ABSTRACT
Cold-chain environment could extend the survival duration of SARS-CoV-2 and increases the risk of transmission. However, the effect of clod-chain environmental factors and packaging materials on SARS-CoV-2 stability and the efficacy of intervention measures to inactivate SARS-CoV-2 under cold-chain environment remains uncertain. This study aimed to unravel cold-chain environmental factors that preserved the stability of SARS-CoV-2 and disinfection measures against SARS-CoV-2 under the cold-chain environment. The spike gene of SARS-CoV-2 isolated from Wuhan hu-1 was used to construct the SARS-CoV-2 pseudovirus and used as model of the SARS-CoV-2 virus. The decay rate of SARS-CoV-2 pseudovirus in the cold-chain environment, various types of packaging material surfaces i.e., PE plastic, stainless steel, Teflon and cardboard, and in frozen seawater was investigated. The influence of LED visible light(wavelength 450 nm-780 nm) and airflow movement on the stability of SARS-CoV-2 pseudovirus at -18{degrees}C were subsequently assessed. The results show that SARS-CoV-2 pseudovirus decayed more rapidly on porous cardboard surface compared with the non-porous surfaces including PE plastic, stainless steel and Teflon. Compared with 25{degrees}C, the decay rate of SARS-CoV-2 pseudovirus was significantly lower at low temperature. Seawater preserved viral stability both at -18{degrees}C and repeated freeze-thawing cycles compared with deionized water. LED visible light illumination and airflow movement environment at -18{degrees}C reduced the SARS-CoV-2 pseudovirus stability. In conclusion, our results indicate cold-chain temperature and seawater as risk factors for SARS-CoV-2 transmission and LED visible light illumination and airflow movement as possible disinfection measures of SARS-CoV-2 under the cold-chain environment.
Subject(s)
Severe Acute Respiratory SyndromeABSTRACT
The COVID-19 pandemic has resulted in millions of deaths and affected socioeconomic structure worldwide and the search for new antivirals and treatments are still ongoing. In the search for new drug target and to increase our understanding of the disease, we used large scale immunofluorescence to explore the host cell response to SARS-CoV-2 infection. Among the 602 host proteins studied in this host response screen, changes in abundance and subcellular localization were observed for 97 proteins, with 45 proteins showing increased abundance and 10 reduced abundances. 20 proteins displayed changed localization upon infection and an additional 22 proteins displayed altered abundance and localization, together contributing to diverse reshuffling of the host cell protein landscape. We then selected existing and approved small-molecule drugs (n =123) against our identified host response proteins and identified 3 compounds - elesclomol, crizotinib and rimcazole, that significantly reduced antiviral activity. Our study introduces a novel, targeted and systematic approach based on host protein profiling, to identify new targets for drug repurposing. The dataset of ~75,000 immunofluorescence images from this study are published as a resource available for further studies.
Subject(s)
Severe Acute Respiratory Syndrome , COVID-19ABSTRACT
A novel coronavirus has rapidly spread to almost every country in the world, causing over 233 million confirmed cases of coronavirus disease 2019 (COVID-19) and over 209,761,242 deaths by late September 2021. Binding the receptor binding domain (RBD) to the host cell surface receptor protein, angiotensin converter enzyme (ACE2), is a key step in virus infection. In this study, we applied a pulsed electric field to the RBD/ACE2 complex based on molecular dynamics simulation and demonstrated that the electric field affects the structure and binding affinity of the complex. Additionally, residue Y505 is the crucial medium for the effects of electric field on the complex. Overall, these results may help apply an external electric field to virus suppression.
Subject(s)
COVID-19ABSTRACT
As the COVID-19 pandemic continues to impact the world, data is being gathered and analyzed to better understand the disease. Recognizing the potential for visual analytics technologies to support exploratory analysis and hypothesis generation from longitudinal clinical data, a team of collaborators worked to apply existing event sequence visual analytics technologies to a longitudinal clinical data from a cohort of 998 patients with high rates of COVID-19 infection. This paper describes the initial steps toward this goal, including: (1) the data transformation and processing work required to prepare the data for visual analysis, (2) initial findings and observations, and (3) qualitative feedback and lessons learned which highlight key features as well as limitations to address in future work.
Subject(s)
COVID-19ABSTRACT
The COVID-19 vaccination efficacy depends on serum production level of the neutralizing IgG antibody (NA) specific to the receptor binding domain of SARS-Cov-2 spike protein. Therefore, a high-throughput rapid assay to measure the total SARS-CoV-2 NA level is urgently needed for COVID-19 serodiagnosis, convalescent plasma therapy, vaccine development, and assessment. Here, we developed a nanoplasmonic immunosorbent assay (NanoPISA) platform for one-step rapid quantification of SARS-CoV-2 NAs in clinical serum samples for high-throughput evaluation of COVID-19 vaccine effectiveness. The NanoPISA platform enhanced by the use of nanoporous hollow gold nanoparticle coupling was able to detect SARS-CoV-2 NAs with a limit of detection of 0.1 ng/mL within 15 min. The one-step NanoPISA for SARS-CoV-2 NA detection in clinical specimens yielded good results, comparable to those obtained in the gold standard seroneutralization test and the surrogate virus neutralizing ELISA. Collectively, our findings indicate that the one-step NanoPISA may offer a rapid and high-throughput NA quantification platform for evaluating the effectiveness of COVID-19 vaccines.
Subject(s)
Severe Acute Respiratory Syndrome , COVID-19ABSTRACT
The recent COVID-19 pandemic has brought about a surge of crowd-sourced initiatives aimed at simulating the proteins of the SARS-CoV-2 virus. A bottleneck currently exists in translating these simulations into tangible predictions that can be leveraged for pharmacological studies. Here we report on extensive electrostatic calculations done on an exascale simulation of the opening of the SARS-CoV-2 spike protein, performed by the Folding@home initiative. We compute the electric potential as the solution of the non-linear Poisson-Boltzmann equation using a parallel sharp numerical solver. The inherent multiple length scales present in the geometry and solution are reproduced using highly adaptive Octree grids. We analyze our results focusing on the electro-geometric properties of the receptor-binding domain and its vicinity. This work paves the way for a new class of hybrid computational and data-enabled approaches, where molecular dynamics simulations are combined with continuum modeling to produce high-fidelity computational measurements serving as a basis for protein bio-mechanism investigations.
Subject(s)
COVID-19ABSTRACT
Dysfunctional immune response in the COVID-19 patients is a recurrent theme impacting symptoms and mortality, yet the detailed understanding of pertinent immune cells is not complete. We applied single-cell RNA sequencing to 284 samples from 205 COVID-19 patients and controls to create a comprehensive immune landscape. Lymphopenia and active T and B cell responses were found to coexist and associated with age, sex and their interactions with COVID-19. Diverse epithelial and immune cell types were observed to be virus-positive and showed dramatic transcriptomic changes. Elevation of ANXA1 and S100A9 in virus-positive squamous epithelial cells may enable the initiation of neutrophil and macrophage responses via the ANXA1-FPR1 and S100A8/9-TLR4 axes. Systemic up-regulation of S100A8/A9, mainly by megakaryocytes and monocytes in the peripheral blood, may contribute to the cytokine storms frequently observed in severe patients. Our data provide a rich resource for understanding the pathogenesis and designing effective therapeutic strategies for COVID-19.
Subject(s)
Carcinoma, Squamous Cell , Lymphopenia , COVID-19ABSTRACT
BACKGROUND: Sepsis is an infection-induced aggressive and life-threatening organ dysfunction with high morbidity and mortality worldwide. Infection-associated inflammation and coagulation promote the progression of adverse outcomes in sepsis. Here, we report that phospho-Tyr705 of STAT3 (pY-STAT3), not total STAT3, contributes to systemic inflammation and coagulopathy in sepsis. METHODS: Cecal ligation and puncture (CLP)-induced septic mice were treated with BP-1-102, Napabucasin, or vehicle control respectively and then assessed for systemic inflammation, coagulation response, lung function and survival. Human pulmonary microvascular endothelial cells (HPMECs) and Raw264.7 cells were exposed to lipopolysaccharide (LPS) with pharmacological or genetic inhibition of pY-STAT3. Cells were assessed for inflammatory and coagulant factor expression, cell function and signaling. RESULTS: Pharmacological inhibition of pY-STAT3 expression by BP-1-102 reduced the proinflammatory factors, suppressed coagulation activation, attenuated lung injury, alleviated vascular leakage and improved the survival rate in septic mice. Pharmacological or genetic inhibition of pY-STAT3 diminished LPS-induced cytokine production in macrophages and protected pulmonary endothelial cells via the IL-6/JAK2/STAT3, NF-κB and MAPK signaling pathways. Moreover, the increase in procoagulant indicators induced by sepsis such as tissue factor (TF), the thrombin-antithrombin complex (TAT) and D-Dimer were down-regulated by pY-STAT3 inhibition. CONCLUSIONS: Our results revealed a therapeutic role of pY-STAT3 in modulating the inflammatory response and defective coagulation during sepsis. Video Abstract.
ABSTRACT
The spread of SARS-CoV-2 virus in the ongoing global pandemics has led to infections of millions of people and losses of many lives. The rapid, accurate and convenient SARS-CoV-2 virus detection is crucial for controlling and stopping the pandemics. Diagnosis of patients in the early stage infection are so far limited to viral nucleic acid or antigen detection in human nasopharyngeal swab or saliva samples. Here we developed a method for rapid and direct optical measurement of SARS-CoV-2 virus particles in one step nearly without any sample preparation using a spike protein specific nanoplasmonic resonance sensor. We demonstrate that we can detect as few as 30 virus particles in one step within 15 minutes and can quantify the virus concentration linearly in the range of 103 vp/ml to 106 vp/ml. Measurements shown on both generic microplate reader and a handheld smartphone connected device suggest that our low-cost and rapid detection method may be adopted quickly under both regular clinical environment and resource-limited settings.
ABSTRACT
The outbreak of COVID-19 pandemic has exposed an urgent need for effective contact tracing solutions through mobile phone applications to prevent the infection from spreading further. However, due to the nature of contact tracing, public concern on privacy issues has been a bottleneck to the existing solutions, which is significantly affecting the uptake of contact tracing applications across the globe. In this paper, we present a blockchain-enabled privacy-preserving contact tracing scheme: BeepTrace, where we propose to adopt blockchain bridging the user/patient and the authorized solvers to desensitize the user ID and location information. Compared with recently proposed contract tracing solutions, our approach shows higher security and privacy with the additional advantages of being battery friendly and globally accessible. Results show viability in terms of the required resource at both server and mobile phone perspectives. Through breaking the privacy concerns of the public, the proposed BeepTrace solution can provide a timely framework for authorities, companies, software developers and researchers to fast develop and deploy effective digital contact tracing applications, to conquer COVID-19 pandemic soon. Meanwhile, the open initiative of BeepTrace allows worldwide collaborations, integrate existing tracing and positioning solutions with the help of blockchain technology.
Subject(s)
COVID-19ABSTRACT
Background Although the existing cases of COVID-19 in China have been reducing since late February 2020, the confirmed cases are surging abroad. Improving public knowledge regarding COVID-19 is critical to control the epidemic. The study aimed to determine the China’s public knowledge of COVID-19 and attitude towards the control measures.Methods A cross-sectional study was conducted in 48 hours, from 29 February 2020, 22:30 to 2 March 2020, 22:30, based on a self-administered web-based questionnaire. The survey was conducted on the WeChat network. Exponential non-discriminative snowball sampling were applied. The questionnaire was voluntarily submitted by WeChat users. The questionnaire covered the basic demographic information, public knowledge about epidemiological and clinical characteristics of COVID-19, psychological state, and attitude towards overall control measures. The primary outcome was the Chinese public knowledge regarding COVID-19 and the attitude towards the control measures and secondary outcome was psychological state of the public during this epidemic.Results The study included 10,905 participants and 10,399 valid questionnaires were included for analysis. Participants with tertiary education, younger age and healthcare workers had better overall knowledge compared with other participants (all P<0.05). About 91.9% of the participants believed in person-to-person transmission and 39.1% believed in animal-to-person transmission. No significant correlation between anxiety and regional number of existing cases was found, while participants in Hubei were more anxious than those in other regions. In general, 74.1% of participants acknowledged the effectiveness of overall control measures and it was negatively correlated with regional number of existing cases (r=-0.492, P=0.007).Conclusions In conclusion, the survey revealed that Chinese public had overall good knowledge regarding COVID-19 except for those indeterminate knowledge. With the dynamic change of global epidemic situation and more researches, further study would be conducted to explore the change of public knowledge and attitude about COVID-19 in the future.
Subject(s)
Anxiety Disorders , COVID-19ABSTRACT
The infected and fatal cases of Coronavirus Disease 2019 (COVID-19) keep increasing around the world, to explore the infection routes and pathogenesis of 2019-nCoV could be meaningful for prevention and treatment of COVID-19. Previous studies showed that the oral cavity is at potentially high risk of 2019-nCoV infection. The ACE2 receptor of 2019-nCoV was reported could express on oral epithelium and salivary glands, and 2019-nCoV could be detected in patients’ saliva. Recently, the amblygeustia were found to widely exist in the COVID-19 patients. To explore the potential mechanism of amblygeustia, we performed further analysis via independent in-house single-cell profiles. Our results showed that ACE2 was inclined to express in taste cells, which indicated that 2019-nCoV may invade into taste cells at the early stage of COVID-19, and lead to the amblygeustia of patients. Above findings about the 2019-nCoV and COVID-19 in oral cavity are valuable and enlightening for future epidemic prevention strategy.