Identification of hospitalized mortality of patients with COVID-19 by machine learning models based on blood inflammatory cytokines

Coronavirus disease 2019 (COVID-19) spread worldwide and presented a significant threat to people's health. Inappropriate disease assessment and treatment strategies bring a heavy burden on healthcare systems. Our study aimed to construct predictive models to assess patients with COVID-19 who may have poor prognoses early and accurately. This research performed a retrospective analysis on two cohorts of patients with COVID-19. Data from the Barcelona cohort were used as the training set, and data from the Rotterdam cohort were used as the validation set. Cox regression, logistic regression, and different machine learning methods including random forest (RF), support vector machine (SVM), and decision tree (DT) were performed to construct COVID-19 death prognostic models. Based on multiple clinical characteristics and blood inflammatory cytokines during the first day of hospitalization for the 138 patients with COVID-19, we constructed various models to predict the in-hospital mortality of patients with COVID-19. All the models showed outstanding performance in identifying high-risk patients with COVID-19. The accuracy of the logistic regression, RF, and DT models is 86.96, 80.43, and 85.51%, respectively. Advanced age and the abnormal expression of some inflammatory cytokines including IFN-α, IL-8, and IL-6 have been proven to be closely associated with the prognosis of patients with COVID-19. The models we developed can assist doctors in developing appropriate COVID-19 treatment strategies, including allocating limited medical resources more rationally and early intervention in high-risk groups.

Role of Neutrophils on the Ocular Surface.

The ocular surface is a gateway that contacts the outside and receives stimulation from the outside. The corneal innate immune system is composed of many types of cells, including epithelial cells, fibroblasts, natural killer cells, macrophages, neutrophils, dendritic cells, mast cells, basophils, eosinophils, mucin, and lysozyme. Neutrophil infiltration and degranulation occur on the ocular surface. Degranulation, neutrophil extracellular traps formation, called NETosis, and autophagy in neutrophils are involved in the pathogenesis of ocular surface diseases. It is necessary to understand the role of neutrophils on the ocular surface. Furthermore, there is a need for research on therapeutic agents targeting neutrophils and neutrophil extracellular trap formation for ocular surface diseases.

Corrigendum to: Genomic epidemiology reveals the reduction of the introduction and spread of SARS-CoV-2 after implementing control strategies in Republic of Korea, 2020.

[This corrects the article DOI: 10.1093/ve/veab077.].

Genomic evidence of SARS-CoV-2 reinfection in the Republic of Korea.

As the coronavirus disease 2019 (COVID-19) pandemic continues, reinfection is likely to become increasingly common. However, confirming COVID-19 reinfection is difficult because it requires whole-genome sequencing of both infections to identify the degrees of genetic differences. Since the first reported case of reinfection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the Republic of Korea in April 2020, four additional cases were classified as suspected reinfection cases. We performed whole-genome sequencing of viral RNA extracted from swabs obtained at the initial infection and reinfection stages of these four suspected cases. The interval between initial infection and reinfection of all four suspected cases was more than 3 months. All four patients were young (10-29 years), and they displayed mild symptoms or were asymptomatic during the initial infection and reinfection episodes. The analysis of genome sequences combined with the epidemiological results revealed that only two of the four cases were confirmed as reinfection, and both were reinfected with the Epsilon variant. Due to the prolonged COVID-19 pandemic, the possibility of reinfections with SARS-CoV-2 variants is increasing, as reported in our study. Therefore, continuous monitoring of cases is necessary.

Genomic epidemiology reveals the reduction of the introduction and spread of SARS-CoV-2 after implementing control strategies in Republic of Korea, 2020.

Genomic epidemiology is a core component in investigating the spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, the efficacy of control strategies in South Korea was evaluated using genomic epidemiology based on viral genome sequences of 2,065 SARS-CoV-2 cases identified in South Korea from January 2020 to December 2020. Phylogenetic analysis revealed that the majority of viruses introduced from inbound travelers did not further spread throughout South Korea; however, four distinct subgroups (KR.1-4, belonging to B.1.497, B.1, K.1 and B.41) of viruses caused local epidemics. After the introduction of enhanced social distancing, the viral population size and daily case numbers decreased, and KR.2-4 subgroups were extinguished from South Korea. Nevertheless, there was a subsequent increase in KR.1 subgroups after the downgrading of social distancing level. These results indicate that the international traveler quarantine system implemented in South Korea along with social distancing measures efficiently reduced the introduction and spread of SARS-CoV-2, but it was not completely controlled. An improvement of control strategies will be required to better control SARS-CoV-2, its variants, and future pandemic viruses.

Discovery and Genetic Characterization of Novel Paramyxoviruses Related to the Genus Henipavirus in Crocidura Species in the Republic of Korea.

Paramyxoviruses, negative-sense single-stranded RNA viruses, pose a critical threat to human public health. Currently, 78 species, 17 genera, and 4 subfamilies of paramyxoviruses are harbored by multiple natural reservoirs, including rodents, bats, birds, reptiles, and fish. Henipaviruses are critical zoonotic pathogens that cause severe acute respiratory distress and neurological diseases in humans. Using reverse transcription-polymerase chain reaction, 115 Crocidura species individuals were examined for the prevalence of paramyxovirus infections. Paramyxovirus RNA was observed in 26 (22.6%) shrews collected at five trapping sites, Republic of Korea. Herein, we report two genetically distinct novel paramyxoviruses (genus: Henipavirus): Gamak virus (GAKV) and Daeryong virus (DARV) isolated from C. lasiura and C. shantungensis, respectively. Two GAKVs and one DARV were nearly completely sequenced using next-generation sequencing. GAKV and DARV contain six genes (3'-N-P-M-F-G-L-5') with genome sizes of 18,460 nucleotides and 19,471 nucleotides, respectively. The phylogenetic inference demonstrated that GAKV and DARV form independent genetic lineages of Henipavirus in Crocidura species. GAKV-infected human lung epithelial cells elicited the induction of type I/III interferons, interferon-stimulated genes, and proinflammatory cytokines. In conclusion, this study contributes further understandings of the molecular prevalence, genetic characteristics and diversity, and zoonotic potential of novel paramyxoviruses in shrews.

The Psychological Effect of Forming WeChat Groups Between Medical Staff and Patients With COVID-19.

Background: This study was conducted in order to explore the effect of psychological intervention based on the use of WeChat with coronavirus disease 2019 (COVID-19) patients. Methods: A total of 65 patients with COVID-19, from two wards, were divided into an experimental group and a control group with the ward as the basic unit. Communication concerning routine treatment and nursing was established between the medical staff and patients in the experimental group via WeChat groups. Within 48 h of admission, at 7 days, and on discharge, all 65 patients completed two self-evaluation questionnaires: the Positive and Negative Affect Schedule (PANAS) and the Hospital Anxiety and Depression Scale (HADS). Hospital stay statistics and a satisfaction survey on discharge were also collated for both groups of patients. Results: The PANAS scores of the experimental group were 26.61 ± 7.99 points on admission, 20.81 ± 5.48 points at 7 days, and 19.58 ± 6.61 points on discharge (P < 0.05). The scores of HADS in the experimental group were 27.74 ± 9.35 points on admission, 12.19 ± 1.92 points at 7 days, and 11.71 ± 3.64 points on discharge (P < 0.05). The differences in the PANS and HADS scores between the experimental and control groups at 7 days and on discharge were statistically significant. The discharge satisfaction ratings of the two groups of patients were 99.87 ± 0.34 and 98.68 ± 1.09 points, the difference being statistically significant (t = 5.827, P < 0.05). Conclusion: Establishing WeChat groups between medical staff and patients with COVID-19 and building a bridge for better communication improved patients' positive mentality and their compliance with doctors, shortened their hospital stay, and promoted their recovery.

Interferon-armed RBD dimer enhances the immunogenicity of RBD for sterilizing immunity against SARS-CoV-2 (preprint)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global crisis, urgently necessitating the development of safe, efficacious, convenient-to-store, and low-cost vaccine options. A major challenge is that the receptor-binding domain (RBD)-only vaccine fails to trigger long-lasting protective immunity if used solely for vaccination. To enhance antigen processing and cross-presentation in draining lymph nodes (DLNs), we developed an interferon (IFN)-armed RBD dimerized by immunoglobulin fragment (I-R-F). I-R-F efficiently directs immunity against RBD to DLN. A low dose of I-R-F induces not only high titer long-lasting neutralizing antibodies but also comprehensive T cell responses than RBD, and even provides comprehensive protection in one dose without adjuvant. This study shows that the I-R-F vaccine provides rapid and complete protection throughout upper and lower respiratory tracts against high dose SARS-CoV-2 challenge in rhesus macaques. Due to its potency and safety, this engineered vaccine may become one of the next-generation vaccine candidates in the global race to defeat COVID-19.

School-Based Participatory Response for Reopening During the COVID-19 Pandemic: A Case Study of a Metropolitan High School Implementing the Health Promoting School.

Purpose: This study aimed to analyze how a private high school in Seoul developed and executed a "school disinfection strategy" to ensure the students' right to study in a safe environment, and also to analyze the lessons learned from this process. Methods: This was a case study of school health in a community-based school reopening during the COVID-19 pandemic. The study target was a 64-year-old private high school with 12 classes for each grade with a total of 1,100 students. Results: A "school disinfection strategy" was set up at individual and class environment levels to protect students from the risk of infection. In addition, school health activities were carried out with a "personal protection safety belt" and "community protection safety belt" for effective implementation. To ensure a safe educational environment for high school students and to ensure smooth execution of face-to-face classes (in-person teaching), the "prevention safety belt strategy" was introduced in accordance with governmental guidelines to sequentially implement various preventive measures necessary to guarantee environmental safety of schools. Activating personal prevention safety belts by checking the symptoms of students when entering the school and during each class, and providing self-made disinfectants by spraying alcohol on wet-wipes were cost-effective and sustainable methods used in this school to prevent the spread of infection. Conclusions: The experience of developing a prevention safety belt strategy to adapt the guidelines of the local education office to the school situation was presented. Focusing on the school community, as well as individual students and teachers, the concept of prevention safety belts helped to unite and stimulate voluntary participation of students in health promotion activities.

Contrasting SARS-CoV-2 Epidemics in Singapore: Cohort Studies in Migrant Workers and the General Population (preprint)

Background: From January 2020, Singapore implemented comprehensive measures to suppress SARS-CoV-2. Community transmission has been limited, although explosive outbreaks have occurred in migrant worker dormitories.Methods: We conducted longitudinal SARS-CoV-2 serology studies among 478 residents of a SARS-CoV-2 affected migrant worker dormitory between May and July 2020, and 937 community-dwelling adult Singapore residents with sera collected before September 2019 and in November/December 2020. We tested sera for SARS-CoV-2 neutralising antibodies and used Bayesian methods to estimate infection incidence accounting for test sensitivity and specificity.Findings: We estimated that <2 per 1000 adult residents in the community were infected with SARS-CoV-2 in 2020 (cumulative seroprevalence: 0.16% (95% CrI: 0.008% - 0.72%), approximately 4 times higher than the national notified case incidence. In contrast, in the migrant worker cohort, nearly two-thirds had been infected by July 2020 (cumulative seroprevalence: 63.8% (95% CrI: 57.9% - 70.3%); no symptoms were reported in almost all of these infections.Conclusions: Our findings demonstrate that SARS-CoV-2 suppression is possible with rapid implementation of border restrictions, case isolation, contact tracing, quarantining and social distancing measures. However, the risk of large-scale epidemics in densely-populated environments requires specific consideration in preparedness planning. Prioritising these settings in vaccination strategies should minimise risk of future resurgences and potential for spillover to the wider community.Funding: This work was funded by the Wellcome Trust grant (221013/Z/20/Z), the NUS Efforts Against COVID-19 fund and the Singapore National Medical Research Council (STPRG-FY19-001 and COVID19RF-003).Declaration of Interests: L-FW and WNC are co-inventors of a patent application for the cPass test kit. The remaining authors declare no competing interests in relation to this work.Ethics Approval Statement: The community cohort study was approved by the National University of Singapore Institutional Review Board (reference H-20-032).

Genomic Surveillance of SARS-CoV-2: Distribution of Clades in the Republic of Korea in 2020.

Since a novel beta-coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in December 2019, there has been a rapid global spread of the virus. Genomic surveillance was conducted on samples isolated from infected individuals to monitor the spread of genetic variants of SARS-CoV-2 in Korea. The Korea Disease Control and Prevention Agency performed whole genome sequencing of SARS-CoV-2 in Korea for 1 year (January 2020 to January 2021). A total of 2,488 SARS-CoV-2 cases were sequenced (including 648 cases from abroad). Initially, the prevalent clades of SARS-CoV-2 were the S and V clades, however, by March 2020, GH clade was the most dominant. Only international travelers were identified as having G or GR clades, and since the first variant 501Y.V1 was identified (from a traveler from the United Kingdom on December 22nd, 2020), a total of 27 variants of 501Y.V1, 501Y.V2, and 484K.V2 have been classified (as of January 25th, 2021). The results in this study indicated that quarantining of travelers entering Korea successfully prevented dissemination of the SARS-CoV-2 variants in Korea.

Highly functional virus-specific cellular immune response in asymptomatic SARS-CoV-2 infection (preprint)

The efficacy of virus-specific T cells in clearing pathogens involves a fine balance between their antiviral and inflammatory features. SARS-CoV-2-specific T cells in individuals who clear SARS-CoV-2 infection without symptoms or disease could reveal non-pathological yet protective characteristics. We therefore compared the quantity and function of SARS-CoV-2-specific T cells in a cohort of asymptomatic individuals (n=85) with that of symptomatic COVID-19 patients (n=76), at different time points after antibody seroconversion. We quantified T cells reactive to structural proteins (M, NP and Spike) using ELISpot assays, and measured the magnitude of cytokine secretion (IL-2, IFN-{gamma}, IL-4, IL-6, IL-1{beta}, TNF- and IL-10) in whole blood following T cell activation with SARS-CoV-2 peptide pools as a functional readout. Frequencies of T cells specific for the different SARS-CoV-2 proteins in the early phases of recovery were similar between asymptomatic and symptomatic individuals. However, we detected an increased IFN-{gamma} and IL-2 production in asymptomatic compared to symptomatic individuals after activation of SARS-CoV-2-specific T cells in blood. This was associated with a proportional secretion of IL-10 and pro-inflammatory cytokines (IL-6, TNF- and IL-1{beta}) only in asymptomatic infection, while a disproportionate secretion of inflammatory cytokines was triggered by SARS-CoV-2-specific T cell activation in symptomatic individuals. Thus, asymptomatic SARS-CoV-2 infected individuals are not characterized by a weak antiviral immunity; on the contrary, they mount a robust and highly functional virus-specific cellular immune response. Their ability to induce a proportionate production of IL-10 might help to reduce inflammatory events during viral clearance.

Unheeded SARS-CoV-2 protein? Look deep into negative-sense RNA (preprint)

SARS-CoV-2 is a novel ssRNA+ virus from the Coronaviridae family, which has caused the global COVID-19 pandemic. The genome of SARS-CoV-2 is one of the largest of RNA viruses, comprising of 26 known protein-coding loci. This study aimed to explore the coding potential of negative-strand RNA intermediate for its potential to contain additional protein coding-loci. Surprisingly, we have found several putative ORFs and one brandt new functional SARS-CoV-2 protein-coding loci and called it Avo1 (Ambient viral ORF1). This sequence is located on negative-sense RNA intermediate and bona fide coding for 81 amino acid residues long protein and contains strong Kozak sequence for translation on eukaryotic ribosomes. In silico translated protein Avo1 has a predominantly alpha-helical structure. The existence of Avo1 gene is supported also by its evolutionarily and structural conservation in RaTG13 bat coronavirus. The nucleotide sequence of Avo1 also contains a unique SREBP2 binding site which is closely related to the so-called cytokine storm in severe COVID-19 patients. Altogether, our results suggest the existence of still undescribed SARS-CoV-2 protein, which may play an important role in the viral lifecycle and COVID-19 pathogenesis.

2019 Tabletop Exercise for Laboratory Diagnosis and Analyses of Unknown Disease Outbreaks by the Korea Centers for Disease Control and Prevention.

OBJECTIVES: The Korea Centers for Disease Control and Prevention has published "A Guideline for Unknown Disease Outbreaks (UDO)." The aim of this report was to introduce tabletop exercises (TTX) to prepare for UDO in the future. METHODS: The UDO Laboratory Analyses Task Force in Korea Centers for Disease Control and Prevention in April 2018, assigned unknown diseases into 5 syndromes, designed an algorithm for diagnosis, and made a panel list for diagnosis by exclusion. Using the guidelines and laboratory analyses for UDO, TTX were introduced. RESULTS: Since September 9th, 2018, the UDO Laboratory Analyses Task Force has been preparing TTX based on a scenario of an outbreak caused by a novel coronavirus. In December 2019, through TTX, individual missions, epidemiological investigations, sample treatments, diagnosis by exclusions, and next generation sequencing analysis were discussed, and a novel coronavirus was identified as the causal pathogen. CONCLUSION: Guideline and laboratory analyses for UDO successfully applied in TTX. Conclusions drawn from TTX could be applied effectively in the analyses for the initial response to COVID-19, an ongoing epidemic of 2019 - 2020. Therefore, TTX should continuously be conducted for the response and preparation against UDO.

Age and chest radiography as possible parameters for rapid triage in COVID-19 outbreak surge (preprint)

BackgroundTo evaluate the utility of age and chest radiography(CXR) in triaging COVID-19 patients for hospitalization versus isolation in non-hospital facilities, we examined how age and CXR at diagnosis were associated with clinical needs from late-January to early-April. MethodsClinical status of all COVID-19 cases was monitored for national disease surveillance. Cases were isolated in hospitals until SARS-CoV-2 RNA was undetectable on PCR. Age and CXR results on admission were analysed for association with oxygen supplementation and mechanical ventilation, the outcomes of interest.ResultsTill 4 April 2020, there were 1,481 COVID-19 cases in Singapore. Overall, 11.4% required supplemental oxygen while 4.8% required mechanical ventilation and intensive care. The respective proportions increased to 40.9% and 16.5% for cases aged ≥70 years. As a predictor of subsequent mechanical ventilation, age had an area under the receiver operator characteristic curve(AUROC) of 0.772 (95%CI:0.699-0.845). A combined criterion of either an abnormal CXR or age≥55 years had a sensitivity of 86.7% and specificity of 58.0% for the same outcome. A similar performance was observed for predicting oxygen supplementation needs.ConclusionsAge and CXR at diagnosis may be valuable in excluding severe disease, allowing safe triage for isolation in non-hospital facilities. 

Emergence of the D614A mutation in the spike protein of SARS-CoV-2: Imported cases to the South Korea (preprint)

We identified imported cases of a novel D614A mutation in the spike glycoprotein of SARS-CoV-2 in the South Korea. SARS-CoV-2 harboring the novel mutation was isolated from returning travelers from Uzbekistan. These results emphasized the possibility that new mutations have emerged in that area.

SARS-CoV-2 manipulates the SR-B1-mediated HDL uptake pathway for its entry (preprint)

The recently emerged pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly, leading to a global COVID-19 pandemic. Binding of the viral spike protein (SARS-2-S) to cell surface receptor angiotensin-converting enzyme 2 (ACE2) mediates host cell infection. In the present study, we demonstrate that in addition to ACE2, the S1 subunit of SARS-2-S binds to HDL and that SARS-CoV-2 hijacks the SR-B1-mediated HDL uptake pathway to facilitate its entry. SR-B1 facilitates SARS-CoV-2 entry into permissive cells by augmenting virus attachment. MAb (monoclonal antibody)-mediated blocking of SARS-2-S-HDL binding and SR-B1 antagonists strongly inhibit HDL-enhanced SARS-CoV-2 infection. Notably, SR-B1 is co-expressed with ACE2 in human pulmonary and extrapulmonary tissues. These findings revealed a novel mechanism for SARS-CoV-2 entry and could provide a new target to treat SARS-CoV-2 infection.

Cholesterol Metabolism--Impact for SARS-CoV-2 Infection Prognosis, Entry, and Antiviral Therapies (preprint)

Abstract The recently emerged pathogenic SARS-coronavirus 2 (SARS-CoV-2) has spread rapidly, leading to a global pandemic. In this study, we show that SARS-CoV-2 infection was associated with clinically significant lower level of HDL cholesterol (HDL-C), which can be used as indicators of disease severity and poor prognosis. Importantly, we found the spike protein of SARS-CoV-2 (SARS-2-S) bound to HDL. Antagonists of HDL receptor-Scavenger receptor class B type I (SR-B1), strongly inhibited SARS-CoV-2 infection. Notably, the lipids transfer function of SR-B1 was indispensable for this inhibition, offering explanations for the reduced serum HDL level observed in COVID-19 patients. Basing on findings here, we speculate that SR-B1-mediated pulmonary HDL-vitamin E uptake could participate in mediating SARS-CoV-2 infection of lung cells, and the unique expression profile of SR-B1 may also affect SARS-CoV-2 cell and tissue tropism. These findings might help to provide further insights into viral transmission, pathological characteristics and reveal therapeutic targets.