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1.
J Clin Virol ; 150-151: 105162, 2022 Jun.
Article in English | MEDLINE | ID: covidwho-1796529

ABSTRACT

A recently identified SARS-CoV-2 variant, Lambda, has spread to many countries around the world. Here, we measured and evaluated the reduced sensitivity of Lambda variant to the neutralization by plasma polyclonal antibodies elicited by the natural SARS-CoV-2 infection and inactivated vaccine. The combination of two substitutions appearing in the RBD of spike protein (L452Q and F490S) resulted in noticeably reduced neutralization against Lambda variant. F490S contributed more than L452Q in affecting the neutralization. In addition, the neutralization test with 12 published nAbs binding to RBD of SARS-CoV-2 with defined structures suggested that Lambda variant resisted the neutralization by some antibodies from Class 2 and Class 3. Overall, these results suggest that pre-existing antibody neutralization established by natural infection from non-Lambda variants or immunization could be significantly decreased, re-emphasizing the importance of ongoing viral mutation monitoring.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Neutralizing , Antibodies, Viral , Humans , Neutralization Tests , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus
2.
J Psychosoc Nurs Ment Health Serv ; : 1-7, 2022 Apr 13.
Article in English | MEDLINE | ID: covidwho-1789488

ABSTRACT

Using a cluster sampling method, 248 nurses from frontline departments of three large general hospitals in Sichuan Province, China, were selected as participants in the current study. Risk perception and coping methods during the coronavirus disease 2019 (COVID-19) pandemic, negative emotions and psychological workload, and awareness of social support among nurses were studied. Negative emotions among nurses increased significantly, with fear being the most common (73.4%, n = 182). Psychological workload of nurses in close contact with patients with COVID-19 was higher than that of nurses in other positions (p < 0.05). Family was the major source of social support. Social support was negatively associated with depression (-0.206, p < 0.05), obsessive-compulsiveness/anxiety (-0.185, p < 0.05), and hypochondriasis (-0.234, p < 0.05). Psychological workload of nurses was positively correlated with depression (0.251, p < 0.05), neurasthenia (0.242, p < 0.05), and obsessive-compulsiveness/anxiety (0.231, p < 0.05). Nursing staff in frontline departments encountered psychological workload burdens to varying degrees during the COVID-19 pandemic. Thus, it is important to implement and strengthen psychological counseling for nurses in close contact positions, and to seek family and social support for nurses. [Journal of Psychosocial Nursing and Mental Health Services, xx(x), xx-xx.].

3.
Healthcare (Basel) ; 10(2)2022 Feb 01.
Article in English | MEDLINE | ID: covidwho-1715255

ABSTRACT

During the process of disease diagnosis, overdiagnosis can lead to potential health loss and unnecessary anxiety for patients as well as increased medical costs, while underdiagnosis can result in patients not being treated on time. To deal with these problems, we construct a partially observable Markov decision process (POMDP) model of chronic diseases to study optimal diagnostic policies, which takes into account individual characteristics of patients. The objective of our model is to maximize a patient's total expected quality-adjusted life years (QALYs). We also derive some structural properties, including the existence of the diagnostic threshold and the optimal diagnosis age for chronic diseases. The resulting optimization is applied to the management of coronary heart disease (CHD). Based on clinical data, we validate our model, demonstrate how the quantitative tool can provide actionable insights for physicians and decision makers in health-related fields, and compare optimal policies with actual clinical decisions. The results indicate that the diagnostic threshold first decreases and then increases as the patient's age increases, which contradicts the intuitive non-decreasing thresholds. Moreover, diagnostic thresholds were higher for women than for men, especially at younger ages.

6.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-324402

ABSTRACT

In June 2020, Arizona, U.S., emerged as one of the world's worst coronavirus disease 2019(COVID-19) spots after the stay-at-home order was lifted in the middle of May. However, with the decisions to reimpose restrictions, the number of COVID-19 cases has been declining, and Arizona is considered to be a good model in slowing the epidemic. In this paper, we aimed to examine the COVID-19 situation in Arizona and assess the impact of human mobility change. We constructed the mobility integrated metapopulation susceptible-infectious-removed model and fitted to publicly available datasets on COVID-19 cases and mobility changes in Arizona. Our simulations showed that by reducing human mobility, the peak time was delayed, and the final size of the epidemic was decreased in all three regions. Our analysis suggests that rapid and effective decision making is crucial to control human mobility and, therefore, COVID-19 epidemics. Until a vaccine is available, reimplementations of mobility restrictions in response to the increase of new COVID-19 cases might need to be considered in Arizona and beyond.

7.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-323581

ABSTRACT

The outbreak of COVID-19 disrupts the life of many people in the world. The state of Arizona in the U.S. emerges as one of the country's newest COVID-19 hot spots. Accurate forecasting for COVID-19 cases will help governments to implement necessary measures and convince more people to take personal precautions to combat the virus. It is difficult to accurately predict the COVID-19 cases due to many human factors involved. This paper aims to provide a forecasting model for COVID-19 cases with the help of human activity data from the Google Community Mobility Reports. To achieve this goal, a specific partial differential equation (PDE) is developed and validated with the COVID-19 data from the New York Times at the county level in the state of Arizona in the U.S. The proposed model describes the combined effects of transboundary spread among county clusters in Arizona and human actives on the transmission of COVID-19. The results show that the prediction accuracy of this model is well acceptable (above 94\%). Furthermore, we study the effectiveness of personal precautions such as wearing face masks and practicing social distancing on COVID-19 cases at the local level. The localized analytical results can be used to help to slow the spread of COVID-19 in Arizona. To the best of our knowledge, this work is the first attempt to apply PDE models on COVID-19 prediction with the Google Community Mobility Reports.

8.
Front Public Health ; 9: 835500, 2021.
Article in English | MEDLINE | ID: covidwho-1674416

ABSTRACT

This study aims to evaluate the changes in the credit risk of the health care industry in China due to the COVID-19 epidemic by the modified KMV (named by Kealhofer, Mcquown, and Vasicek) model to calculate the default distances. We observe that the overall default distance mainly first decreased and then increased before and after the COVID-19 epidemic control in China; after the epidemic was controlled, the overall credit risk was reduced by 22.8%. Specifically, as shown in subdivided industries, health care equipment and health care facilities have larger credit risk fluctuations, while health care suppliers, health care distributors, and health care services have smaller fluctuations. These results can contribute to our understanding of why the COVID-19 epidemic in China could be controlled earlier, and software facilities are more important than hardware facilities in public health safety. Our methodological innovation is to use the GARCH (generalized autoregressive conditional heteroskedasticity) model and threshold regression model to modify the important parameters of the KMV model. This method has good accuracy in the Chinese environment.


Subject(s)
COVID-19 , China/epidemiology , Health Care Sector , Humans , Industry , SARS-CoV-2
9.
Front Immunol ; 12: 816745, 2021.
Article in English | MEDLINE | ID: covidwho-1662588

ABSTRACT

COVID-19 patients show heterogeneous and dynamic immune features which determine the clinical outcome. Here, we built a single-cell RNA sequencing (scRNA-seq) dataset for dissecting these complicated immune responses through a longitudinal survey of COVID-19 patients with various categories of outcomes. The data reveals a highly fluctuating peripheral immune landscape in severe COVID-19, whereas the one in asymptomatic/mild COVID-19 is relatively steady. Then, the perturbed immune landscape in peripheral blood returned to normal state in those recovered from severe COVID-19. Importantly, the imbalance of the excessively strong innate immune response and delayed adaptive immunity in the early stage of viral infection accelerates the progression of the disease, indicated by a transient strong IFN response and weak T/B-cell specific response. The proportion of abnormal monocytes appeared early and rose further throughout the severe disease. Our data indicate that a dynamic immune landscape is associated with the progression and recovery of severe COVID-19, and have provided multiple immune biomarkers for early warning of severe COVID-19.


Subject(s)
Adaptive Immunity/immunology , COVID-19/immunology , Interferons/immunology , B-Lymphocytes/immunology , Humans , Immunity, Innate/immunology , SARS-CoV-2/immunology , T-Lymphocytes/immunology
10.
Cell Discov ; 7(1): 60, 2021 Aug 04.
Article in English | MEDLINE | ID: covidwho-1541177

ABSTRACT

Severe coronavirus disease 2019 (COVID-19) is often indicated by lymphopenia and increased myelopoiesis; however, the underlying mechanism is still unclear, especially the alteration of hematopoiesis. It is important to explore to what extent and how hematopoietic stem cells contribute to the impairment of peripheral lymphoid and myeloid compartments in COVID-19 patients. In this study, we used single-cell RNA sequencing to assess bone marrow mononuclear cells from COVID-19 patients with peripheral blood mononuclear cells as control. The results showed that the hematopoietic stem cells in these patients were mainly in the G1 phase and prone to apoptosis, with immune activation and anti-viral responses. Importantly, a significant accumulation of immature myeloid progenitors and a dramatic reduction of lymphoid progenitors in severe cases were identified, along with the up-regulation of transcription factors (such as SPI1, LMO4, ETS2, FLI1, and GATA2) that are important for the hematopoietic stem cell or multipotent progenitor to differentiate into downstream progenitors. Our results indicate a dysregulated hematopoiesis in patients with severe COVID-19.

11.
Sustainability ; 13(22):12932, 2021.
Article in English | ProQuest Central | ID: covidwho-1538521

ABSTRACT

Cruise tourism on the Yangtze River Basin has developed rapidly in recent years. However, it is still facing such challenges as homogenization of itinerary and shore attraction arrangement, as well as aging cruise ships and simplification of service facilities, while it is also difficult to satisfy hierarchical and personalized tourist needs. To change such circumstances, new-build river cruise ships are inevitable. Complexity of market supply and demand environment, together with variability of tourist preferences, have increased market uncertainties of new-build cruise products. This study aims to assess market risks of new-build river cruise ships first by identifying risk factors, from the perspective of supply and demand under the actual conditions of the Yangtze River cruise market, then by evaluating potential impacts, caused by risk factors based on multi-criteria decision-making considerations. Fuzzy AHP-PROMETHEE was employed to prioritize the risk factors. The results reveal that among the most significant market risk factors are the following, in sequence: backwardness of support facilities;sudden security crisis;homogenization of cruise products;simplification of tourism route design;and inadequate management of the tourism market. Such findings will provide beneficial insights for strategic and sustainable development of river cruises on the Yangtze River.

13.
Applied Sciences ; 11(20):9671, 2021.
Article in English | ProQuest Central | ID: covidwho-1480549

ABSTRACT

The information cluster that supports the final decision in a decision task is usually presented as a series of information. According to the serial position effect, the decision result is easily affected by the presentation order of the information. In this study, we seek to investigate how the presentation mode of commodities and the informativeness on a shopping website will influence online shopping decisions. To this end, we constructed two experiments via a virtual online shopping environment. The first experiment suggests that the serial position effect can induce human computer interaction decision-making bias, and user decision-making results in separate evaluation mode are more prone to the recency effect, whereas user decision-making results in joint evaluation mode are more prone to the primacy effect. The second experiment confirms the influence of explicit and implicit details of information on the decision bias of the human computer interaction caused by the serial position effect. The results of the research will be better applied to the design and development of shopping websites or further applied to the interactive design of complex information systems to alleviate user decision-making biases and induce users to make more rational decisions.

14.
J Appl Genet ; 63(1): 159-167, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1469782

ABSTRACT

During SARS-CoV-2 proliferation, the translation of viral RNAs is usually the rate-limiting step. Understanding the molecular details of this step is beneficial for uncovering the origin and evolution of SARS-CoV-2 and even for controlling the pandemic. To date, it is unclear how SARS-CoV-2 competes with host mRNAs for ribosome binding and efficient translation. We retrieved the coding sequences of all human genes and SARS-CoV-2 genes. We systematically profiled the GC content and folding energy of each CDS. Considering that some fixed or polymorphic mutations exist in SARS-CoV-2 and human genomes, all algorithms and analyses were applied to both pre-mutate and post-mutate versions. In SARS-CoV-2 but not human, the 5-prime end of CDS had lower GC content and less RNA structure than the 3-prime part, which was favorable for ribosome binding and efficient translation initiation. Globally, the fixed and polymorphic mutations in SARS-CoV-2 had created an even lower GC content at the 5-prime end of CDS. In contrast, no similar patterns were observed for the fixed and polymorphic mutations in human genome. Compared with human RNAs, the SARS-CoV-2 RNAs have less RNA structure in the 5-prime end and thus are more favorable of fast translation initiation. The fixed and polymorphic mutations in SARS-CoV-2 are further amplifying this advantage. This might serve as a strategy for SARS-CoV-2 to adapt to the human host.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Mutation , Pandemics , RNA, Messenger/genetics
15.
Evol Bioinform Online ; 17: 11769343211052013, 2021.
Article in English | MEDLINE | ID: covidwho-1463169

ABSTRACT

SARS-CoV-2 needs to efficiently make use of the resources from hosts in order to survive and propagate. Among the multiple layers of regulatory network, mRNA translation is the rate-limiting step in gene expression. Synonymous codon usage usually conforms with tRNA concentration to allow fast decoding during translation. It is acknowledged that SARS-CoV-2 has adapted to the codon usage of human lungs so that the virus could rapidly proliferate in the lung environment. While this notion seems to nicely explain the adaptation of SARS-CoV-2 to lungs, it is unable to tell why other viruses do not have this advantage. In this study, we retrieve the GTEx RNA-seq data for 30 tissues (belonging to over 17 000 individuals). We calculate the RSCU (relative synonymous codon usage) weighted by gene expression in each human sample, and investigate the correlation of RSCU between the human tissues and SARS-CoV-2 or RaTG13 (the closest coronavirus to SARS-CoV-2). Lung has the highest correlation of RSCU to SARS-CoV-2 among all tissues, suggesting that the lung environment is generally suitable for SARS-CoV-2. Interestingly, for most tissues, SARS-CoV-2 has higher correlations with the human samples compared with the RaTG13-human correlation. This difference is most significant for lungs. In conclusion, the codon usage of SARS-CoV-2 has adapted to human lungs to allow fast decoding and translation. This adaptation probably took place after SARS-CoV-2 split from RaTG13 because RaTG13 is less perfectly correlated with human. This finding depicts the trajectory of adaptive evolution from ancestral sequence to SARS-CoV-2, and also well explains why SARS-CoV-2 rather than other viruses could perfectly adapt to human lung environment.

16.
PLoS One ; 15(8): e0238490, 2020.
Article in English | MEDLINE | ID: covidwho-1388885

ABSTRACT

SARS-CoV-2 is still rampaging throughout the world while the many evolutionary studies on it are simultaneously springing up. Researchers have simply utilized the public RNA-seq data to find out the so-called SNPs in the virus genome. The evolutionary analyses were largely based on these mutations. Here, we claim that we reliably detected A-to-G RNA modifications in the RNA-seq data of SARS-CoV-2 with high signal to noise ratios, presumably caused by the host's deamination enzymes. Intriguingly, since SARS-CoV-2 is an RNA virus, it is technically impossible to distinguish SNPs and RNA modifications from the RNA-seq data alone without solid evidence, making it difficult to tell the evolutionary patterns behind the mutation spectrum. Researchers should clarify their biological significance before they automatically regard the mutations as SNPs or RNA modifications. This is not a problem for DNA organisms but should be seriously considered when we are investigating the RNA viruses.


Subject(s)
Betacoronavirus/genetics , Evolution, Molecular , Polymorphism, Single Nucleotide , RNA, Viral/genetics , Base Sequence , COVID-19 , Coronavirus Infections , Humans , Mutation Rate , Pandemics , Pneumonia, Viral , RNA-Seq , SARS-CoV-2
17.
Nat Commun ; 12(1): 250, 2021 01 11.
Article in English | MEDLINE | ID: covidwho-1387324

ABSTRACT

Understanding the mechanism for antibody neutralization of SARS-CoV-2 is critical for the development of effective therapeutics and vaccines. We recently isolated a large number of monoclonal antibodies from SARS-CoV-2 infected individuals. Here we select the top three most potent yet variable neutralizing antibodies for in-depth structural and functional analyses. Crystal structural comparisons reveal differences in the angles of approach to the receptor binding domain (RBD), the size of the buried surface areas, and the key binding residues on the RBD of the viral spike glycoprotein. One antibody, P2C-1F11, most closely mimics binding of receptor ACE2, displays the most potent neutralizing activity in vitro and conferred strong protection against SARS-CoV-2 infection in Ad5-hACE2-sensitized mice. It also occupies the largest binding surface and demonstrates the highest binding affinity to RBD. More interestingly, P2C-1F11 triggers rapid and extensive shedding of S1 from the cell-surface expressed spike glycoprotein, with only minimal such effect by the remaining two antibodies. These results offer a structural and functional basis for potent neutralization via disruption of the very first and critical steps for SARS-CoV-2 cell entry.


Subject(s)
Angiotensin-Converting Enzyme 2/chemistry , Angiotensin-Converting Enzyme 2/metabolism , Antibodies, Monoclonal/chemistry , Antibodies, Neutralizing/immunology , COVID-19/immunology , SARS-CoV-2/immunology , Animals , Antibodies, Monoclonal/immunology , Antibodies, Monoclonal/therapeutic use , Antibodies, Viral/immunology , Binding Sites , COVID-19/drug therapy , COVID-19/virology , Disease Models, Animal , Epitopes , HEK293 Cells , Humans , Mice , Mice, Inbred BALB C , Models, Molecular , Protein Binding , Protein Conformation , Receptors, Virus/immunology , Receptors, Virus/metabolism , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism , Virus Internalization
18.
J Immunol ; 207(7): 1848-1856, 2021 10 01.
Article in English | MEDLINE | ID: covidwho-1377034

ABSTRACT

Immune cell responses are strikingly altered in patients with severe coronavirus disease 2019 (COVID-19), but the immunoregulatory process in these individuals is not fully understood. In this study, 23 patients with mild and 22 patients with severe COVID-19 and 6 asymptomatic carriers of COVID-19 were enrolled, along with 44 healthy controls (HC). Peripheral immune cells in HC and patients with COVID-19 were comprehensively profiled using mass cytometry. We found that in patients with severe COVID-19, the number of HLA-DRlow/- monocytes was significantly increased, but that of mucosal-associated invariant T (MAIT) cells was greatly reduced. MAIT cells were highly activated but functionally impaired in response to Escherichia coli and IL-12/IL-18 stimulation in patients with severe COVID-19, especially those with microbial coinfection. Single-cell transcriptome analysis revealed that IFN-stimulated genes were significantly upregulated in peripheral MAIT cells and monocytes from patients with severe COVID-19. IFN-α pretreatment suppressed MAIT cells' response to E. coli by triggering high levels of IL-10 production by HLA-DRlow/--suppressive monocytes. Blocking IFN-α or IL-10 receptors rescued MAIT cell function in patients with severe COVID-19. Moreover, plasma from patients with severe COVID-19 inhibited HLA-DR expression by monocytes through IL-10. These data indicate a unique pattern of immune dysregulation in severe COVID-19, which is characterized by enrichment of suppressive HLA-DRlow/- monocytes associated with functional impairment of MAIT cells through the IFN/IL-10 pathway.


Subject(s)
COVID-19/immunology , Escherichia coli Infections/immunology , Escherichia coli/physiology , Interleukin-10/metabolism , Monocytes/immunology , Mucosal-Associated Invariant T Cells/immunology , SARS-CoV-2/physiology , Adolescent , Adult , Asymptomatic Diseases , Cells, Cultured , Child , Coinfection , Disease Progression , Female , Humans , Immune Tolerance , Lymphocyte Activation , Male , Middle Aged , Severity of Illness Index , Young Adult
20.
Symmetry (20738994) ; 13(7):1264-1264, 2021.
Article in English | Academic Search Complete | ID: covidwho-1332178

ABSTRACT

We consider a k-nearest neighbor-based nonparametric lack-of-fit test of constant regression in presence of heteroscedastic variances. The asymptotic distribution of the test statistic is derived under the null and local alternatives for a fixed number of nearest neighbors. Advantages of our test compared to classical methods include: (1) The response variable can be discrete or continuous regardless of whether the conditional distribution is symmetric or not and can have variations depending on the predictor. This allows our test to have broad applicability to data from many practical fields;(2) this approach does not need nonlinear regression function estimation that often affects the power for moderate sample sizes;(3) our test statistic achieves the parametric standardizing rate, which gives more power than smoothing-based nonparametric methods for moderate sample sizes. Our numerical simulation shows that the proposed test is powerful and has noticeably better performance than some well known tests when the data were generated from high frequency alternatives or binary data. The test is illustrated with an application to gene expression data and an assessment of Richards growth curve fit to COVID-19 data. [ABSTRACT FROM AUTHOR] Copyright of Symmetry (20738994) is the property of MDPI and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

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