diagnosis and clinical intervention. Methods Six COVID-19 patients with positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were enrolled from the Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine from Jan. 1 to Feb. 22, 2020. The epidemiological history, clinical manifestations, imaging data and laboratory indicators were retrospectively analyzed. Results All six patients had a clear travel or residence history in Wuhan. Four patients had fever, three had cough, two had upper respiratory tract symptoms such as runny nose and sore throat, and two had systemic symptoms such as headache and muscle ache. Chest computed tomography (CT) showed that all the six patients had abnormal manifestations in bilateral lungs, and the lower lung lesions were more common than the upper lung lesions. The main manifestations were multiple ground-glass opacities, consolidation shadows, crazy paving sign and different degrees of fibrosis in lateral field of bilateral lungs. Chest CT examination later after onset showed lung consolidation and severe fibrosis. Conclusion The imaging of COVID-19 has special characteristics. Combined with the epidemiological history, clinical manifestations and the detection of SARS-CoV-2 nucleic acid, COVID-19 can be effectively diagnosed in the early stage.

Accurately Differentiating COVID-19, Other Viral Infection, and Healthy Individuals Using Multimodal Features via Late Fusion Learning (preprint)

Effectively identifying COVID-19 patients using non-PCR clinical data is critical for the optimal clinical outcomes. Currently, there is a lack of comprehensive understanding of various biomedical features and appropriate technical approaches to accurately detecting COVID-19 patients. In this study, we recruited 214 confirmed COVID-19 patients in non-severe (NS) and 148 in severe (S) clinical type, 198 non-infected healthy (H) participants and 129 non-COVID viral pneumonia (V) patients. The participants' clinical information (23 features), lab testing results (10 features), and thoracic CT scans upon admission were acquired as three input feature modalities. To enable late fusion of multimodality data, we developed a deep learning model to extract a 10-feature high-level representation of the CT scans. Exploratory analyses showed substantial differences of all features among the four classes. Three machine learning models (k-nearest neighbor kNN, random forest RF, and support vector machine SVM) were developed based on the 43 features combined from all three modalities to differentiate four classes (NS, S, V, and H) at once. All three models had high accuracy to differentiate the overall four classes (95.4%-97.7%) and each individual class (90.6%-99.9%). Multimodal features provided substantial performance gain from using any single feature modality. Compared to existing binary classification benchmarks often focusing on single feature modality, this study provided a novel and effective breakthrough for clinical applications. Findings and the analytical workflow can be used as clinical decision support for current COVID-19 and other clinical applications with high-dimensional multimodal biomedical features.

Proteomic Profiling in Biracial Cohorts Implicates DC-SIGN as a Mediator of Genetic Risk in COVID-19 (preprint)

COVID-19 is one of the most consequential pandemics in the last century, yet the biological mechanisms that confer disease risk are incompletely understood. Further, heterogeneity in disease outcomes is influenced by race, though the relative contributions of structural/social and genetic factors remain unclear. Very recent unpublished work has identified two genetic risk loci that confer greater risk for respiratory failure in COVID-19: the ABO locus and the 3p21.31 locus. To understand how these loci might confer risk and whether this differs by race, we utilized proteomic profiling and genetic information from three cohorts including black and white participants to identify proteins influenced by these loci. We observed that variants in the ABO locus are associated with levels of CD209/DC-SIGN, a known binding protein for SARS-CoV and other viruses, as well as multiple inflammatory and thrombotic proteins, while the 3p21.31 locus is associated with levels of CXCL16, a known inflammatory chemokine. Thus, integration of genetic information and proteomic profiling in biracial cohorts highlights putative mechanisms for genetic risk in COVID-19 disease.

The SARS-CoV-2 receptor-binding domain elicits a potent neutralizing response without antibody-dependent enhancement (preprint)

The SARS-coronavirus 2 (SARS-CoV-2) spike (S) protein mediates entry of SARS-CoV-2 into cells expressing the angiotensin-converting enzyme 2 (ACE2). The S protein engages ACE2 through its receptor-binding domain (RBD), an independently folded 197-amino acid fragment of the 1273-amino acid S-protein protomer. Antibodies to the RBD domain of SARS-CoV (SARS-CoV-1), a closely related coronavirus which emerged in 2002-2003, have been shown to potently neutralize SARS-CoV-1 S-protein-mediated entry, and the presence of anti-RBD antibodies correlates with neutralization in SARS-CoV-2 convalescent sera. Here we show that immunization with the SARS-CoV-2 RBD elicits a robust neutralizing antibody response in rodents, comparable to 100 {micro}g/ml of ACE2-Ig, a potent SARS-CoV-2 entry inhibitor. Importantly, anti-sera from immunized animals did not mediate antibody-dependent enhancement (ADE) of S-protein-mediated entry under conditions in which Zika virus ADE was readily observed. These data suggest that an RBD-based vaccine for SARS-CoV-2 could be safe and effective.