Dual Multi-scale Mean Teacher Network for Semi-supervised Infection Segmentation in Chest CT Volume for COVID-19 (preprint)

Automated detecting lung infections from computed tomography (CT) data plays an important role for combating COVID-19. However, there are still some challenges for developing AI system. 1) Most current COVID-19 infection segmentation methods mainly relied on 2D CT images, which lack 3D sequential constraint. 2) Existing 3D CT segmentation methods focus on single-scale representations, which do not achieve the multiple level receptive field sizes on 3D volume. 3) The emergent breaking out of COVID-19 makes it hard to annotate sufficient CT volumes for training deep model. To address these issues, we first build a multiple dimensional-attention convolutional neural network (MDA-CNN) to aggregate multi-scale information along different dimension of input feature maps and impose supervision on multiple predictions from different CNN layers. Second, we assign this MDA-CNN as a basic network into a novel dual multi-scale mean teacher network (DM${^2}$T-Net) for semi-supervised COVID-19 lung infection segmentation on CT volumes by leveraging unlabeled data and exploring the multi-scale information. Our DM${^2}$T-Net encourages multiple predictions at different CNN layers from the student and teacher networks to be consistent for computing a multi-scale consistency loss on unlabeled data, which is then added to the supervised loss on the labeled data from multiple predictions of MDA-CNN. Third, we collect two COVID-19 segmentation datasets to evaluate our method. The experimental results show that our network consistently outperforms the compared state-of-the-art methods.

Pre-existing anti-HCoV-OC43 immunity influences the durability and cross-reactivity of humoral response to SARS-CoV-2 vaccination

Purpose This study was conducted in order to properly understand whether prior seasonal human coronavirus (HCoV) immunity could impact the potential cross-reactivity of humoral responses induced by SARS-CoV-2 vaccine, thereby devising universal coronavirus vaccines for future outbreaks. Methods We performed enzyme-linked immunosorbent assay (ELISA) to quantify the immunoglobulin G (IgG) antibody levels to spike (S) protein and S1 subunit of HCoVs (HCoV-OC43, HCoV-HKU1, HCoV-NL63, and HCoV-229E), and ELISA [anti-RBD and anti-nucleoprotein (N)], chemiluminescence immunoassay assays (anti-RBD), pseudovirus neutralization test, and authentic viral neutralization test to detect the binding and neutralizing antibodies to SARS-CoV-2 in the vaccinees. Results We found that the antibody of seasonal HCoVs did exist before vaccination and could be boosted by SARS-CoV-2 vaccine. A further analysis demonstrated that the prior S and S1 IgG antibodies of HCoV-OC43 were positively correlated with anti-RBD and neutralization antibodies to SARS-CoV-2 at 12 and 24 weeks after the second vaccination, and the correlation is more statistically significant at 24 weeks. The persistent antibody levels of SARS-CoV-2 were observed in vaccinees with higher pre-existing HCoV-OC43 antibodies. Conclusion Our data indicate that inactivated SARS-CoV-2 vaccination may confer cross-protection against seasonal coronaviruses in most individuals, and more importantly, the pre-existing HCoV-OC43 antibody was associated with protective immunity to SARS-CoV-2, supporting the development of a pan-coronavirus vaccine.

Clinical Characteristics of Omicron SARS-CoV-2 Variant Infection After Non-mRNA-Based Vaccination in China

Introduction To date, little is known about the real-world protective role of Chinese inactivated and recombinant coronavirus disease 2019 (COVID-19) vaccines under the background of the long-term “Dynamic Zero COVID-19 Case” (i.e., no infection source) in China, especially when facing the widespread Omicron severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant infection. Methods In this prospective, single-center cohort study, the clinical characteristics of post-vaccination Omicron SARS-CoV-2 variant infection were investigated in the initial largest outbreak of Omicron SARS-CoV-2 variant infection that occurred between the 8 January, 2022 and 29 January, 2022 in Anyang City, Henan Province, China. The primary endpoints were the rates of severe and critical diseases or death. The secondary endpoints were the SARS-CoV-2 shedding duration and length of hospitalization. Results A total of 380 post-vaccination patients infected with the Omicron SARS-CoV-2 variant were enrolled. The median age was 18 (interquartile range [IQR] 17–35) years, 219 (57.6%) cases were female, and 247 (65.0%) cases were students. Before confirmation of Omicron SARS-CoV-2 variant infection, patients had 3 (IQR 2–4) days of dry cough (40.3%), nasal congestion (26.3%), and sore throat (26.3%). On admission, 294 (77.4%) cases had normal chest computerized tomography (CT) imaging. Additionally, only 5 (1.3%), 30 (7.9%), 4 (4/342, 1.2%), and 7 (7/379, 0.2%) patients had lymphocyte counts <800 per mm3, C-reactive protein levels >10 mg/L, lactate dehydrogenase levels ≥250 U/L, and D-dimer levels ≥0.5 mg/L on admission, respectively. During hospitalization, 308 (81.1%) and 72 (18.9%) were identified as mild and moderate cases, respectively, and no one progressed to severe and critical types, with a SARS-CoV-2 shedding period and length of hospital stay of 17 (IQR 12–22) and 19 (IQR 15–24) days, respectively. Conclusion The current study found that approximately 80% of individuals infected with the Omicron SARS-CoV-2 variant were mild, approximately 20% of patients were moderate, and no severe, critical, or fatal cases were identified in a prospective cohort including 380 participants vaccinated with non-mRNA-based vaccines. Discussion This study supports the consideration of policy adjustments and changes to prevent and control the Omicron-predominant COVID-19 in China and other regions with high SARS-CoV-2 vaccination rates.

Development of Equine Polyclonal Antibodies as a Broad-Spectrum Therapy Against SARS-CoV-2 Variants (preprint)

The Coronavirus disease 19 (COVID-19) pandemic has accumulated over 550 million confirmed cases and more than 6.34 million deaths worldwide. Although vaccinations has largely protected the population through the last two years, the effect of vaccination has been increasingly challenged by the emerging SARS-CoV-2 variants. Although several therapeutics including both monoclonal antibodies and small molecule drugs have been used clinically, high cost, viral escape mutations, and potential side effects have reduced their efficacy. There is an urgent need to develop a low cost treatment with wide-spectrum effect against the novel variants of SARS-CoV-2. Here we report a product of equine polyclonal antibodies that showed potential broad spectrum neutralization effect against the major variants of SARS-CoV-2. The equine polyclonal antibodies were generated by horse immunization with the receptor binding domain (RBD) of SARS-CoV-2 spike protein and purified from equine serum. A high binding affinity between the generated equine antibodies and the RBD was observed. Although designed against the RBD of the early wild type strain sequenced in 2020, the equine antibodies also showed a highly efficient neutralization capacity against the major variants of SARS-CoV-2, including the recent BA.2 Omicron variant (IC50 =1.867g/ml) in viral neutralization assay in Vero E6 cells using live virus cultured. The broad-spectrum neutralization capacity of the equine antibodies was further confirmed using pseudovirus neutralization assay covering the major SARS-CoV-2 variants including wild type, alpha, beta, delta, and omicron, showing effective neutralization against all the tested strains. Ex vivo reconstructed human respiratory organoids representing nasal, bronchial, and lung epitheliums were employed to test the treatment efficacy of the equine antibodies. Antibody treatment protected the human nasal, bronchial, and lung epithelial organoids against infection of the novel SARS-CoV-2 variants challenging public health, the Delta and Omicron BA.2 isolates, by reducing >95% of the viral load. The equine antibodies were further tested for potential side effects in a mouse model by inhalation and no significant pathological feature was observed. Equine antibodies, as a mature medical product, have been widely applied in the treatment of infectious diseases for more than a century, which limits the potential side effects and are capable of large scale production at a low cost. A cost-effective, wide-spectrum equine antibody therapy effective against the major SARS-CoV-2 variants can contribute as an affordable therapy to cover a large portion of the world population, and thus potentially reduce the transmission and mutation of SARS-CoV-2.

Cover Image, Volume 94, Number 5, May 2022

Front Cover Caption: The cover image is based on the Research Article Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift by Tao Li et al., https://doi.org/10.1002/jmv.27596.

Relationship between meteorological factors, air pollutants and hand, foot and mouth disease from 2014 to 2020 (preprint)

Background: Meteorological factors and air pollutants have been reported to be associated with hand, foot, and mouth disease (HFMD) epidemics before the introduction of vaccine. However, there is limited evidence from studies with long-term dimensions.Methods: We collected the daily HFMD counts, weather and air pollution data from 2014 to 2020 in Chengdu. Distributed lag non-linear models (DLNM) were used to assess the associations of meteorological factors and air pollutants on HFMD cases. Results: From 2014-2020, high relative humidity and precipitation and extremely high and low levels of PM10, O3, SO2 and CO increased the risk of HFMD. In pre-vaccination period, extreme high and low temperatures, PM10 and NO2, low precipitation and high concentrations of PM2.5 and O3 significantly increase the risk of HFMD; In post-vaccination period, low temperature and high relative humidity, O3, NO2 and CO can significantly increase the incidence of HFMD; During the period of COVID-19, only low temperature will significantly increase the risk of HFMD; Low concentration of air pollutants has the greatest impact on the 6-14 age group, while the high concentration of air pollutants has the greatest impact on the 0-1 age group.Conclusions: Our study suggest that high relative humidity and precipitation and extremely high and low levels of PM10, O3, SO2 and CO increased the risk of HFMD from 2014 to 2020. The results of this study provide a reference for local authorities to formulate intervention measures and establish an environment-based disease early warning system.

Electrochemical detection of 25-hydroxyvitamin D3 using an oligonucleotide aptasensor

Vitamin D deficiency remains a serious health issue in many developing countries and regions with a deficiency of sunlight. And although the demand for vitamin D testing has increased dramatically in recent years, finding new methods for efficient rapid testing remain at the forefront for clinical diagnosis and public health prevention. Herein, we are introducing an electrochemical aptasensor for the detection of 25-hydroxyvitamin D3 (25(OH)D3), comparing two aptamers platforms. The oligonucleotide aptamers were immobilized on gold surfaces using a disulfide linker, followed by monitoring the electrochemical response by cyclic voltammetry (CV), square wave voltammetry (SWV), and electrochemical impedance spectroscopy (EIS). Our studies revealed that the aptamer VDBA14 possessing a 5′-terminal disulfide recognizes the vitamin target. This electrochemical aptasensor exhibited a wide linear range of 1–1000 nM and a limit of detection (LOD) of 0.085 nM for the detection of 25(OH)D3. The aptasensor also allows the detection of 25(OH)D3 in human serum sample with high sensitivity and selectivity, indicating that the proposed electrochemical aptasensor may have potential applications in clinical diagnosis.

Clinical Outcomes of COVID-19 Cases and Influencing Factors of Severe Cases in Qingdao City: A Retrospective Cohort Study (preprint)

BackgroundTo analyze the clinical outcomes of COVID-2019 cases and the influencing factors of severe cases in Qingdao City and provide theoretical reference basis for optimizing medical treatment and the strategies of epidemic prevention and control. MethodsThe demographical, epidemiological, clinical data of 81 confirmed COVID-2019 cases in Qingdao City were collected via epidemiological investigation and clinical process tracking. The status of cure, discharge, clinical outcome and influencing factors were analyzed in our study. ResultsAmong the 81 cases，12(14.81%) and 55(67.90%) were mild and ordinary, 9(11.11%) and 4(4.94%) were severe and critical, and 1 critical cases (1.23%) developed into fatal, with the fatality rate 1.23%. The median time from onset of symptoms to hospital admission were 3.67 days (IQR, 1.75 to 6.71). The median duration of illness were 21.00 days (IQR, 16.00 to 26.00) and the median length of hospitalization were 15.63 days (IQR, 11.60 to 20.50). The median time for progression to severe cases was 6.00 days after onset (IQR, 5.00-10.00). The median duration of severe cases was 8.00 days (IQR, 6.25-14.00). Age older than 40 years old (OR=5.797, 95%CI: 1.064~31.568) and first chest CT abnormal (OR=0.1140, 95%CI: 0.014~0.923) were the influencing factors of COVID-2019 severe cases. ConclusionsOlder age and first chest CT normal would be more prone to develop to severe cases of COVID-2019. During the epidemic period, it was necessary to classify and manage cases according to the needs of prevention and control in order to ensure the rational allocation of medical resources.

Distribution of ACE2, CD147, cyclophilins, CD26 and other SARS-CoV-2 associated molecules in human tissues and immune cells in health and disease (preprint)

BackgroundMorbidity and mortality from COVID-19 caused by novel coronavirus SARS-CoV-2 is accelerating worldwide and novel clinical presentations of COVID-19 are often reported. The range of human cells and tissues targeted by SARS-CoV-2, its potential receptors and associated regulating factors are still largely unknown. The aim of our study was to analyze the expression of known and potential SARS-CoV-2 receptors and related molecules in the extensive collection of primary human cells and tissues from healthy subjects of different age and from patients with risk factors and known comorbidities of COVID-19. MethodsWe performed RNA sequencing and explored available RNA-Seq databases to study gene expression and co-expression of ACE2, CD147 (BSG), CD26 (DPP4) and their direct and indirect molecular partners in primary human bronchial epithelial cells, bronchial and skin biopsies, bronchoalveolar lavage fluid, whole blood, peripheral blood mononuclear cells (PBMCs), monocytes, neutrophils, DCs, NK cells, ILC1, ILC2, ILC3, CD4+ and CD8+ T cells, B cells and plasmablasts. We analyzed the material from healthy children and adults, and from adults in relation to their disease or COVID-19 risk factor status. ResultsACE2 and TMPRSS2 were coexpressed at the epithelial sites of the lung and skin, whereas CD147 (BSG), cyclophilins (PPIA and PPIB), CD26 (DPP4) and related molecules were expressed in both, epithelium and in immune cells. We also observed a distinct age-related expression profile of these genes in the PBMCs and T cells from healthy children and adults. Asthma, COPD, hypertension, smoking, obesity, and male gender status generally led to the higher expression of ACE2- and CD147-related genes in the bronchial biopsy, BAL or blood. Additionally, CD147-related genes correlated positively with age and BMI. Interestingly, we also observed higher expression of ACE2- and CD147-related genes in the lesional skin of patients with atopic dermatitis. ConclusionsOur data suggest different receptor repertoire potentially involved in the SARS-CoV-2 infection at the epithelial barriers and in the immune cells. Altered expression of these receptors related with age, gender, obesity and smoking, as well as with the disease status might contribute to COVID-19 morbidity and severity patterns.

Thymosin alpha-1 Protected T Cells from Excessive Activation in Severe COVID-19 (preprint)

Two typical features of uncontrolled inflammation, cytokine storm and lymphopenia, are associated with the severity of coronavirus disease 2019 (COVID-19), demonstrating that both innate and adaptive immune responses are involved in the development of this disease. Recent studies have explored the contribution of innate immune cells to the pathogenesis of the infection. However, the impact of adaptive immunity on this disease remains unknown. In order to clarify the role of adaptive immune response in COVID-19, we characterized the phenotypes of lymphocytes in PBMCs from patients at different disease stages using single-cell RNA sequencing (scRNA-seq) technology. Dynamics of the effector cell levels in lymphocytes revealed a distinct feature of adaptive immunity in severely affected patients, the coincidence of impaired cellular and enhanced humoral immune responses, suggesting that dysregulated adaptive immune responses advanced severe COVID-19. Excessive activation and exhaustion were observed in CD8 T effector cells, which might contribute to the lymphopenia. Interestingly, expression of Prothymosin alpha (PTMA), the proprotein of Tα1, was significantly increased in a group of CD8 T memory stem cells, but not in excessively activated T cells. We further showed that Tα1 significantly promoted the proliferation of activated T cells in vitro and relieved the lymphopenia in COVID-19 patients. Our data suggest that protection of T cells from excessive activation might be critical for the prevention of severe COVID-19.