Clinical features and viral etiology of acute respiratory infection in an outpatient fever clinic during COVID-19 pandemic in a tertiary hospital in Nanjing, China.

BACKGROUND: Clinical feature and viral etiology for acute respiratory infection (ARI) in the community was unknown during coronavirus disease 2019 (COVID-19) pandemic. OBJECTIVE: In a retrospective study, we aimed to characterize the clinical feature and etiology for the ARI patients admitted to the outpatient fever clinic in Nanjing Drum Tower Hospital between November 2020 and March 2021. METHODS: Fifteen common respiratory pathogens were tested using pharyngeal swabs by multiplex reverse transcriptase-polymerase chain reaction assays. RESULTS: Of the 242 patients, 56 (23%) were tested positive for at least one viral agent. The predominant viruses included human rhinovirus (HRV) (5.4%), parainfluenza virus type III (PIV-III) (5.0%), and human coronavirus-NL63 (HCoV-NL63) (3.7%). Cough, sputum, nasal obstruction, and rhinorrhea were the most prevalent symptoms in patients with viral infection. Elderly and the patients with underlying diseases were susceptible to pneumonia accompanied with sputum and chest oppression. Three (5.4%) patients in virus infection group, whereas 31 (16.7%) in non-viral infection group (p = 0.033), were empirically prescribed with antiviral agents. Among 149 patients who received antibiotic therapy, 30 (20.1%) patients were later identified with viral infection. CONCLUSION: Our study indicated the importance of accurate diagnosis of ARI, especially during the COVID-19 pandemic, which might facilitate appropriate clinical treatment.

RabbitV: fast detection of viruses and microorganisms in sequencing data on multi-core architectures.

MOTIVATION: Detection and identification of viruses and microorganisms in sequencing data plays an important role in pathogen diagnosis and research. However, existing tools for this problem often suffer from high runtimes and memory consumption. RESULTS: We present RabbitV, a tool for rapid detection of viruses and microorganisms in Illumina sequencing datasets based on fast identification of unique k-mers. It can exploit the power of modern multi-core CPUs by using multi-threading, vectorization, and fast data parsing. Experiments show that RabbitV outperforms fastv by a factor of at least 42.5 and 14.4 in unique k-mer generation (RabbitUniq) and pathogen identification (RabbitV), respectively. Furthermore, RabbitV is able to detect COVID-19 from 40 samples of sequencing data (255GB in FASTQ format) in only 320 seconds. AVAILABILITY: RabbitUniq and RabbitV are available at https://github.com/RabbitBio/RabbitUniq and https://github.com/RabbitBio/RabbitV. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Disrupted rhythms of life, work and entertainment and their associations with psychological impacts under the stress of the COVID-19 pandemic: A survey in 5854 Chinese people with different sociodemographic backgrounds

Background & aim: The coronavirus disease 2019 (COVID-19) pandemic has affected the life and work of people worldwide. The present study aimed to evaluate the rhythm disruptions of life, work, and entertainment, and their associations with the psychological impacts during the initial phase of the COVID-19 pandemic. Method: A cross-sectional study was conducted from the 10th to 17th March 2020 in China. A structured e-questionnaire containing general information, the Chinese version of Brief Social Rhythm Scale, and Zung's self-rating scales of depression and anxiety (SDS and SAS) was posted and collected online through a public media (i.e. EQxiu online questionnaire platform). Scores in sleeping, getting up, and socializing (SGS) rhythm and eating, physical practice, and entertainment (EPE) rhythm were compared among and between participants with different sociodemographic backgrounds including gender, age, education, current occupation, annual income, health status, and chronic disease status. Correlations of SDS and SAS with SGS-scale and EPE-scale were also analyzed. Results: Overall, 5854 participants were included. There were significant differences in the scores of SGS-scale and EPE-scale among people with different sociodemographic backgrounds. The scores were significantly higher in the groups with female gender, low education level, lower or higher than average income, poor health status, ages of 26-30 years or older than 61 years, nurses and subjects with divorce or widow status. There were also significant differences in SAS and SDS scores among people with different sociodemographic backgrounds (all P< 0.05). The overall prevalence of depression and anxiety was 24.3% and 12.6%, respectively, with nurses having the highest rates of depression (32.94%) and anxiety (18.98%) among the different occupational groups. SGS-scale was moderately correlated with SDS and SAS, and disruption of SGS rhythm was an independent risk factor for depression and anxiety. Conclusion: Social rhythm disruption was independently associated with depression and anxiety. Interventions should be applied to people vulnerable to the rhythm disruption during the COVID-19 pandemic. (PsycInfo Database Record (c) 2022 APA, all rights reserved)

Germinal center responses to SARS-CoV-2 mRNA vaccines in healthy and immunocompromised individuals.

Vaccine-mediated immunity often relies on the generation of protective antibodies and memory B cells, which commonly stem from germinal center (GC) reactions. An in-depth comparison of the GC responses elicited by SARS-CoV-2 mRNA vaccines in healthy and immunocompromised individuals has not yet been performed due to the challenge of directly probing human lymph nodes. Herein, through a fine-needle aspiration-based approach, we profiled the immune responses to SARS-CoV-2 mRNA vaccines in lymph nodes of healthy individuals and kidney transplant recipients (KTXs). We found that, unlike healthy subjects, KTXs presented deeply blunted SARS-CoV-2-specific GC B cell responses coupled with severely hindered T follicular helper cell, SARS-CoV-2 receptor binding domain-specific memory B cell, and neutralizing antibody responses. KTXs also displayed reduced SARS-CoV-2-specific CD4 and CD8 T cell frequencies. Broadly, these data indicate impaired GC-derived immunity in immunocompromised individuals and suggest a GC origin for certain humoral and memory B cell responses following mRNA vaccination.

Development and Validation of a New Prognostic Scoring System for COVID-19.

This study aimed to develop and validate a bedside risk analysis system for predicting the clinical severity and prognosis of patients with coronavirus disease 2019 (COVID-19). In total, 444 COVID-19 patients were included and randomly assigned in a 2:1 ratio to 2 groups: derivation group and validation group. The new scoring system comprised of the following 8 variables: history of malignant diseases, history of diabetes mellitus, dyspnea, respiratory rate >24 breaths/min, C-reactive protein level >14 mg/L, white blood cell count >8×109/L, platelets count <180 × 1012/L, and lymphocyte count <1 × 109/L. The sensitivity analysis revealed that this new scoring system was more efficient than the sequential organ failure assessment scoring system on the first day of admission. The receiver characteristic curve analysis revealed that the new risk scoring predicted the severe cases of COVID-19 infection with an area under the curve of 0.831 (95% confidence interval [CI]: 0.783-0.879) and 0.798 (95% CI: 0.727-0.869) in the derivation and validation groups, respectively. This proposed risk score system is a fairly reliable and robust tool for evaluating the severity and prognosis of patients with COVID-19. This may help in the early identification of severe COVID-19 patients with poor prognosis, requiring more intense interventions.

Baidu Jieduan granules, traditional Chinese medicine, in the treatment of moderate coronavirus disease-2019 (COVID-19): study protocol for an open-label, randomized controlled clinical trial.

BACKGROUND: Currently, coronavirus disease-2019 (COVID-19) is continuously and rapidly circulating, resulting in serious and extensive effects on human health. Due to the absence of antiviral medicine for COVID-19 thus far, there is a desperate need to develop effective medicine. Traditional Chinese medicine (TCM) has been widely applied in the treatment of epidemic diseases in China, with the aim of achieving clinical efficacy and decreasing the use of antibiotics and glucocorticoids. The aim of this study was to evaluate the efficacy and safety of Baidu Jieduan granules in treating COVID-19. METHODS/DESIGN: This multicentre, open-label, randomized controlled trial will be conducted in 300 patients with COVID-19. The patients will be randomly (1:1) divided into a treatment group and a control group. All patients will receive standard therapy at the same time. Patients in the experimental group will receive Baidu Jieduan granule treatment twice a day for 14 days. The outcomes will be assessed at baseline and at 3, 5, 7 and 14 days after treatment initiation. The primary outcome will be the rate of symptom (fever, fatigue and coughing) recovery. Adverse events (AEs) will be monitored throughout the trial. DISCUSSION: The study will provide high-quality clinical evidence to support the efficacy and safety of Baidu Jieduan granules in the treatment of moderate COVID-19, and enrich the theory and practice of TCM in treating COVID-19. TRIAL REGISTRATION: Chinese Clinical Trial Registry ChiCTR2000029869 . Registered on 15 February 2020.

Traditional Chinese medicine shenhuang granule in patients with severe/critical COVID-19: A randomized controlled multicenter trial.

BACKGROUND: Coronavirus disease 2019 (COVID-19) is still a pandemic, with a high mortality rate in severe/critical cases. Therapies based on the Shenghuang Granule have proved helpful in viral infection and septic shock. HYPOTHESIS/PURPOSE: The objective of the current study was to compare the efficacy and safety of the traditional Chinese medicine, Shenhuang Granule, with standard care in hospitalized patients with severe/critical COVID-19. STUDY DESIGN AND METHODS: This was an open-label, multicenter, randomized, controlled clinical trial. At 4 medical centers, a total of 111 severe/critical patients were randomly assigned to receive Shenhuang Granule (SHG group) twice a day for 14 days, in addition to standard care, or to receive standard care alone (Control group). The maximal follow up time was 75 days. The clinical endpoint was clinical improvement and mortality. RESULTS: 54 patients were assigned to the control group and 57 to the SHG group. The overall mortality was 75.9% (41/54) in the control group, and 38.6% (22/57) in the SHG group (p < 0.01 vs. control). The post hoc analysis showed that in the severe category, the mortality of the control group vs. the SHG group was 58.8% (10/17) vs. 5.3% (1/19) (p < 0.01); while in the critical category, it was 83.8% (31/37) vs. 55.3% (21/38) (p < 0.05). In the severe category, the mortality of patients who eventually received an invasive ventilator in the control vs. the SHG group was 58.8% (10/17) vs. 0 (0/19) (p < 0.01). Administration of SHG was associated with increased lymphocytes and decreased adverse events. CONCLUSION: Shenhuang Granule is a promising integrative therapy for severe and critical COVID-19.

The difference of disrupted rhythms of life, work and entertainment between patients with FGIDs and healthy people and their associations with psychological disorders under COVID-19 pandemic.

AIMS: To investigate the differences in disrupted rhythms between healthy people and patients with functional gastrointestinal disorders (FGIDs) and their associations with mood disorders during the coronavirus disease 2019 (COVID-19) pandemic. METHODS: The rhythm scales were composed of subscales 1 and 2 for the assessment of life-work and entertainment rhythms, respectively; Zung's Self-Rating Anxiety Scale (SAS) and Self-Rating Depression Scale (SDS) were used to assess mood disorders. RESULTS: A total of 671 patients with FGIDs and 4373 healthy people successfully participated. The scores of subscales 1 and 2 for patients with FGIDs were significantly higher than those for healthy people (p < .005). The SAS and SDS scores, their prevalence rates were significantly higher than those for the healthy group (all p < .001). Health status, current occupation, life-work rhythm, SDS, and SAS were independent related factors of FGIDs. The score of life-work-entertainment rhythm was significantly positively correlated with SDS and SAS (both p < .001). CONCLUSION: Disrupted rhythms in patients with FGIDs under the COVID-19 pandemic were more frequently and significantly positively associated with mood disorders.

Immediate psychological impact on nurses working at 42 government-designated hospitals during COVID-19 outbreak in China: A cross-sectional study.

BACKGROUND: During an epidemic of a novel infectious disease, frontline nurses suffer from unprecedented psychological stress. This study aimed to assess the immediate psychological impact on frontline nurses in China. METHODS: A multicenter, cross-sectional survey of frontline nurses was conducted via online questionnaires. Symptoms of depression, anxiety, somatic disorders, and suicidal ideation were evaluated. Demographic, stress, and support variables were entered into logistic regression analysis to identify the impact factors. FINDINGS: Of the 4,692 nurses who completed the survey, 9.4% (n = 442) were considered to have depressive symptoms, 8.1% (n = 379) represented anxiety, and 42.7% (n = 2,005) had somatic symptom. About 6.5% (n = 306) respondents had suicidal ideation. DISCUSSION: The study showed that the overall mental health of frontline nurses was generally poor during COVID-19 outbreak, and several impact factors associated with nurses' psychological health were identified. Further research is needed to ascertain whether training and support strategies are indeed able to mitigate psychological morbidities.

D-Dimer as a Prognostic Indicator in Critically Ill Patients Hospitalized With COVID-19 in Leishenshan Hospital, Wuhan, China.

Background: D-dimer is a small protein fragment and high levels of D-dimer have been associated with increased mortality in patients presenting to emergency departments with infection. Previous studies have reported increased levels of D-dimer in COVID-19; however, it is unclear whether an increased D-dimer level provides early warning of poor prognosis. Therefore, this study aimed to assess the usefulness of D-dimer as an early indicator of prognosis in patients with coronavirus disease (COVID-19). Methods: We conducted a retrospective study of patients with COVID-19 admitted to Leishenshan Hospital in Wuhan, China, from February 15 to March 30, 2020. The final date of follow-up was April 11, 2020. Results: Of the 1,643 patients with COVID-19, 691 had elevated D-dimer levels. Their median age was 65 years. Of the patients with elevated D-dimer levels, 45% had comorbidities, with cardiovascular disease (205 [29.7%]) being the most common. Patients with elevated D-dimer were more likely to require treatment with high-flow oxygen, anticoagulation, antibiotics, and admission to the intensive care unit They were also more likely to have increased interleukin-6, monocytes, and lymphocytes. Patients with elevated D-dimer levels had significantly higher mortality than those with normal or low D-dimer levels. Conclusion: In patients with COVID-19, elevated D-dimer was associated with abnormal immunity, underlying disease, increased disease severity, and increased mortality. Taken together, D-dimer may be a marker for the early warning of disease severity and increased risk of death. These findings provide insights into the potential risk of elevated D-dimer in patients with COVID-19.

Suicidal and self-harm ideation among Chinese hospital staff during the COVID-19 pandemic: Prevalence and correlates.

The COVID-19 pandemic put global medical systems under massive pressure for its uncertainty, severity, and persistence. For detecting the prevalence of suicidal and self-harm ideation (SSI) and its related risk factors among hospital staff during the COVID-19 pandemic, this cross-sectional study collected the sociodemographic data, epidemic-related information, the psychological status and need, and perceived stress and support from 11507 staff in 46 hospitals by an online survey from February 14 to March 2, 2020. The prevalence of SSI was 6.47%. Hospital staff with SSI had high family members or relatives infected number and the self-rated probability of infection. Additionally, they had more perceived stress, psychological need, and psychological impact. On the contrary, hospital staff without SSI reported high self-rated health, willingness to work in a COVID-19 ward, confidence in defeating COVID-19, and perceived support. Furthermore, they reported better marital or family relationship, longer sleep hours, and shorter work hours. The infection of family members or relatives, poor marital status, poor self-rated health, the current need for psychological intervention, perceived high stress, perceived low support, depression, and anxiety were independent factors to SSI. A systematic psychological intervention strategy during a public health crisis was needed for the hospital staff's mental well-being.

Severity Detection for the Coronavirus Disease 2019 (COVID-19) Patients Using a Machine Learning Model Based on the Blood and Urine Tests.

The recent outbreak of the coronavirus disease-2019 (COVID-19) caused serious challenges to the human society in China and across the world. COVID-19 induced pneumonia in human hosts and carried a highly inter-person contagiousness. The COVID-19 patients may carry severe symptoms, and some of them may even die of major organ failures. This study utilized the machine learning algorithms to build the COVID-19 severeness detection model. Support vector machine (SVM) demonstrated a promising detection accuracy after 32 features were detected to be significantly associated with the COVID-19 severeness. These 32 features were further screened for inter-feature redundancies. The final SVM model was trained using 28 features and achieved the overall accuracy 0.8148. This work may facilitate the risk estimation of whether the COVID-19 patients would develop the severe symptoms. The 28 COVID-19 severeness associated biomarkers may also be investigated for their underlining mechanisms how they were involved in the COVID-19 infections.

Epidemiologic and clinical characteristics of 42 deaths caused by SARS-CoV-2 infection in Wuhan, China: A retrospective study.

This study described the epidemiologic and clinical characteristics of patients who died from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and pointed out the potential risk factors associated with fatal outcomes. Retrospective data from 42 death cases due to SARS-CoV-2 infection at Tongji Hospital Affiliated to Huazhong University of Science and Technology, Wuhan, China was analyzed. Demographics, clinical detection, laboratory findings, and treatments of the deceased were collected and analyzed. The average time between onset of symptoms and admission to the hospitals was 11 ± 5 days of hospitalization. Among the deceased, 60% were with co-morbidities. All of them were having fever and bilateral pneumonia on computed tomography, abnormal infection-related biomarkers, and renal impairment. Abnormal blood coagulation parameters that appeared in more than half of them, were consistent with disseminated intravascular coagulation. All of the patients were treated in the ICU. Based on the fact that SARS-CoV-2 infection carries a risk of mortality, we may infer a few older male patients with underlying comorbidities are likely to have the increased risk. Impaired consciousness level, markers of renal impairment and coagulation abnormalities may be poor prognostic factors.