Development of a multiplex qRT-PCR assay for the detection of porcine epidemic diarrhea virus, porcine transmissible gastroenteritis virus and porcine Deltacoronavirus.

Currently, porcine coronaviruses are prevalent in pigs, and due to the outbreak of COVID-19, porcine coronaviruses have become a research hotspot. porcine epidemic diarrhea virus (PEDV), Transmissible Gastroenteritis Virus (TGEV), and Porcine Deltacoronavirus (PDCoV) mentioned in this study mainly cause diarrhea in pigs. These viruses cause significant economic losses and pose a potential public health threat. In this study, specific primers and probes were designed according to the M gene of PEDV, the S gene of TGEV, and the M gene of PDCoV, respectively, and TaqMan probe-based multiplex real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was developed for the simultaneous detection of PEDV, TGEV, and PDCoV. This method has high sensitivity and specificity, and the detection limit of each virus can reach 2.95 × 100 copies/µl. An assay of 160 clinical samples from pigs with diarrhea showed that the positive rates of PEDV, TGEV, and PDCoV were 38.13, 1.88, and 5.00%; the coinfection rates of PEDV+TGEV, PEDV+PDCoV, TGEV+PDCoV, PEDV+TGEV+PDCoV were 1.25, 1.25, 0, 0.63%, respectively. The positive coincidence rates of the multiplex qRT-PCR and single-reaction qRT-PCR were 100%. This method is of great significance for clinical monitoring of the porcine enteric diarrhea virus and helps reduce the loss of the breeding industry and control the spread of the disease.

Knowledge, attitudes, and practice related to the prone positioning of patients among intensive care unit nurses working in COVID-19 units: A cross-sectional study in China.

BACKGROUND: An increasing number of studies persistently demonstrate that prone position ventilation can significantly improve the oxygenation index and blood oxygen saturation for most patients (70-80%) with acute respiratory distress syndrome (ARDS). Studies have also shown that the awake prone position was both safe and effective in helping patients with coronavirus disease 2019 (COVID-19) breathe spontaneously. However, the prone position is not widely adopted when treating patients with COVID-19 or ARDS from other causes. Basic knowledge, positive attitudes, and correct practices among the nursing staff are necessary to increase the use of prone positions, reduce the incidence of complications associated with prone positions, and improve the quality and safety of health care. AIM: This study aimed to investigate the knowledge, attitudes, and practice of prone positioning of patients among intensive care unit (ICU) nurses working in COVID-19 units and provide suggestions for improvement. STUDY DESIGN: ICU nurses were recruited from two designated tertiary hospitals for COVID-19 treatment in Shanghai, China, in April 2022, using convenience sampling. A questionnaire survey focusing on the dimensions of knowledge, attitudes, and practice of the prone position with 42 items, was conducted. RESULTS: A total of 132 ICU nurses participated. The scores on the overall questionnaire and the dimensions of knowledge, attitudes, and practice of prone position were 167.28 (95% CI, 161.70-172.86), 78.35 (95% CI, 76.04-80.66), 32.08 (95% CI, 31.51-32.65), and 56.85 (95% CI, 52.42-61.28) respectively. The overall average score was 79.66% (95% CI, 0.77-0.82). The results of multiple linear regression analysis showed that prior experience in treating patients with COVID-19 and professional titles were related to the level of knowledge, attitudes, and practice of prone position. CONCLUSIONS: The ICU nurses strongly believed in the effectiveness of prone positioning, but their knowledge and practice levels need improvement. The experience in treating patients with COVID-19 and professional titles were related to the level of knowledge, attitudes, and practice of prone position. Nursing managers should ensure that ICU nurses are well trained in prone positioning and help enhance the knowledge and attitudes toward prone positioning to promote its widespread use. RELEVANCE TO CLINICAL PRACTICE: Clinical guidelines and in-service training modules need to be developed to promote the use of prone positioning and reduce prone position-related complications.

Development of a multiplex RT-PCR method for the detection of four porcine enteric coronaviruses.

Porcine enteric coronaviruses are pathogens that cause viral diarrhea in pigs and are widely prevalent worldwide. Moreover, studies have shown that some porcine enteric coronaviruses can infect humans and poultry. In order to effectively monitor these viruses, it is necessary to establish a multiple detection method to understand their prevalence and conduct in-depth research. Common porcine enteric coronaviruses include Porcine epidemic diarrhea virus (PEDV), Porcine transmissible gastroenteritis virus (TGEV), Porcine delta coronavirus (PDCoV), and Swine acute diarrhea syndrome coronavirus (SADS-CoV). Pigs infected with these viruses have the common clinical symptoms that are difficult to distinguish. A quadruplex RT-PCR (reverse transcription-polymerase chain reaction) method for the simultaneous detection of PEDV, PDCoV, TGEV and SADS-CoV was developed. Four pairs of specific primers were designed for the PEDV M gene, PDCoV N gene, TGEV S gene and SADS-CoV RdRp gene. Multiplex RT-PCR results showed that the target fragments of PDCoV, SADS-CoV, PEDV and TGEV could be amplified by this method. and the specific fragments with sizes of 250 bp, 368 bp, 616 bp and 801 bp were amplified, respectively. This method cannot amplify any fragment of nucleic acids of Seneca Valley virus (SVV), Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and Atypical Porcine Pestivirus (APPV), and has good specificity. The lowest detection limits of PDCoV, PEDV, TGEV and SADS-CoV were 5.66 × 105 copies/µL, 6.48 × 105 copies/µL, 8.54 × 105 copies/µL and 7.79 × 106 copies/µL, respectively. A total of 94 samples were collected from pig farms were analyzed using this method. There were 15 positive samples for PEDV, 3 positive samples for mixed infection of PEDV and PDCoV, 2 positive samples for mixed infection of PEDV and TGEV, and 1 positive sample for mixed infection of PEDV, TGEV, and PDCoV. Multiplex RT-PCR method could detect four intestinal coronaviruses (PEDV, PDCoV, TGEV, and SADS-CoV) in pigs efficiently, cheaply and accurately, which can be used for clinical large-scale epidemiological investigation and diagnosis.

Inhibitors of HIV-1 and Cathepsin L Proteases Identified from the Insect Gall of Hypericum kouytchense.

Hypericum kouytchense Lévl is a semi-evergreen plant of the Hypericaceae family. Its roots and seeds have been used in a number of traditional remedies for antipyretic, detoxification, anti-inflammatory, antimicrobial and antiviral functions. However, to date, no bioactivity compounds have been characterized from the insect gall of H. kouytchens. In this study, we evaluated the antiviral activities of different extracts from the insect gall of H. kouytchen against cathepsin L, HIV-1 and renin proteases and identified the active ingredients using UPLC-HRMS. Four different polar extracts (HW, H30, H60 and H85) of the H. kouytchense insect gall exhibited antiviral activities with IC50 values of 10.0, 4.0, 3.2 and 17.0 µg/mL against HIV-1 protease; 210.0, 34.0, 24.0 and 30.0 µg/mL against cathepsin L protease; and 180.0, 65.0, 44.0 and 39.0 µg/mL against human renin, respectively. Ten compounds were identified and quantified in the H. kouytchense insect gall extracts. Epicatechin, eriodictyol and naringenin chalcone were major ingredients in the extracts with contents ranging from 3.9 to 479.2 µg/mg. For HIV-1 protease, seven compounds showed more than 65% inhibition at a concentration of 1000.0 µg/mL, especially for hypericin and naringenin chalcone with IC50 values of 1.8 and 33.0 µg/mL, respectively. However, only hypericin was active against cathepsin L protease with an IC50 value of 17100.0 µg/mL, and its contents were from 0.99 to 11.65 µg/mg. Furthermore, we attempted to pinpoint the interactions between the active compounds and the proteases using molecular docking analysis. Our current results imply that the extracts and active ingredients could be further formulated and/or developed for potential prevention and treatment of HIV or SARS-CoV-2 infections.

Bioinformatics analysis of potential common pathogenic mechanisms for COVID-19 infection and primary Sjogren's syndrome.

Background: Accumulating evidence has revealed that the prevalence of Coronavirus 2019 (COVID-19) was significantly higher in patients with primary Sjogren's syndrome (pSS) compared to the general population. However, the mechanism remains incompletely elucidated. This study aimed to further investigate the molecular mechanisms underlying the development of this complication. Methods: The gene expression profiles of COVID-19 (GSE157103) and pSS (GSE40611) were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the common differentially expressed genes (DEGs) for pSS and COVID-19, functional annotation, protein-protein interaction (PPI) network, module construction and hub gene identification were performed. Finally, we constructed transcription factor (TF)-gene regulatory network and TF-miRNA regulatory network for hub genes. Results: A total of 40 common DEGs were selected for subsequent analyses. Functional analyses showed that cellular components and metabolic pathways collectively participated in the development and progression of pSS and COVID-19. Finally, 12 significant hub genes were identified using the cytoHubba plugin, including CMPK2, TYMS, RRM2, HERC5, IFI44L, IFI44, IFIT2, IFIT1, IFIT3, MX1, CDCA2 and TOP2A, which had preferable values as diagnostic markers for COVID-19 and pSS. Conclusions: Our study reveals common pathogenesis of pSS and COVID-19. These common pathways and pivotal genes may provide new ideas for further mechanistic studies.

Phylogeography and evolutionary dynamics analysis of porcine delta-coronavirus with host expansion to humans.

From 2003 onwards, three pandemics have been caused by coronaviruses: severe acute respiratory syndrome coronavirus (SARS-CoV); middle east respiratory syndrome coronavirus (MERS-CoV); and, most recently, SARS-CoV-2. Notably, all three were transmitted from animals to humans. This would suggest that animals are potential sources of epidemics for humans. The emerging porcine delta-coronavirus was reported to infect children. This is a red flag that marks the ability of PDCoV to break barriers of cross-species transmission to humans. Therefore, we conducted molecular genetic analysis of global clade PDCoV to characterize spatiotemporal patterns of viral diffusion and genetic diversity. PDCoV was classified into three major lineages, according to distribution and phylogenetic analysis of PDCoV. It can be inferred based on the analysis results of the currently known PDCoV strains that PDCoV might originate in Asia. We also selected six special spike amino acid sequences to align and analyze to find seven significant mutation sites. The accumulation of these mutations may enhance dynamic movements, accelerating spike protein membrane fusion events and transmission. Altogether, our study offers a novel insight into the diversification, evolution, and interspecies transmission and origin of PDCoV and emphasizes the need to study the zoonotic potential of the PDCoV and comprehensive surveillance and enhanced biosecurity precautions for PDCoV.

Space-Time Variation and Spatial Differentiation of COVID-19 Confirmed Cases in Hubei Province Based on Extended GWR

Clarifying the regional transmission mechanism of COVID-19 has practical significance for effective protection. Taking 103 county-level regions of Hubei Province as an example, and taking the fastest-spreading stage of COVID-19, which lasted from 29 January 2020, to 29 February 2020, as the research period, we systematically analyzed the population migration, spatio-temporal variation pattern of COVID-19, with emphasis on the spatio-temporal differences and scale effects of related factors by using the daily sliding, time-ordered data analysis method, combined with extended geographically weighted regression (GWR). The results state that: Population migration plays a two-way role in COVID-19 variation. The emigrants’ and immigrants’ population of Wuhan city accounted for 3.70% and 73.05% of the total migrants’ population respectively;the restriction measures were not only effective in controlling the emigrants, but also effective in preventing immigrants. COVID-19 has significant spatial autocorrelation, and spatio-temporal differentiation has an effect on COVID-19. Different factors have different degrees of effect on COVID-19, and similar factors show different scale effects. Generally, the pattern of spatial differentiation is a transitional pattern of parallel bands from east to west, and also an epitaxial radiation pattern centered in the Wuhan 1 + 8 urban circle. This paper is helpful to understand the spatio-temporal evolution of COVID-19 in Hubei Province, so as to provide a reference for similar epidemic prevention.

Prognostic Value of a Clinical Biochemistry-Based Nomogram for Coronavirus Disease 2019.

Background: This study aimed to explore the predictive value of a clinical biochemistry-based nomogram in COVID-19. Methods: The plasma or serum concentrations/levels of carcinoembryonic antigen (CEA) and other biomarkers, e.g., C-reactive protein (CRP), white blood cell (WBC), interleukin-6 (IL-6), ferritin (Fer), procalcitonin (PCT), lymphocyte percentage (L%), D-dimer (D2), and neutrophils percentage (Neu%), were assessed in 314 hospitalized patients with confirmed COVID-19. The area under the curve was used to estimate the diagnostic and prognostic value for COVID-19. Cox and logistic regression analyses were used to estimate the independent prognostic risk factors for the survival of patients with COVID-19. Results: Receiver operating characteristic (ROC) curves were used to determine the area under the curve (AUC) values for CEA, IL-6, CRP, PCT, Fer, D-dimer levels and L%, Neu%, and WBC to assess disease classification. The critical values for these markers to predict severe disease type were then determined. The hazard ratio of prognosis for risk of COVID-19 identified CEA, WBC, CRP, PCT, Fer, D-dimer, Neu%, and L% as independent prognostic factors. For the nomogram of overall survival (OS), the C-index was 0.84, demonstrating a good discriminative performance. Conclusions: An OS nomogram for the clinical diagnosis and treatment of COVID-19 was constructed using biomarkers. These data will be useful for the diagnosis, management, and therapy of COVID-19.

The impact of social distancing during COVID-19: A conditional process model of negative emotions, alienation, affective disorders, and post-traumatic stress disorder.

Background The social distancing during COVID-19 is likely to cause a feeling of alienation, which may pose a threat to the public's mental health. Our research aims to examine the relationship between negative emotions and Post-Traumatic Stress Disorder (PTSD), considering the mediation effect of alienation and how it is moderated by anxiety and depression. Methods For this, the current study conducted a cross-sectional survey on 7145 participants during the outbreak of COVID-19, via online questionnaires comprised of a self-designed Negative emotions questionnaire, Symptom Check List 90 (SCL-90), PTSD Checklist-civilian version (PCL-C), and Adolescent Students Alienation Scale (ASAS). Results A total of 6666 pieces of data from the general population were included in the statistical analysis. The descriptive statistics showed a relatively mild level of mental disorders. Besides, results of Conditional Process Model analysis supported our hypotheses that negative emotions and alienation were both predictors for PTSD symptoms, and their direct and indirect effects were all moderated by the level of anxiety. Limitations This study was limited by the generality and causality of the conclusion. The moderating effect of depression was left for further study due to the collinearity problem of variables. Conclusions Social distancing may have an impact on individuals' mental health by the feeling of alienation, which was moderated by affective disorders. Clinical psychologists should identify individuals' particular cognition and mental disorders to provide a more accurate and adequate intervention for them.

Clinical characteristics and risk factors for in-hospital mortality of lung cancer patients with COVID-19: A multicenter, retrospective, cohort study.

BACKGROUND: Data on clinical, laboratory, and radiographic characteristics and risk factors for in-hospital mortality of lung cancer patients with COVID-19 are scarce. Here, we aimed to characterize the early clinical features of lung cancer patients with COVID-19 and identify risk factors associated with in-hospital mortality. METHODS: All consecutive lung cancer patients with laboratory-confirmed COVID-19 admitted to 12 hospitals in Hubei province, China, from 3 January to 6 May 2020 were included in the study. Patients without definite clinical outcomes during the period were excluded. Data on initial clinical, laboratory and radiographic findings were compared between survivors and nonsurvivors. Univariable and multivariable logistic regression analyses were used to explore the risk factors associated with in-hospital mortality. RESULTS: Of the 45 lung cancer patients (median [interquartile range] age, 66 [58-74] years; 68.9% males) included, 34 (75.6%) discharged and 11 (24.4%) died. Fever (73.3%) and cough (53.3%) were the dominant initial symptoms, and respiratory symptoms were common. Lung cancer patients also presented atypical appearances of COVID-19. In the multivariable analysis, prolonged prolongation prothrombin time (PT) (OR = 2.1, 95% CI: 1.00-4.41, P = 0.0497) and elevated high sensitivity cardiac troponin I (hs-TNI) (OR = 7.65, 95% CI: 1.24-47.39, P = 0.0287) were associated with an increased risk of in-hospital mortality. CONCLUSIONS: Lung cancer patients with COVID-19 have high in-hospital mortality. Prolonged PT and elevated hs-TNI are independent risk factors for in-hospital mortality of lung cancer patients with COVID-19. KEY POINTS: SIGNIFICANT FINDINGS OF THE STUDY: Lung cancer patients with COVID-19 have atypical early symptoms and imaging features. The prolonged prothrombin time and elevated high sensitivity cardiac troponin I are independent risk factors for in-hospital mortality of lung cancer patients with COVID-19. WHAT THIS STUDY ADDS: This study characterizes the early clinical features of lung cancer patients with COVID-19 in China, and identifies the risk factors associated with in-hospital mortality of lung cancer patients with COVID-19.

Characteristics of in peripheral blood of 70 hospitalized patients and 8 diarrhea patients with COVID-19.

Objective: To analyze the blood test indicators of patients after infection of COVID-19 in Chongqing and analyze the clinical indicators of 8 patients with diarrhea. Materials and Methods: From January 26, 2019 to February 13, 2020, 70 patients diagnosed with 2019-nCoV according to the World Health Organization interim guidance for NCP and divided into diarrhea and non-diarrhea groups. The laboratory tests liver and kidney function, blood routine, coagulation function, and immune status. Results: The study population included 70 hospitalized patients with confirmed CONV-2019. NCP patients (43males and 27 females) with a mean age of 48.57±17.80 (9~82) years and only 4.3% of patients have lung-related diseases. The positive rate of ESR, CRP, PT, IL6, lymphocyte count, GGT, Prealbumin and CD4 was more than 50%. We further analyzed the differences between 8 diarrhea patients and 62 non-diarrhea patients. Among these indicators, only Lymphocyte, CRP, Prealbumin and Cystatin C positive rate is more than 50%. Although there is no statistical difference in GGT, 100% of the 7 patients tested decreased. Conclusion: Our data recommended that the ESR, CRP, PT, IL6, lymphocyte count, GGT, prealbumin and CD4 have important value in the diagnosis of COVID-19, and the decrease of GGT may be an important indicator for judging the intestinal dysfunction of patients.

A Trial of Lopinavir-Ritonavir in Adults Hospitalized with Severe Covid-19.

BACKGROUND: No therapeutics have yet been proven effective for the treatment of severe illness caused by SARS-CoV-2. METHODS: We conducted a randomized, controlled, open-label trial involving hospitalized adult patients with confirmed SARS-CoV-2 infection, which causes the respiratory illness Covid-19, and an oxygen saturation (Sao2) of 94% or less while they were breathing ambient air or a ratio of the partial pressure of oxygen (Pao2) to the fraction of inspired oxygen (Fio2) of less than 300 mm Hg. Patients were randomly assigned in a 1:1 ratio to receive either lopinavir-ritonavir (400 mg and 100 mg, respectively) twice a day for 14 days, in addition to standard care, or standard care alone. The primary end point was the time to clinical improvement, defined as the time from randomization to either an improvement of two points on a seven-category ordinal scale or discharge from the hospital, whichever came first. RESULTS: A total of 199 patients with laboratory-confirmed SARS-CoV-2 infection underwent randomization; 99 were assigned to the lopinavir-ritonavir group, and 100 to the standard-care group. Treatment with lopinavir-ritonavir was not associated with a difference from standard care in the time to clinical improvement (hazard ratio for clinical improvement, 1.31; 95% confidence interval [CI], 0.95 to 1.80). Mortality at 28 days was similar in the lopinavir-ritonavir group and the standard-care group (19.2% vs. 25.0%; difference, -5.8 percentage points; 95% CI, -17.3 to 5.7). The percentages of patients with detectable viral RNA at various time points were similar. In a modified intention-to-treat analysis, lopinavir-ritonavir led to a median time to clinical improvement that was shorter by 1 day than that observed with standard care (hazard ratio, 1.39; 95% CI, 1.00 to 1.91). Gastrointestinal adverse events were more common in the lopinavir-ritonavir group, but serious adverse events were more common in the standard-care group. Lopinavir-ritonavir treatment was stopped early in 13 patients (13.8%) because of adverse events. CONCLUSIONS: In hospitalized adult patients with severe Covid-19, no benefit was observed with lopinavir-ritonavir treatment beyond standard care. Future trials in patients with severe illness may help to confirm or exclude the possibility of a treatment benefit. (Funded by Major Projects of National Science and Technology on New Drug Creation and Development and others; Chinese Clinical Trial Register number, ChiCTR2000029308.).

Risk Factors Associated With Acute Respiratory Distress Syndrome and Death in Patients With Coronavirus Disease 2019 Pneumonia in Wuhan, China.

Importance: Coronavirus disease 2019 (COVID-19) is an emerging infectious disease that was first reported in Wuhan, China, and has subsequently spread worldwide. Risk factors for the clinical outcomes of COVID-19 pneumonia have not yet been well delineated. Objective: To describe the clinical characteristics and outcomes in patients with COVID-19 pneumonia who developed acute respiratory distress syndrome (ARDS) or died. Design, Setting, and Participants: Retrospective cohort study of 201 patients with confirmed COVID-19 pneumonia admitted to Wuhan Jinyintan Hospital in China between December 25, 2019, and January 26, 2020. The final date of follow-up was February 13, 2020. Exposures: Confirmed COVID-19 pneumonia. Main Outcomes and Measures: The development of ARDS and death. Epidemiological, demographic, clinical, laboratory, management, treatment, and outcome data were also collected and analyzed. Results: Of 201 patients, the median age was 51 years (interquartile range, 43-60 years), and 128 (63.7%) patients were men. Eighty-four patients (41.8%) developed ARDS, and of those 84 patients, 44 (52.4%) died. In those who developed ARDS, compared with those who did not, more patients presented with dyspnea (50 of 84 [59.5%] patients and 30 of 117 [25.6%] patients, respectively [difference, 33.9%; 95% CI, 19.7%-48.1%]) and had comorbidities such as hypertension (23 of 84 [27.4%] patients and 16 of 117 [13.7%] patients, respectively [difference, 13.7%; 95% CI, 1.3%-26.1%]) and diabetes (16 of 84 [19.0%] patients and 6 of 117 [5.1%] patients, respectively [difference, 13.9%; 95% CI, 3.6%-24.2%]). In bivariate Cox regression analysis, risk factors associated with the development of ARDS and progression from ARDS to death included older age (hazard ratio [HR], 3.26; 95% CI 2.08-5.11; and HR, 6.17; 95% CI, 3.26-11.67, respectively), neutrophilia (HR, 1.14; 95% CI, 1.09-1.19; and HR, 1.08; 95% CI, 1.01-1.17, respectively), and organ and coagulation dysfunction (eg, higher lactate dehydrogenase [HR, 1.61; 95% CI, 1.44-1.79; and HR, 1.30; 95% CI, 1.11-1.52, respectively] and D-dimer [HR, 1.03; 95% CI, 1.01-1.04; and HR, 1.02; 95% CI, 1.01-1.04, respectively]). High fever (≥39 °C) was associated with higher likelihood of ARDS development (HR, 1.77; 95% CI, 1.11-2.84) and lower likelihood of death (HR, 0.41; 95% CI, 0.21-0.82). Among patients with ARDS, treatment with methylprednisolone decreased the risk of death (HR, 0.38; 95% CI, 0.20-0.72). Conclusions and Relevance: Older age was associated with greater risk of development of ARDS and death likely owing to less rigorous immune response. Although high fever was associated with the development of ARDS, it was also associated with better outcomes among patients with ARDS. Moreover, treatment with methylprednisolone may be beneficial for patients who develop ARDS.