Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein driving the genesis of Omicron variants (preprint)

Continued evolution of SARS-CoV-2 generates variants to challenge antibody immunity established by infection and vaccination. A connection between population immunity and genesis of virus variants has long been suggested but its molecular basis remains poorly understood. Here, we identify a class of SARS-CoV-2 neutralising public antibodies defined by their shared usage of VL6-57 light chains. Although heavy chains of diverse genotypes are utilized, convergent HCDR3 rearrangements have been observed among these public antibodies to cooperate with germline VL6-57 LCDRs to target a convergent epitope defined by RBD residues S371-S373-S375. Antibody repertoire analysis identifies that this class of VL6-57 antibodies is present in SARS-CoV-2-naive individuals and is clonally expanded in most COVID-19 patients. We confirm that Omicron specific substitutions at S371, S373 and S375 mediate escape of antibodies of the VL6-57 class. These findings support that this class of public antibodies constitutes immune pressure promoting the introduction of S371L/F-S373P-S375F in Omicron variants. The results provide further molecular evidences to support that antigenic evolution of SARS-CoV-2 is driven by antibody mediated population immunity.

Identification of potentional immunological biomarkers of COVID-19 by blood transcriptome analysis (preprint)

Backgroud:The COVID-19 pandemic has swept the globe since 2019, threatening people's health. Many studies indicate that infection is closely related to immune response disorder. We searched for potential immune-related biomarkers through systems biological analysis, and performed immune infiltration analysis on relevant data. Methods and findings: We used CIBERSORT to analyze the blood transcriptomics data of the controls, the mild COVID-19 patients, and the severe COVID-19 patients. And we further obtained the essential infiltration immune cells of COVID-19 by the Wilcoxon test and LASSO algorithm. Then we used a limma package to find significant DE-IRGs. The GO and pathways analysis of these important immune genes were also applied. Subsequently, we used STRING and Cytoscape to screen hub genes and evaluated their value as a potential biomarker according to their expression at different stages and the ROC curve. Moreover, the results were verified by high-throughput data. Finally, we formed a TFs-mRNA-miRNA regulatory network diagram. Through the analysis above, we obtained four important immune cells. And the immune-related gene chip of the blood samples was analyzed to figure out the 36 significant DE-IRGs. Based on the operations above, we confirmed six immune-related hub genes involved in the pathogenesis of COVID-19 and analyzed their relationship with critical immune cells. Conclusions:It was concluded that TLR2, CAMP, S100A9, BCL6, CD4, and IL7R could be used as potential biomarkers to provide corresponding value for the diagnosis and the prognosis of COVID-19.

Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes. (preprint)

SARS-CoV-2 spike protein (S) is structurally dynamic and has been observed by cryo-EM to adopt a variety of prefusion conformations that can be categorized as locked, closed and open. The locked conformations feature tightly packed trimers with structural elements incompatible with RBD in "up" position. For SARS-CoV-2 S, it has been shown that the locked conformations are transient under neutral pH. Probably due to their transience, locked conformations remain largely uncharacterized for SARS-CoV-1 S. Intriguingly, locked conformations were the only conformations captured for S proteins of bat and pangolin origin SARS-related coronaviruses. In this study, we introduced x1, x2, and x3 disulfides into SARS-CoV-1 S. Some of these disulfides have been shown to preserve rare locked conformations when introduced to SARS-CoV-2 S. Introduction of these disulfides allowed us to image a variety of locked and other rare conformations for SARS-CoV-1 S by cryo-EM. We identified bound cofactors and structural features that are associated with SARS-CoV-1 S locked conformations. We compare newly determined structures to other available spike structures of Sarbecoviruses to identify conserved features and discuss their possible functions.

SARS-CoV-2 breakthrough infections induce somatically hypermutated broadly neutralizing antibodies against heterologous variants (preprint)

Currently circulating SARS-CoV-2 Omicron variants feature highly mutated spike proteins with extraordinary abilities in evading acute-infection-induced germline antibodies isolated earlier in the pandemic. We identified that memory B cells from Delta variant breakthrough-infection patients expressed antibodies with more extensive somatic hypermutations (SHMs) allowing isolation of a number of broadly neutralizing antibodies with activities against heterologous variants of concerns (VOCs) including Omicron variant. Structural studies identified that SHM introduced altered amino acids and highly unusual HCDR2 insertions respectively in two representative broadly neutralizing antibodies - YB9-258 and YB13-292. Previously, insertion/deletion were rarely reported for antiviral antibodies except for those induced by HIV-1 chronic infections. Identified SHMs involved heavily in epitope recognition, they broadened neutralization breadth by rendering antibodies resistant to VOC mutations highly detrimental to previously isolated antibodies targeting similar epitopes. These data provide molecular mechanisms for enhanced immunity to heterologous SARS-CoV-2 variants after repeated antigen exposures with implications for future vaccination strategy.

Clinical and Virological Features of the First Occurrence of COVID-19 Delta Variant in Anhui Province, China (preprint)

Objectives Since the outbreak of coronavirus disease 2019 (COVID-19), it has caused serious casualties worldwide. In recent months, the virus has mutated into an increasingly infectious form (Delta variant) and spread rapidly.Methods In the current study, we analyzed the clinical, epidemiological and viral genetic characteristics of the first four imported Delta cases in Anhui Province, China.Results The four imported Delta cases developed chest inflammation, tissue damage and recovered after admission, the serum high-sensitivity C-reactive protein (hs-CRP) and CRP levels showed a first increasing and then decreasing trend. The changes of hs-CRP /CRP and serum neutralizing antibodies (Nab) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) levels were associated with the regression of chest lesions. The combination of genetic sequencing and epidemiological analysis suggested that the SARS-CoV-2 delta variant infection of these four patients may originate from Russia.Conclusions Our study found the certain correlations of serum hs-CRP/CRP and Nab levels with the occurrence, development and outcome of COVID-19 delta variant, suggesting that monitoring hs-CRP/CRP and Nab levels of COVID-19 delta variant patients at hospital admission may be useful for understanding the severity of patients’ current conditions.

A population antibody response against SARS-CoV-2 with differential neutralization activities towards the Delta and Omicron variants (preprint)

Population antibody response is believed to be important in selection of new variant viruses. We identified that SARS-CoV-2 infections elicit a population immune response mediated by a lineage of VH1-69 germline antibodies. The representative antibody R1-32 targets a novel semi-cryptic epitope defining a new class of RBD targeting antibodies. Binding to this non-ACE2 competing epitope leading to spike destruction impairing virus entry. Based on epitope location, neutralization mechanism and analysis of antibody binding to spike variants we propose that recurrent substitutions at 452 and 490 are associated with immune evasion of this population antibody response. These substitutions, including L452R found in the Delta variant, disrupt interaction mediated by the VH1-69 specific hydrophobic HCDR2 to impair antibody-antigen association allowing variants to escape. Lacking 452/490 substitutions, the Omicron variant is sensitive to this class of antibodies. Our results provide new insights into SARS-CoV-2 variant genesis and immune evasion.

A human monoclonal antibody potently pan-neutralizes SARS-CoV-2 VOCs by targeting RBD invariant sites (preprint)

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of novel corona virus disease (COVID-19). The neutralizing monoclonal antibodies (mAbs) targeting the receptor binding domain (RBD) of SARS-CoV-2 are among the most promising strategies to prevent and treat COVID-19. However, SARS-CoV-2 variants of concern (VOCs) profoundly reduced the efficacies of most of mAbs and vaccines approved for clinical use. Herein, we demonstrated mAb 35B5 efficiently neutralizes both wild-type (WT) SARS-CoV-2 and VOCs, including B.1.617.2 (delta) variant, in vitro and in vivo. Cryo-electron microscopy (cryo-EM) revealed that 35B5 neutralizes SARS-CoV-2 by targeting a unique epitope that avoids the prevailing mutation sites on RBD identified in circulating VOCs, providing the molecular basis for its pan-neutralizing efficacy. The 35B5-binding epitope could also be exploited for the rational design of a universal SARS-CoV-2 vaccine.

Analysis of COVID-19 chest ct in asymptomatic infection transferred to diagnosis patients

Objective: To analyze the clinical classification and chest CT manifestations of coronavirus disease 2019(COVID-19)in asymptomatic infection transferred to diagnosis, and improve image understanding of asymptomatic infection COVID-19.

Discrimination and social exclusion in the outbreak of COVID-19

This paper is aimed to document the observed social exclusion and discrimination in the outbreak of COVID-19 across the world and inside of China. Discrimination and social exclusion has occurred in various forms, while 25.11% of respondents overseas experienced discrimination in the breakout of COVID-19, and 90% of respondents inside of China exhibited discriminatory attitudes. The discrimination and social exclusion also lead to a range of damaging social outcomes. Thus, this is an urgent call for the inclusiveness in policy and media in the face of this public health emergency.

Research progress on potential drug interactions of anti-Coronavirus disease 2019 drugs

From the December 2019, coronavirus disease 2019 (COVID-19) was outbreak at home and abroad. Besides antiviral therapy, patients should be treated for complications, therefore a combination of drugs for treatment in Clinic need to be taken. Although recently published guidelines have repeatedly highlighted the drug interactions between the anti-COVID-l 9 medicines, it has not been detailed. The potential drug - drug interactions were reviewed 0f the anti-COVID-19 drugs, and in order to provide references for the clinical safety and rational use of the anti-COVID-19 drugs.

Mutation and Virulence of SARS-CoV-2 Strains Circulating in Anhui Province, China (preprint)

Background: The genome of SARS-CoV-2 has shown considerable variation during its spreading. Monitoring variations in the virus genome to understand the evolution and spread of the virus is extremely important. Methods: Seven SARS-CoV-2 strains (BB127, BB183, HB030, MAS525, HF3028, FY1494, and SZ005) circulating in Anhui Province, China were isolated and sequenced for evolutionary analysis. Five strains were further cultured in vitro and were subjected to viral growth assay, TCID50 assay, and detection of spike protein expression. Next generation sequence (NGS) analysis were applied to investigate the mutation frequencies throughout the whole genome at different time gradients in vitro. Findings: Our observations revealed that in vitro cultured SARS-CoV-2 virus had much higher mutation frequency (up to ~20 times) than that in infected patients, and the mutation in nonstructural protein 14 (nsp14) might increase the genomic mutation frequency. Different strains had various amount of spike protein which may positively correlated with the virus replication capacity but may be influenced by other viral factors. Interpretation: Our study suggested that SARS-CoV-2 has the potential to diversify under favorable conditions. Monitoring viral mutations is not only helpful for better understanding of virus evolution and virulence change, but also the key to prevent virus transmission and disease progression. SARS-CoV-2 genomic variation analysis may also provide potential ideas for more efficient vaccine development and clinical treatment. Funding: This work is funded by Special Project for Emergency Scientific and Technological Research on New Coronavirus Infection (YG, No. YD9110002001), Emergency Research Project of Novel Coronavirus Infection of Anhui Province (Grant numbers 202004a07020002; 202004a07020004), Postdoctoral Research Foundation of China (2020M670084ZX) and the Fundamental Research Funds for the Central Universities (WK9110000166; WK9110000167).Declaration of Interests: We declare no competing interests.Ethics Approval Statement: The study was conformed to the principles of the Declaration ofHelsinki and approved by the Ethics Committee of the First Affiliated Hospital of USTC..

Molecular epidemiology of SARS-CoV-2 clusters caused by asymptomatic cases in Anhui Province, China (preprint)

Background: COVID-19 is a newly emerging disease caused by a novel coronavirus (SARS-CoV-2), which spread globally in early 2020. Asymptomatic carriers of the virus contribute to the propagation of this disease, and the existence of asymptomatic infection has caused widespread fear and concern in the control of this pandemic. Methods: : In this study, we investigated the origin and transmission route of SARS-CoV-2 in Anhui’s two clusters, analyzed the role and infectiousness of asymptomatic patients in disease transmission, and characterized the complete spike gene sequences in the Anhui strains. Results: : We conducted an epidemiological investigation of two clusters caused by asymptomatic infections sequenced the spike gene of viruses isolated from 12 patients. All cases of the two clusters we investigated had clear contact histories, both from Wuhan, Hubei province. The viruses isolated from two outbreaks in Anhui were found to show a genetically close link to the virus from Wuhan. In addition, new single nucleotide variations were discovered in the spike gene. Conclusions: : Both clusters may have resulted from close contact and droplet-spreading and asymptomatic infections were identified as the initial cause. We also analyzed the infectiousness of asymptomatic cases and the challenges to the current epidemic to provided information for the development of control strategies.

Nonstructural protein 7 and 8 complexes of SARS-CoV-2 (preprint)

The pandemic outbreak of coronavirus disease 2019 (COVID-19) across the world has led to millions of infection cases and caused a global public health crisis. Current research suggests that SARS-CoV-2 is a highly contagious coronavirus that spreads rapidly through communities. To understand the mechanisms of viral replication, it is imperative to observe coronavirus viral replicase, a huge protein complex comprising up to 16 viral nonstructural and associated host proteins, which is the most promising antiviral target for inhibiting viral genome replication and transcription. Recently, several components of the viral replicase complex in SARS-CoV-2 have been solved to provide a basis for the design of new antiviral therapeutics. Here, we report the crystal structure of the SARS-CoV2 nsp7-8 tetramer, which comprises two copies of each protein representing nsp7’s full-length and the C-terminus of nsp8 owing to N-terminus proteolysis during the process of crystallization. We also identified a long helical extension and highly flexible N-terminal domain of nsp8, which is preferred for interacting with single-stranded nucleic acids.

SARS-CoV-2 suppresses mRNA expression of selenoproteins associated with ferroptosis, ER stress and DNA synthesis (preprint)

A significant, positive association between selenium status and prognosis of SARS-CoV-2 infection has been identified among COVID-19 patients in China. Moreover, a German study revealed a pronounced deficit of serum selenium and SELENOP concentrations in COVID-19 patients, and selenium deficiency was associated with mortality risk from COVID-19. The present study investigated the influence of SARS-CoV-2 on gene expression of host selenoproteins which mediate many beneficial actions of selenium. We found that SARS-CoV-2 suppressed mRNA expression of selenoproteins associated with ferroptosis (GPX4), endoplasmic reticulum stress (SELENOF, SELENOK, SELENOM and SELENOS) and DNA synthesis (TXNRD3), while SARS-CoV-2 increased gene expression of IL-6 (an inflammatory cytokine positively correlated with severity of COVID-19), in Vero cells. These results provide a deeper insight into the connection between selenium and SARS-CoV-2 pathogenesis.

Distribution Of Medical Institutions In Cold Regions Of China Based On Public Health Emergencies (preprint)

Background：Recently, investments in the construction of medical resources have been increasing annually China, and consequently, the allocation of these resources has improved. However, the outbreak of covid-19 in 2020 highlights the problems in the distribution of medical institutions. After the occurrence of public health emergencies, the joint action of different levels of medical and health institutions can bring the role of urban medical and health system into full play. Therefore, after a global public health emergency, the study of medical institution distribution needs to be reconsidered.Methods：With the continuous application and development of GIS (Geographic Information System), the application of GIS in civil planning is relatively mature, and research investigating distribution has been conducted in depth. Based on this foundation, this paper analyzes the factors impacting distribution, such as the transportation system, land use characteristics and personal factors, by a weighted spatial separation model of a representative city in a cold region in China. Results：The data were sorted, edited and visually processed through the constructed geodatabase to perform an analysis of the spatial distributions of the factors impacting the accessibility of medical institutions in the study area. A weighted spatial separation model was built and applied to comprehensively consider several factors affecting accessibility, the accessibility of these medical institutions is significantly impacted when the spatial population distribution is considered as a factor in the weighted spatial separation model.Conclusions：The accessibility of medical institutions in this representative cold city in China was comparatively analyzed in this paper through theoretical research, software computations/simulations and model analysis based on the GIS paradigm. This study will help optimize the layout of medical institutions and improve medical equality.Trial registration: An ethics review and approval for this study was not required according to the local legislation and institutional requirements.

Distribution of Medical Institutions in Cold Regions of China Based on Public Health Emergencies (preprint)

Background：Recently, investments in the construction of medical resources have been increasing annually China, and consequently, the allocation of these resources has improved. However, the outbreak of covid-19 in 2020 highlights the problems in the distribution of medical institutions. After the occurrence of public health emergencies, the joint action of different levels of medical and health institutions can bring the role of urban medical and health system into full play. Therefore, after a global public health emergency, the study of medical institution distribution needs to be reconsidered.Methods：With the continuous application and development of GIS, the application of GIS in civil planning is relatively mature, and research investigating distribution has been conducted in depth. Based on this foundation, this paper analyzes the factors impacting distribution, such as the transportation system, land use characteristics and personal factors, by a weighted spatial separation model of a representative city in a cold region in China. Results：The data were sorted, edited and visually processed through the constructed geodatabase to perform an analysis of the spatial distributions of the factors impacting the accessibility of medical institutions in the study area. A weighted spatial separation model was built and applied to comprehensively consider several factors affecting accessibility, the accessibility of these medical institutions is significantly impacted when the spatial population distribution is considered as a factor in the weighted spatial separation model.Conclusions：The accessibility of medical institutions in this representative cold city in China was comparatively analyzed in this paper through theoretical research, software computations/simulations and model analysis based on the GIS paradigm. This study will help optimize the layout of medical institutions and improve medical equality.Trial registration: An ethics review and approval for this study was not required according to the local legislation and institutional requirements.

Distribution of Medical Institutions in Cold Regions of China Based on Public Health Emergencies (preprint)

Background: Recently, investments in the construction of medical resources have been increasing annually China, and consequently, the allocation of these resources has improved. However, the outbreak of covid-19 in 2020 highlights the problems in the distribution of medical institutions. After the occurrence of public health emergencies, the joint action of different levels of medical and health institutions can bring the role of urban medical and health system into full play. Therefore, after a global public health emergency, the study of medical institution distribution needs to be reconsidered.Methods: With the continuous application and development of GIS, the application of GIS in civil planning is relatively mature, and research investigating distribution has been conducted in depth. Based on this foundation, this paper analyzes the factors impacting distribution, such as the transportation system, land use characteristics and personal factors, by a weighted spatial separation model of a representative city in a cold region in China.Results: A weighted spatial separation model was built and applied to comprehensively consider several factors affecting accessibility, including the spatial coverage separation, the service areas separation, the road network separation, the population separation and the weather separation. To calculate the accessibility of medical institutions using a weighted spatial separation model, Harbin was chosen as a case study. The accessibility of medical institutions was analyzed.Conclusions: The accessibility of medical institutions in this representative cold city in China was comparatively analyzed in this paper through theoretical research, software computations/simulations and model analysis based on the GIS paradigm. This study will help optimize the layout of medical institutions and improve medical equality.Trial registration: An ethics review and approval for this study was not required according to the local legislation and institutional requirements.

Survival analysis of hospital length of stay of novel coronavirus (COVID-19) pneumonia patients in Sichuan, China (preprint)

Objective Allocation of medical resource is essential to a strong public health system in response to COVID-19. Analysis of confirmed COVID-19 patients' hospital length of stay in Sichuan can be informative to decision-making in other regions of the world. Design A retrospective cross-sectional study. Data and Method Data from confirmed COVID-19 cases in Sichuan Province were obtained from the National Notifiable Diseases Reporting System (NNDRS) and field survey. We collected information on demographic, epidemiological, clinical characteristics, and the length of hospital stay for confirmed patients. We conducted an exploratory analysis using adjusted multivariate cox-proportional models. Participants A total of 538 confirmed patients of COVID-19 infection in Sichuan Province from January to March 2020. Outcome measure The length of hospital stay after admissions for confirmed patients. Results From January 16, 2020 to March 4, 2020, 538 human cases of COVID-19 infection were laboratory-confirmed, and were hospitalized for treatment. Among these, 271 (50%) were 45 years of age or above, 285 (53%) were male, 450 (84%) were considered as having mild symptoms. The median hospital length of stay was 19 days (interquartile range (IQR): 14-23, Range: 3-41). Adjusted multivariate analysis showed that longer hospital length of stay was associated with factors aged 45 and over (HR: 0.74, 95% CI: 0.60-0.91), those admitted to provincial hospital (HR: 0.73, 95% CI: 0.54-0.99), and those with serious illness (HR: 0.66, 95% CI: 0.48-0.90); living in areas with more than 5.5 healthcare workers per 1000 population (HR: 1.32, 95% CI: 1.05-1.65) was associated with shorter hospital length of stay. There was no gender difference. Conclusions Preparation control measures of COVID-19 should involve the allocation of sufficient medical resources, especially in areas with older vulnerable populations and in areas that lack basic medical resources.

Epidemiological and clinical features of 291 cases with coronavirus disease 2019 in areas adjacent to Hubei, China: a double-center observational study (preprint)

Abstract Background: The clinical outcomes of COVID-19 patients in Hubei and other areas are different. We aim to investigate the epidemiological and clinical characteristics of patient with COVID-19 in Hunan which is adjacent to Hubei. Methods: In this double-center, observational study, we recruited all consecutive patients with laboratory confirmed COVID-19 from January 23 to February 14, 2020 in two designated hospitals in Hunan province, China. Epidemiological and clinical data from patients' electronic medical records were collected and compared between mild, moderate and severe/critical group in detail. Clinical outcomes were followed up to February 20, 2020. Findings: 291 patients with COVID-19 were categorized into mild group (10.0%), moderate group (72.8%) and severe/critical group (17.2%). The median age of all patients was 46 years (49.8% were male). 86.6% patients had an indirect exposure history. The proportion of patients that had been to Wuhan in severe/critical group (48.0% vs 17.2%, p=0.006) and moderate group (43.4% vs 17.2%, p=0.007) were higher than mild group. Fever (68.7%), cough (60.5%), and fatigue (31.6%) were common symptoms especially for severe and critical patients. Typical lung imaging finding were bilateral and unilateral ground glass opacity or consolidation. Leukopenia, lymphopenia and eosinopenia occurred in 36.1%, 22.7% and 50.2% patients respectively. Increased fibrinogen was detected in 45 of 58 (77.6%) patients with available results. 29 of 44 (65.9%) or 22 of 40 (55.0%) patients were positive in Mycoplasma pneumonia or Chlamydia pneumonia antibody test respectively. Compared with mild or moderate group, severe/critical group had a relative higher level of neutrophil, Neutrophil-to-Lymphocyte Ratio, h-CRP, ESR, CK, CK-MB, LDH, D-dimer, and a lower level of lymphocyte, eosinophils, platelet, HDL and sodium (all p<0.01). Most patients received antiviral therapy and Chinese Medicine therapy. As of February 20, 2020, 159 (54.6%) patients were discharged and 2 (0.7%) patients died during hospitalization. The median length of hospital stay in discharged patients was 12 days (IQR: 10-15). Interpretation: The epidemiological and clinical characteristics of COVID-19 patients in Hunan is different from patients in Wuhan. The proportion of patients that had been to Wuhan in severe/critical group and moderate group were higher than mild group. Laboratory and imaging examination can assist in the diagnosis and classification of COVID-19 patients.