Spike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through multiple mechanisms (preprint)

Selective pressures have given rise to a number of SARS-CoV-2 variants during the prolonged course of the COVID-19 pandemic. Recently evolved variants differ from ancestors in additional glycosylation within the spike protein receptor-binding domain (RBD). Details of how the acquisition of glycosylation impacts viral fitness and human adaptation are not clearly understood. Here, we dissected the role of N354-linked glycosylation, acquired by BA.2.86 sub-lineages, as a RBD conformational control element in attenuating viral infectivity. The reduced infectivity could be recovered in the presence of heparin sulfate, which targets the N354 pocket to ease restrictions of conformational transition resulting in a RBD-up state, thereby conferring an adjustable infectivity. Furthermore, N354 glycosylation improved spike cleavage and cell-cell fusion, and in particular escaped one subset of ADCC antibodies. Together with reduced immunogenicity in hybrid immunity background, these indicate a single spike amino acid glycosylation event provides selective advantage in humans through multiple mechanisms.

Clinical characteristics and risk factors of severe COVID-19 in hospitalized neonates with Omicron variant infection: a retrospective study (preprint)

Background Previous study on coronavirus disease 2019 (COVID-19) in neonates was limited, especially in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) Omicron variant. This study aims to analyze the clinical characteristics and identify risk factors associated with severe COVID-19 in neonates infected with Omicron variant.Methods The study population was neonates with COVID-19 who were admitted to The Affiliated Children’s Hospital of Xi’an Jiaotong University in northwest China, from December 10, 2022 to January 20, 2023. Chinese Center for Disease Control and Prevention (CDC) announced that all local COVID-19 cases were infected with Omicron variant during the study period. Clinical and laboratory data was collected retrospectively. We used logistic regression analysis to investigate the risk factors for severe COVID-19, and derived odds ratios (ORs) and the corresponding 95% confidence intervals (CIs) from it.Results A total of 108 neonates have a median age of 18.1 days (interquartile range 9.4–23.0) for diagnosis of COVID-19 including 84 in mild group and 24 in severe group. Of them, 6.5% were premature and 22.2% had severe infection. There were no deaths. The most common clinical manifestations were fever (88.9%) and cough (55.6%), with 5 cases (4.6%) complicated by pneumonia. 4 cases (3.7%) received respiratory support, including 2 cases of high-flow oxygen and 2 cases of non-invasive ventilation. Gestational age at birth (OR: 0.615; 95% CI: 0.393–0.961), neutrophil count (NEU) (OR:0.576; 95% CI : 0.344–0.962) and lymphocyte count (LYM) (OR: 0.159; 95% CI: 0.063–0.401) were independent risk factors for severe COVID-19. The combination of NEU and LYM had the largest receiver operating characteristic area under the curve [0.912 (95% CI:0.830–0.993)] for identifying severe COVID-19, with a sensitivity of 0.833 and a specificity of 0.917.Conclusions The general presentations and outcomes of neonatal COVID-19 caused by Omicron variant were not severe and very few patients required respiratory support. The simultaneous decrease in NEU and LYM can be used to identify severe infection.

Maternal depression, childhood resting-state brain connectivity, and adolescent depression during the COVID-19 outbreak (preprint)

Adolescents of mothers with a history of depression are at two-to-five-fold increased risk for developing depression themselves. These adolescents may be especially vulnerable to depression during the COVID-19 pandemic. To better understand the complex vulnerability processes involved in the transmission of maternal depression risk to adolescent offspring in the context of the pandemic-related stress, we examined potential mediating and moderating factors that link maternal depression history and offspring depressive symptoms, including resting-state functional connectivity (rs-FC) and mothers’ depressive symptoms, in 85 adolescents during the pandemic. Adolescents’ pre-pandemic rs-FC between posterior and anterior cingulate cortex (PCC-ACC) moderated the association between maternal depression history and adolescents’ depressive symptoms during the pandemic, such that maternal depression history predicted adolescents’ symptoms only in youths with heightened pre-pandemic PCC-ACC rs-FC. Mothers’ depressive symptoms during pandemic mediated and moderated the link between maternal depression history and adolescents’ depressive symptoms; specifically, mothers with a history of depression had greater depressive symptoms during pandemic outbreak, which were, in turn, associated with offspring depressive symptoms. Additionally, maternal depression history predicted depressive symptoms in adolescents whose mothers had relatively lower depressive symptoms during the pandemic. Findings speak to the complex mediating and moderating processes involved in the transmission of maternal depression risk to adolescent offspring in the context of the COVID-19 pandemic.

Structural and functional characterizations of altered infectivity and immune evasion of SARS-CoV-2 Omicron variant (preprint)

The SARS-CoV-2 Omicron with increased fitness is spreading rapidly worldwide. Analysis of cryo-EM structures of the Spike (S) from Omicron reveals amino acid substitutions forging new interactions that stably maintain an active conformation for receptor recognition. The relatively more compact domain organization confers improved stability and enhances attachment but compromises the efficiency of viral fusion step. Alterations in local conformation, charge and hydrophobic microenvironments underpin the modulation of the epitopes such that they are not recognized by most NTD- and RBD-antibodies, facilitating viral immune escape. Apart from already existing mutations, we have identified three new immune escape sites: 1) Q493R, 2) G446S and 3) S371L/S373P/S375F that confers greater resistance to five of the six classes of RBD-antibodies. Structure of the Omicron S bound with human ACE2, together with analysis of sequence conservation in ACE2 binding region of 25 sarbecovirus members as well as heatmaps of the immunogenic sites and their corresponding mutational frequencies sheds light on conserved and structurally restrained regions that can be used for the development of broad-spectrum vaccines and therapeutics.

A subset of Memory B-derived antibody repertoire from 3-dose vaccinees is ultrapotent against diverse and highly transmissible SARS-CoV-2 variants, including Omicron (preprint)

Omicron, the most heavily mutated SARS-CoV-2 variant so far, is highly resistant to neutralizing antibodies, raising unprecedented concerns about the effectiveness of antibody therapies and vaccines. We examined whether sera from individuals who received two or three doses of inactivated vaccine, could neutralize authentic Omicron. The seroconversion rates of neutralizing antibodies were 3.3% (2/60) and 95% (57/60) for 2- and 3-dose vaccinees, respectively. For three-dose recipients, the geometric mean neutralization antibody titer (GMT) of Omicron was 15, 16.5-fold lower than that of the ancestral virus (254). We isolated 323 human monoclonal antibodies derived from memory B cells in 3-dose vaccinees, half of which recognize the receptor binding domain (RBD) and show that a subset of them (24/163) neutralize all SARS-CoV-2 variants of concern (VOCs), including Omicron, potently. Therapeutic treatments with representative broadly neutralizing mAbs individually or antibody cocktails were highly protective against SARS-CoV-2 Beta infection in mice. Atomic structures of the Omicron S in complex with three types of all five VOC-reactive antibodies defined the binding and neutralizing determinants and revealed a key antibody escape site, G446S, that confers greater resistance to one major class of antibodies bound at the right shoulder of RBD through altering local conformation at the binding interface. Our results rationalize the use of 3-dose immunization regimens and suggest that the fundamental epitopes revealed by these broadly ultrapotent antibodies are a rational target for a universal sarbecovirus vaccine. One sentence summary A sub-set of antibodies derived from memory B cells of volunteers vaccinated with 3 doses of an inactivated SARS-CoV-2 vaccine work individually as well as synergistically to keep variants, including Omicron, at bay.

A third dose of inactivated vaccine augments the potency, breadth, and duration of anamnestic responses against SARS-CoV-2 (preprint)

Emergence of variants of concern (VOC) with altered antigenic structures and waning humoral immunity to SARS-CoV-2 are harbingers of a long pandemic. Administration of a third dose of an inactivated virus vaccine can boost the immune response. Here, we have dissected the immunogenic profiles of antibodies from 3-dose vaccinees, 2-dose vaccinees and convalescents. Better neutralization breadth to VOCs, expeditious recall and long-lasting humoral response bolster 3-dose vaccinees in warding off COVID-19. Analysis of 171 complex structures of SARS-CoV-2 neutralizing antibodies identified structure-activity correlates, revealing ultrapotent, VOCs-resistant and broad-spectrum antigenic patches. Construction of immunogenic and mutational heat maps revealed a direct relationship between "hot" immunogenic sites and areas with high mutation frequencies. Ongoing antibody somatic mutation, memory B cell clonal turnover and antibody composition changes in B cell repertoire driven by prolonged and repeated antigen stimulation confer development of monoclonal antibodies with enhanced neutralizing potency and breadth. Our findings rationalize the use of 3-dose immunization regimens for inactivated vaccines. One sentence summaryA third booster dose of inactivated vaccine produces a highly sifted humoral immune response via a sustained evolution of antibodies capable of effectively neutralizing SARS-CoV-2 variants of concern.

Pneumothorax Following COVID-19: Based on Autopsy Findings (preprint)

Background  More and more studies showed pneumothorax is a complication of the 2019 novel coronavirus disease (COVID-19). But no autopsy findings of pneumothorax in COVID-19 decedent were reported, and direct relations between pneumothorax and lung pathology in these decedents were not discussed so far.Methods A 62-year-old man with COVID-19 presenting with persistent hypoxemia and suddenly dead, who was treated by mechanical ventilation in the intensive care unit (ICU) for 5 days. A systemic autopsy examination of COVID-19 decedent, including histopathology study, was conducted and the medical record, chest computerized tomography (CT) image were reviewed by forensic pathologists and clinicians. Results Severe pneumothorax, diffuse alveolar damage and airway obstruction were observed. Pneumothorax should be one of the causes of death.Conclusion Pneumothorax, due to SARS-CoV-2 infection, is a fatal complication of COVID-19. Regular examination of chest CT or X-ray and airway management are important to clinical treatment.

Designed Variants of Recombinant ACE2-Fc that Decouple Anti-SARS-CoV-2 Activities from Unwanted Cardiovascular Effects (preprint)

Angiotensin-converting enzyme 2 (ACE2) is the entry receptor for SARS-CoV-2, and recombinant ACE2 decoys are being evaluated as new antiviral therapies. We designed and tested an ACE2-Fc fusion protein, which has the benefits of a long pharmacological half-life and the potential to facilitate immune clearance of the virus. Out of the concern that the intrinsic catalytic activity of ACE2 may unintentionally alter the balance of its hormonal substrates and cause adverse cardiovascular effects in treatment, we performed a mutagenesis screening for inactivating the enzyme. Three mutants, R273A, H378A and E402A, completely lost their enzymatic activity for either surrogate or physiological substrates. All of them remained capable of binding SARS-CoV-2 and could suppress the transduction of a pseudotyped virus in cell culture. This study established new ACE2-Fc candidates as antiviral treatment for SARS-CoV-2 without potentially harmful side effects from ACE2s catalytic actions toward its vasoactive substrates.

Assisting Scalable Diagnosis Automatically via CT Images in the Combat against COVID-19 (preprint)

Introductory paragraphThe pandemic of coronavirus Disease 2019 (COVID-19) caused enormous loss of life globally. 1-3 Case identification is critical. The reference method is using real-time reverse transcription PCR (rRT-PCR) assays, with limitations that may curb its prompt large-scale application. COVID-19 manifests with chest computed tomography (CT) abnormalities, some even before the onset of symptoms. We tested the hypothesis that application of deep learning (DL) to the 3D CT images could help identify COVID-19 infections. Using the data from 920 COVID-19 and 1,073 non-COVID-19 pneumonia patients, we developed a modified DenseNet-264 model, COVIDNet, to classify CT images to either class. When tested on an independent set of 233 COVID-19 and 289 non-COVID-19 patients. COVIDNet achieved an accuracy rate of 94.3% and an area under the curve (AUC) of 0.98. Application of DL to CT images may improve both the efficiency and capacity of case detection and long-term surveillance.

Why do you wear a face mask? Taiwanese public epidemic awareness of COVID-19 from social media behavior (preprint)

BackgroundFacing the COVID-19 epidemic, Taiwan has demonstrated resilience at the initial stage of epidemic prevention and effectively slowed down its spread. This study aims to capture public epidemic awareness toward the COVID-19 through collecting social media- and Internet-based data and elaborate on how the public epidemic awareness rose and played a role in the epidemic prevention in Taiwan during the initial course of COVID-19 spread.MethodsUsing the Google search query volume of COVID-19 and face mask as indicators of public epidemic awareness, we collected the volume of news reports and the mentions on social media about COVID-19 and face masks between December 31, 2019, and February 29, 2020, through big data analysis and sorted the daily total confirmed cases of COVID-19 worldwide and in Taiwan as well as critical mask-related measures implemented by the Taiwanese government to plot the trends in this information and conduct correlation analysis. Additionally, the content analysis was adopted to analyze the transmission of different types of fear information of COVID-19 between December 31, 2019, and March 29, 2020, and their effects on the public.ResultsThe Google search query volume of COVID-19 and face mask was significantly correlated with the number of confirmed cases in Taiwan, the number of news reports on COVID-19 (correlation coefficient: .74–.90). Since the first confirmed cases of COVID-19, public epidemic awareness has increased rapidly, prompting the government to formulate relevant emergency measures. Additionally, the findings from content analysis suggested that the fear of the loss of control best explains why panic behavior occurs in public.ConclusionsConfronting the highly infectious COVID-19, public epidemic awareness is vital. While fear is an inevitable product when an emerging infectious disease occurs, the government can convert resistance into assistance by understanding why fear arises and which fear factors cause excessive panic in public. Moreover, online social media promptly reflect public epidemic awareness, which can be used as a reference for epidemic prevention; this urges the government to deal with the crisis in the form of public opinion.

New Soluble Angiopoietin Analog of C4BP-ANG1 Prevents Pathological Vascular Leakage (preprint)

Vascular leak is a key driver of organ injury in diseases such as Acute Respiratory Distress Syndrome caused by viruses, including COVID-19. Strategies that reduce enhanced permeability and vascular inflammation are promising therapeutic targets. Activation of the Angiopoietin-1 (Angpt1)-Tie2 tyrosine kinase signaling pathway is an important regulator of vascular quiescence. Here we describe the design and construction of a new soluble ANGPT1 mimetic that is a potent activator of endothelial Tie2 in vitro and in vivo. Using a chimeric fusion strategy, we replaced the extracellular matrix (ECM) binding and oligomerization domain of ANGPT1 with a heptameric scaffold derived from the C-terminus of serum complement protein C4-binding protein α (C4BP). We refer to this new fusion protein biologic as C4BP-ANG1, which forms a stable heptamer and induces TIE2 phosphorylation in cultured cells, and in the lung following i.v. injection of mice. Injection of C4BP-ANG1 ameliorates VEGF- and lipopolysaccharide-induced vascular leakage, in keeping with the known functions of Angpt1-Tie2 in maintaining quiescent vascular stability, and therefore is a promising candidate treatment for inflammatory endothelial dysfunction.