Oral Ursodeoxycholic Acid Therapy Failed to Mitigate SARS-CoV-2 Omicron Variants BA.5.2 Infection (preprint)

Background Ursodeoxycholic acid (UDCA) was reported to reduce susceptibility to SARS-CoV-2 infection by downregulating farnesoid X receptor (FXR) -ACE2 signaling. However, we found a different story in real-world clinical studies.Objectives We attempted to verify whether UDCA can effectively prevent SARS-CoV-2 transmission or have positive therapeutic effects in a real-world clinical study.Methods We performed a retrospective study, collected and assessed clinical presentation and laboratory data on patients with liver diseases infected with SARS-CoV-2 Omicron sub-variant BA.5.2 who had been treated with or without UDCA.Results Treatment with UDCA did not prevent infection with the Omicron sub-variant BA.5.2, failed in reducing the duration of infection and hardly mitigated the severity of COVID-19. Meanwhile, the severity of liver diseases, especially TBil, ALP, γ-GT, liver cirrhosis and Child-Pugh classification, should be considered as risk factors for severe COVID-19 in chronic hepatic patients.Conclusion UDCA failed to show inhibitory effects against SARS-CoV-2 infection in complex clinical settings. The regulatory mechanism of the novel UDCA-FXR-ACE2 pathway needs to be further investigated in real-world clinical studies.

First close insight into global daily gapless 1 km PM2.5 pollution, driving factors, and health impact (preprint)

Fine particulate matter (PM2.5) is the largest environmental risk factor impacting human health. While PM2.5 has been measured widely across the world, there has been no high-resolution and gapless global PM2.5 data on a daily scale. We generate a global daily PM2.5 concentration at 1 km resolution using satellite gap-filled aerosol products and machine learning. Daily PM2.5 retrievals agreed well with ground measurements, with sample-, space-, and time-based cross-validated correlations of 0.93, 0.89, and 0.88, respectively. This enables us to unprecedentedly monitor the day-to-day variations of PM2.5, exposure risk, and mortality burden around the globe. More than 96% of the days exceeded the World Health Organization (WHO) recommended daily air quality guidelines (AQG) level (15 μg m-3) in 2020, and 99% of populated areas were exposed to PM2.5 risk at least one day; in particular, the proportions are 91% and 64% similarly in 7 and 30 days, respectively. The annual population-weighted mean PM2.5 concentration was 27.6 μg m-3 (~5.5 times higher than the WHO annual AQG level of 5 μg m-3), resulting in estimated premature deaths of ~4.2 million people and accounting for ~6.6% of total global deaths. Substantial differences are noted in many parts of the world between 2019 and 2020 associated with widespread episodes of wildfires or the COVID-19 shutdowns. The overall air quality in 2020 was significantly better than in 2019 in more than 70% of major cities. The global population-weighted mean PM2.5 decreased by ~5.1%, and the associated number of premature deaths dropped by 56,700.

A general urban spreading pattern of COVID-19 and its underlying mechanism

Currently, the global situation of COVID-19 is aggravating, pressingly calling for efficient control and prevention measures. Understanding the spreading pattern of COVID-19 has been widely recognized as a vital step for implementing non-pharmaceutical measures. Previous studies explained the differences in contagion rates due to the urban socio-political measures, while fine-grained geographic urban spreading pattern still remains an open issue. Here, we fill this gap by leveraging the trajectory data of 197,808 smartphone users (including 17,808 anonymous confirmed cases) in nine cities in China. We find a general spreading pattern in all cities: the spatial distribution of confirmed cases follows a power-law-like model and the spreading centroid human mobility is time-invariant. Moreover, we reveal that long average traveling distance results in a high growth rate of spreading radius and wide spatial diffusion of confirmed cases in the fine-grained geographic model. With such insight, we adopt the Kendall model to simulate the urban spreading of COVID-19 which can well fit the real spreading process. Our results unveil the underlying mechanism behind the spatial-temporal urban evolution of COVID-19, and can be used to evaluate the performance of mobility restriction policies implemented by many governments and to estimate the evolving spreading situation of COVID-19.

Glyco-engineered pentameric SARS-CoV-2 IgMs show superior activities compared to IgG1 orthologues (preprint)

Immunoglobulin M (IgM) is the largest antibody isotype with unique features like extensive glycosylation and oligomerization. Major hurdles in characterizing its properties are difficulties in the production of well-defined multimers. Here we report the expression of two SARS-CoV-2 neutralizing monoclonal antibodies in glycoengineered plants. Isotype switch from IgG1 to IgM resulted in the production of pentameric IgMs, comprising of correctly assembled 21 human protein subunits. All four recombinant monoclonal antibodies carried a highly reproducible human-type N-glycosylation profile, with a single dominant N-glycan species at each glycosite. Both pentameric IgMs exhibited increased antigen binding and virus neutralization potency, up to 390-fold, compared to the parental IgG1. Collectively, the results may impact on the future design of vaccines, diagnostics and antibody-based therapies and emphasize the versatile use of plants for the expression of highly complex human proteins with targeted posttranslational modifications.

Two doses of mRNA vaccine elicit cross-neutralizing memory B-cells against SARS-CoV-2 Omicron variant (preprint)

SARS-CoV-2 Beta and Omicron variants have multiple mutations in the receptor-binding domain (RBD) allowing antibody evasion. Despite the resistance to circulating antibodies in those who received two doses of mRNA vaccine, the third dose prominently recalls cross-neutralizing antibodies with expanded breadth to these variants. Herein, we longitudinally profiled the cellular composition of persistent memory B-cell subsets and their antibody reactivity against these variants following the second vaccine dose. The vaccination elicited a memory B-cell subset with resting phenotype that dominated the other subsets at 4.9 months. Notably, most of the resting memory subset retained the ability to bind the Beta variant, and the memory-derived antibodies cross-neutralized the Beta and Omicron variants at frequencies of 59% and 29%, respectively. The preservation of cross-neutralizing antibody repertoires in the durable memory B-cell subset likely contributes to the prominent recall of cross-neutralizing antibodies following the third dose of the vaccine. One Sentence Summary Fully vaccinated individuals preserve cross-neutralizing memory B-cells against the SARS-CoV-2 Omicron variant.

Treatment Effects of Integrated TCM and Western Medicine Treatment Scheme on COVID-19: A Single-armed Clinical Trial

Backgroud : The outbreak of COVID-19 has brought unprecedented perils to human health and raised public health concerns in more than two hundred countries. Safe and effective treatment scheme is needed urgently. Objective : To evaluate the effects of integrated TCM and western medicine treatment scheme on COVID-19. Methods : A single-armed clinical trial was carried out in Hangzhou Xixi Hospital, an affiliated hospital with Zhejiang Chinese Medical University. 102 confirmed cases were screened out from 725 suspected cases and 93 of them were treated with integrated TCM and western medicine treatment scheme. Results : 83 cases were cured, 5 cases deteriorated, and 5 cases withdrew from the study. No deaths were reported. The mean relief time of fever, cough, diarrhea, and fatigue were (4.78±4.61) days, (7.22±4.99) days, (5.28± 3.39) days, and (5.28± 3.39) days, respectively. It took (14.84±5.50) days for SARS-CoV-2 by nucleic acid amplification-based testing to turn negative. Multivariable cox regression analysis revealed that age, BMI, PISCT, BPC, AST, CK, BS, and UPRO were independent risk factors for COVID-19 treatment. Conclusion : Our study suggested that integrated TCM and western medicine treatment scheme was effective for COVID-19.

Distinct immune cell dynamics mark adverse events and antibody responses of SARS-CoV-2 mRNA vaccine (preprint)

Pfizer/BioNTec BNT162b2 mRNA vaccine robustly elicits neutralizing antibodies against SARS-CoV-2 in clinical trials and real-world settings. However, booster vaccinations are frequently associated with self-limited adverse events. Here, by applying a high-dimensional immune profiling approach to peripheral blood, we linked early vaccine-induced immune dynamics with adverse events and neutralizing antibody responses. The dynamics of two dendritic cell subsets (DC3s and AS-DCs) were identified as the specific correlates for adverse events; the combination of these cell dynamics stratified the vaccinees with severe reactogenicity, while the stratification did not affect the neutralizing antibody titers. Furthermore, the NKT-like cell dynamics that correlated with adverse events and antibody titers were accounted for distinct magnitudes of both events by sex and age. The identified immune correlates for adverse events and antibody responses may pave the way for a rational vaccine strategy for reducing the reactogenicity of mRNA vaccines without compromising the immunogenicity.

Broad Neutralization Activity of SARS-CoV-2 Antibody is Achieved by Coordinated Recognition of Virus Vulnerable Site (preprint)

Potently neutralizing SARS-CoV-2 antibodies often target the receptor binding site (RBS) of spike protein but the variability of RBS epitopes hampers broad neutralization of different clades of coronaviruses and emerging drifted viruses. Here, we identified a human RBS antibody that potently neutralizes SARS-CoV and SARS-CoV-2 variants that belong to clade 1 SARS-related coronavirus. X-ray crystallography revealed coordinated recognition by the heavy chain to conserved sites and the light chain to RBS, allowing for the mimicry of ACE2 binding mode. The minimum footprints in the hypervariable region of RBS contributed to the breadth of neutralization, and the activity was further enhanced by IgG3 switching. Eventually, the coordinated binding resulted in broad neutralization of SARS-CoV and emerging SARS-CoV-2 variants of concern. Furthermore, therapeutic treatment in a hamster model provided protection at low dosage. The structural basis for broadly neutralizing activity informs the design of broad spectrum of therapeutics and vaccines.Funding: This work was supported by Japan Agency for Medical Research and Development grant JP19fk0108111 (TH, YT), JP20fk0108298 (TK, TH, KM, YT), JP20am0101093 (KM), JP20ae0101047 (KM), JP20fk0108251 (HS), and JP20am0101124 (YK), by Ministry of Education, Culture, Sports, Science and Technology grant JPMXS0420100119 (KM) and 20H05773 (TH), by The Naito Foundation (TH), and by Joint Usage/Research Center program of Institute for Frontier Life and Medical Sciences, Kyoto University (KM).Conflict of Interest: AS is an employee of Shionogi & Co., Ltd. MO is a CEO, employee, and shareholder of Trans Chromosomics, Inc. These authors acknowledge a potential conflict of interest and attest that the work contained in this report is free of any bias that might be associated with the commercial goals of the company. TO, YA, MO, TH, KM, and YT declare that an intellectual property application has been filed using the data presented in this paper. The other authors declare that they have no competing interests.Ethical Approval: Animal procedures were approved by the Animal Ethics Committee of the National Institute of Infectious Diseases, Japan, and performed in accordance with the guidelines of the Institutional Animal Care and Use Committee. In vitro escape mutation screening experiments for SARSCoV-2 were performed at the Biosafety Level-3 facility of the Research Center for ZoonosisControl, Hokkaido University, and the National Institute of Infectious Diseases following the institutional guidelines.

SUMOylation restrains ACE2 degradation through TOLLIP-mediated selective autophagy to facilitate the host susceptibility to SARS-CoV-2 infection (preprint)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Alongside investigations into the virology of SARS-CoV-2, understanding the host–virus dependencies are vital for the identification and rational design of effective antiviral therapy. Here, we report the dominant SARS-CoV-2 entry receptor, ACE2, conjugates with small ubiquitin-like modifier 3 (SUMO3) through a proteome-wide protein interaction analysis. We further demonstrate that E3 SUMO ligase PIAS4 prompts the SUMOylation and stabilization of ACE2, whereas deSUMOylation enzyme SENP3 reverses this process. Conjugation of SUMO3 with ACE2 at lysine (K) 187 hampers the K48-linked ubiquitination of ACE2, thus suppressing its subsequent cargo receptor TOLLIP-dependent autophagic degradation. Pharmacological intervention of ACE2 SUMOylation blocks the entry of SARS-CoV-2 and viral infection-triggered immune responses. Collectively, our findings suggest selective autophagic degradation of ACE2 orchestrated by SUMOylation and ubiquitination can be targeted to future antiviral therapy of SARS-CoV-2.

Impact of blood analysis and immune function on the prognosis of patients with COVID-19 (preprint)

Introduction: This retrospective study investigated the implications of changes in blood parameters and cellular immune function in patients with 2019-coronavirus infected disease (COVID-19). Methods: Records were reviewed of 85 patients with COVID-19 between February 4 and 16, 2020. The primary outcome was in-hospital mortality at 28 days. Results: Fourteen patients died. The baseline leukocyte count, neutrophil count and hemoglobin was significantly higher in non-survivors compared with survivors, while the reverse was true of lymphocyte count, platelet, PaO2/FiO2, CD3+ count and CD4+ count. The percentage of neutrophil count > 6.3*109/L in death group was significantly higher than that in survival group, and multivariate logistic regression showed neutrophil count was independently associated with mortality. However, there were not significant difference in IgG, IgM, IgA, C3, C4 and the percentage of IgE > 100 IU/ml between the death group and survival group. Areas under the receiver operating characteristic curves of the following at baseline could significantly predict mortality: leukocyte, neutrophil, lymphocyte, CD3+ and CD4+ counts. Conclusions: For patients with COVID-19, lymphocyte, CD3+ and CD4+ counts that marked decrease suggest a poor outcome. A high neutrophil count is independently associated with mortality. At admission, leukocyte, neutrophil, lymphocyte, CD3+ and CD4+ counts should receive added attention.

Reporting the life tracks of confirmed cases can effective prevent and control the COVID-19 outbreak in China (preprint)

Background: Since late December 2019, a novel coronavirus (COVID-19) has emerged in Wuhan and rapidly spread throughout China. Fears were raised higher, effective policies for prevention and control were concerned. Methods: Till March 3, 91273 confirmed COVID-19 cases were included in. Using Mann-Whitney U test, the provinces that reported the life tracks of confirmed cases to public had lower increased in daily new confirmed cases. Results: Compared with the paired province, Tianjin, Jilin, Gansu, Shanxi, Hainan and Guizhou had significant differences in the number of new confirmed cases and have lower mean rank (P<0.05). Shanghai had a lower mean rank (P=0.175) but no significant difference. Besides, the successful prevention and control work need other effective strategies, such as real time media coverage, isolating the suspected cases or close contacts, delaying the return of work, closing schools, wearing facial masks, and disinfecting the communities, et.al. Conclusions: Strategies must be adjusted in real time according to the epidemic. Reporting the life tracks of confirmed cases was an effective way to control the epidemic. They may be suggestions to other counties with an outbreak of COVID-19.

Characterization of anti-viral immunity in recovered individuals infected by SARS-CoV-2 (preprint)

The WHO has declared SARS-CoV-2 outbreak a public health emergency of international concern. However, to date, there was hardly any study in characterizing the immune responses, especially adaptive immune responses to SARS-CoV-2 infection. In this study, we collected blood from COVID-19 patients who have recently become virus-free and therefore were discharged, and analyzed their SARS-CoV-2-specific antibody and T cell responses. We observed SARS-CoV-2-specific humoral and cellular immunity in the patients. Both were detected in newly discharged patients, suggesting both participate in immune-mediated protection to viral infection. However, follow-up patients (2 weeks post discharge) exhibited high titers of IgG antibodies, but with low levels of virus-specific T cells, suggesting that they may enter a quiescent state. Our work has thus provided a basis for further analysis of protective immunity to SARS-CoV-2, and understanding the pathogenesis of COVID-19, especially in the severe cases. It has also implications in designing an effective vaccine to protect and treat SARS-CoV-2 infection.