Predictive value of immunoglobulin G, activated partial thromboplastin time, platelet, and indirect bilirubin for delayed viral clearance in patients infected with the Omicron variant.

Background: Omicron is the recently emerged highly transmissible severe acute respiratory syndrome coronavirus 2 variant that has caused a dramatic increase in coronavirus disease-2019 infection cases worldwide. This study was to investigate the association between demographic and laboratory findings, and the duration of Omicron viral clearance. Methods: Approximately 278 Omicron cases at the Ruijin Hospital Luwan Branch, Shanghai Jiaotong University School of Medicine were retrospectively analyzed between August 11 and August 31, 2022. Demographic and laboratory data were also collected. The association between demographics, laboratory findings, and duration of Omicron viral clearance was analyzed using Pearson correlation analysis and univariate and multivariate logistic regression. Results: Univariate logistic regression analyses showed that a prolonged viral clearance time was significantly associated with older age and lower immunoglobulin (Ig) G and platelet (PLT) levels. Using multinomial logistic regression analyses, direct bilirubin, IgG, activated partial thromboplastin time (APTT), and PLT were independent factors for longer viral shedding duration. The model combining direct bilirubin, IgG, APTT, and PLT identifies patients infected with Omicron whose viral clearance time was ≥7 days with 62.7% sensitivity and 83.4% specificity. Conclusion: These findings suggest that direct bilirubin, IgG, PLT, and APTT are significant risk factors for a longer viral shedding duration in patients infected with Omicron. Measuring levels of direct bilirubin, IgG, PLT, and APTT is advantageous to identify patients infected with Omicron with longer viral shedding duration.

Emergency department treatment process planning: a field research, case analysis, and simulation approach.

Background: The coronavirus disease 2019 (COVID-19) has forced accelerated optimization of Emergency Department (ED) process, and simulation tools offer an alternative approach to strategic assessment and selection. Methods: Field research and case analysis methods were used to obtain the treatment process and medical records information from the ED of a general hospital. Minitab was used for analysis of the measurement system, and Arena was applied for simulation modelling. We established a framework for the triage protocol of ordinary and quarantined patients, analysed bottlenecks in the treatment time of the hospital's ED, and proposed an optimised management strategy. Results: The computed tomography (CT) pre-scheduling strategy simulation results demonstrated that longer CT room preparation times for quarantined people before their arrival (Tp) resulted in reduced CT scan and waiting times for quarantined patients, but these times were longer for ordinary patients. The nucleic acid priority strategy simulation results demonstrated that when the average daily number of ordinary patients (λc) was relatively stable, the hospital could guide ordinary patients to perform nucleic acid testing first followed by CT testing. However, when λc fluctuated greatly, the hospital could appropriately reduce the proportion of preferential nucleic acid testing. Furthermore, when λc was overloaded, the nucleic acid priority strategy showed no advantages. The joint analysis results demonstrated that the optimal strategy selection was significantly affected by the severity of the epidemic. The nucleic acid detection sample size optimisation strategy demonstrated that optimizing the sample size of each batch according to the number of patients could effectively reduce the waiting times for nucleic acid testing (Tn). Conclusions: Simulation tools are an alternative method for strategic evaluation and selection that do not require external factors.

VOC-alarm: mutation-based prediction of SARS-CoV-2 variants of concern.

SUMMARY: Mutation is the key for a variant of concern (VOC) to overcome selective pressures, but this process is still unclear. Understanding the association of the mutational process with VOCs is an unmet need. Motivation: Here, we developed VOC-alarm, a method to predict VOCs and their caused COVID surges, using mutations of about 5.7 million SARS-CoV-2 complete sequences. We found that VOCs rely on lineage-level entropy value of mutation numbers to compete with other variants, suggestive of the importance of population-level mutations in the virus evolution. Thus, we hypothesized that VOCs are a result of a mutational process across the globe. Results: Analyzing the mutations from January 2020 to December 2021, we simulated the mutational process by estimating the pace of evolution, and thus divided the time period, January 2020-March 2022, into eight stages. We predicted Alpha, Delta, Delta Plus (AY.4.2) and Omicron (B.1.1.529) by their mutational entropy values in the Stages I, III, V and VII with accelerated paces, respectively. In late November 2021, VOC-alarm alerted that Omicron strongly competed with Delta and Delta plus to become a highly transmissible variant. Using simulated data, VOC-alarm also predicted that Omicron could lead to another COVID surge from January 2022 to March 2022. AVAILABILITY AND IMPLEMENTATION: Our software implementation is available at https://github.com/guangxujin/VOC-alarm. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The Good Samaritan Parable Revisited: A Survey During the COVID-19 Pandemic.

From an integrative approach of parable interpretation that combines ethical, evolutionary, historical, and psychological perspectives, the current research empirically examined the purely theorized assumption elucidating the behaviors of the priest, Levite, and Samaritan in the good Samaritan parable (Luke 10:25-37) by the regulatory focus theory. In one experiment conducted during the COVID-19 outbreak, 93 Polish participants were randomly assigned to a simulated vignette of the good Samaritan parable where either the prevention or promotion regulatory focus was manipulated. The results confirmed a certain favorable tendency to offer quasi-realistic help in both the regulatory focus conditions. The finding highlights a dynamic association in goal pursuit motivation and prosocial behavior in a pandemic context regarding the good Samaritan parable. The current study is among rare empirical research which reflects a challenge people respond to offer help in simulated scenarios as original as the good Samaritan parable.

Decreased Incidence of Influenza During the COVID-19 Pandemic.

Background: The aim of this study was to analyse changes in influenza detection rates of the influenza seasons 2017/2018, 2018/2019, 2019/2020, and 2020/2021 and the changes in personal awareness of protection during the COVID-19 pandemic. Methods: This retrospective study included patients tested for influenza virus A and B from November 2017 to March 2021 at the Affiliated People's Hospital of Ningbo University (Ningbo, China). Influenza virus A and B tested by direct RT-PCR. A small group of 100 regular participants in influenza virus detection were surveyed on the use of protective measures in four different influenza seasons. Results: There were 14,902, 14,762, 25,070, and 1107 tests of influenza virus A and B in the four influenza periods, for total positive rates of 32.45%, 35.77%, 29.40%, and 0.54%, respectively. In the two periods of four influenza seasons, from November to January, the total number of influenza samples was 8530, 4980, 22,925, 868; from February to March, the number of tests was 6372, 9782, 2145, 239. Total number of tests and positive rate decreased significantly from February/March onwards of the 2019/2020 season, coinciding with the beginning of COVID-19. The proportion of people taking protective measures also increased during the 2019/20 and 2020/21 flu seasons. Conclusion: The influenza virus has a high incidence in this area. The diagnosis rate of influenza decreased after the start of the COVID-19 pandemic. The COVID-19 pandemic had an important impact on the detection rates for influenza virus.

Clinical Features and Chest CT Manifestations of Coronavirus Disease 2019 (COVID-19) in a Single-Center Study in Shanghai, China.

OBJECTIVE. Confronting the new coronavirus infection known as coronavirus disease 2019 (COVID-19) is challenging and requires excluding patients with suspected COVID-19 who actually have other diseases. The purpose of this study was to assess the clinical features and CT manifestations of COVID-19 by comparing patients with COVID-19 pneumonia with patients with non-COVID-19 pneumonia who presented at a fever observation department in Shanghai, China. MATERIALS AND METHODS. Patients were retrospectively enrolled in the study from January 19 through February 6, 2020. All patients underwent real-time reverse transcription-polymerase chain reaction (RT-PCR) testing. RESULTS. Eleven patients had RT-PCR test results that were positive for severe acute respiratory syndrome coronavirus 2, whereas 22 patients had negative results. No statistical difference in clinical features was observed (p > 0.05), with the exception of leukocyte and platelet counts (p < 0.05). The mean (± SD) interval between onset of symptoms and admission to the fever observation department was 4.40 ± 2.00 and 5.52 ± 4.00 days for patients with positive and negative RT-PCR test results, respectively. The frequency of opacifications in patients with positive results and patients with negative results, respectively, was as follows: ground-glass opacities (GGOs), 100.0% versus 90.9%; mixed GGO, 63.6% versus 72.7%; and consolidation, 54.5% versus 77.3%. In patients with positive RT-PCR results, GGOs were the most commonly observed opacification (seen in 100.0% of patients) and were predominantly located in the peripheral zone (100.0% of patients), compared with patients with negative results (31.8%) (p = 0.05). The median number of affected lung lobes and segments was higher in patients with positive RT-PCR results than in those with negative RT-PCR results (five vs 3.5 affected lobes and 15 vs nine affected segments; p < 0.05). Although the air bronchogram reticular pattern was more frequently seen in patients with positive results, centrilobular nodules were less frequently seen in patients with positive results. CONCLUSION. At the point during the COVID-19 outbreak when this study was performed, imaging patterns of multifocal, peripheral, pure GGO, mixed GGO, or consolidation with slight predominance in the lower lung and findings of more extensive GGO than consolidation on chest CT scans obtained during the first week of illness were considered findings highly suspicious of COVID-19.

Detection of Respiratory Infections Using RGB-Infrared Sensors on Portable Device

Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronaviruses 2 (SARS-CoV-2) has become a serious global pandemic in the past few months and caused huge loss to human society worldwide. For such a large-scale pandemic, early detection and isolation of potential virus carriers is essential to curb the spread of the pandemic. Recent studies have shown that one important feature of COVID-19 is the abnormal respiratory status caused by viral infections. During the pandemic, many people tend to wear masks to reduce the risk of getting sick. Therefore, in this paper, we propose a portable non-contact method to screen the health conditions of people wearing masks through analysis of the respiratory characteristics from RGB-infrared sensors. We first accomplish a respiratory data capture technique for people wearing masks by using face recognition. Then, a bidirectional GRU neural network with an attention mechanism is applied to the respiratory data to obtain the health screening result. The results of validation experiments show that our model can identify the health status of respiratory with 83.69% accuracy, 90.23% sensitivity and 76.31% specificity on the real-world dataset. This work demonstrates that the proposed RGB-infrared sensors on portable device can be used as a pre-scan method for respiratory infections, which provides a theoretical basis to encourage controlled clinical trials and thus helps fight the current COVID-19 pandemic. The demo videos of the proposed system are available at: https://doi.org/10.6084/m9.figshare.12028032.

Nucleic acid and antibody assay results in Chinese patients with coronavirus disease 2019 (COVID-19).

AIM: To evaluate the nucleic acid and antibody test results of patients with Coronavirus Disease 2019 (COVID-19) in China. METHODS: All patients with laboratory-confirmed SARS-CoV-2 infection from Jan to Apr 2020were retrospectively analyzed. Clinical characteristics and laboratory test results were obtained from electronic medical records. Patients were divided into three groups based on antibody production, and compared for laboratory test results. RESULTS: Of 73 patients aged11-82 years, 12 (16.4%), 28 (38.4%), 25 (34.2%) and 8 (11.0%)were ≤ 30, 31-50, 51-70,and ≥ 71 years old, respectively. Thirty-four (46.6%) patients were male. Most individuals had mild symptoms, and no patient died during treatment. All patients were tested positive for SARS-CoV-2 in sputum and nasopharyngeal samples, and 40 (54.8%) were also tested positive in stool. Nine(12.3%) patients were re-positivefor SARS-CoV-2, as assessed by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) after discharge. Sixty-five (89.0%) patients had IgM or IgG antibodies against SARS-CoV-2.Among the four age groups, there was no difference in IgG antibody production (P = 0.664).CD3, CD4, CD8 and CD19 cell counts between the antibody producing and non-producing groups showed no significant differences (all P > 0.05).The antibodies disappeared within two months in four patients. Lymphocyte count, C-reactive protein, IL-6, lactate dehydrogenase, alanine aminotransferase, creatinine and D-Dimer levels were similar in the three groups (all P > 0.05). CONCLUSIONS: Patients after recovery from COVID-19 can be tested positive for SARS-CoV-2.Some patients may produce antibodies only for a short time, or even no antibodies at all.

COVID-19 and early-stage lung cancer both featuring ground-glass opacities: a propensity score-matched study.

BACKGROUND: Radiological manifestations of coronavirus disease 2019 (COVID-19) featured ground-glass opacities (GGOs), especially in the early stage, which might create confusion in differential diagnosis with early lung cancer. We aimed to specify the radiological characteristics of COVID-19 and early lung cancer and to unveil the discrepancy between them. METHODS: One hundred and fifty-seven COVID-19 patients and 374 early lung cancer patients from four hospitals in China were retrospectively enrolled. Epidemiological, clinical, radiological, and pathological characteristics were compared between the two groups using propensity score-matched (PSM) analysis. RESULTS: COVID-19 patients had more distinct symptoms, tended to be younger (P<0.0001), male (P<0.0001), and had a higher body mass index (P=0.014). After 1:1 PSM, 121 matched pairs were identified. Regarding radiological characteristics, patients with a single lesion accounted for 17% in COVID-19 and 89% in lung cancer (P<0.0001). Most lesions were peripherally found in both groups. Lesions in COVID-19 involved more lobes (median 3.5 vs. 1; P<0.0001) and segments (median 6 vs. 1; P<0.0001) and tended to have multiple types (67%) with patchy form (54%). Early lung cancer was more likely to have a single type (92%) with oval form (66%). Also, COVID-19 and early lung cancer either had some distinctive features on computed tomography (CT) images. CONCLUSIONS: Both COVID-19 and early lung cancers showed GGOs, with similar but independent features. The imaging characteristics should be fully understood and combined with epidemiological history, pathogen detection, laboratory tests, short-term CT reexamination, and pathological results to aid differential diagnosis.

Pulmonary vascular enlargement on thoracic CT for diagnosis and differential diagnosis of COVID-19: a systematic review and meta-analysis.

BACKGROUND: The 2019 coronavirus disease (COVID-19) has become a global pandemic. To date, although many studies have reported on the computed tomography (CT) manifestations of COVID-19, the vascular enlargement sign (VES) of COVID-19 has not been deeply examined, with the few available studies reporting an inconsistent prevalence. We thus performed a systematic review and meta-analysis based on the best available studies to estimate the prevalence and identify the underlying differential diagnostic value of VES. METHODS: We searched nine English and Chinese language databases up to April 23, 2020. Studies that evaluated CT features of COVID-19 patients and reported VES, with or without comparison with other pneumonia were included. The methodologic quality was assessed using Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2). Meta-analyses with random effects models were performed to calculate the aggregate prevalence and pooled odds ratios (ORs) of VES. We also conducted meta-regression and subgroup analyses to analyze heterogeneity. RESULTS: VES findings from a total of 1969 patients were summarized and pooled across 22 studies. Our analysis demonstrated that the prevalence of VES among COVID-19 patients was 69.37% [95% confidence interval (CI): 57.40-79.20%]. Compared with non-COVID-19 patients, VES manifestation was more frequently observed in confirmed COVID-19 patients (OR =6.43, 95% CI: 3.39-12.22). Studies that explicitly defined distribution of VES in the lesion area demonstrated a significantly higher prevalence (P=0.03). Subgroup analyses also revealed a relatively higher VES rate in studies with a sample size larger than 50, but the difference was not statistically significant. No significant difference in VES rates was found between different countries (China/Italy), regions (Hubei/outside Hubei), average age groups (over/less than 50-year-old), or slice thicknesses of CT scan. Extensive heterogeneity was identified across most estimates (I2>80%). Some of the variations (R2=19.73%) could be explained by VES distribution, and sample size. No significant publication bias was seen (P=0.29). CONCLUSIONS: VES on thoracic CT was found in almost two-thirds of COVID-19 patients, and was more prevalent compared with that of the non-COVID-19 patients, supporting a promising role for VES in identifying pneumonia caused by coronavirus.

Establishing a standardized FUO emergency department: design and practice in dealing with COVID-19.

BACKGROUND: Since the outbreak of COVID-19 in January, 2020, the fever of unknown origin (FUO) emergency department has become the first station for disease prevention and identification in hospitals. Establishing a standardized FUO emergency department within a short period of time has become the key to preventing and controlling COVID-19 in densely populated Chinese cities. METHODS: Based on the lean management model, the research group established a process of less-link visits, which sees reduced contact between patients and physicians during diagnosis and treatment, and zero-contact consultation through lean workflow and value stream analysis. Three steps were implemented to improve the operations of the FUO emergency department: the rapid establishment of an isolation zone, the refinement of duty and protection configuration, and the use of Internet and technology to establish a full-process follow-up consultation system. RESULTS: (I) Tests related to COVID-19 screening are all completed in the FUO emergency department; (II) 12 new isolated observation rooms have been built; (III) hospital visiting time, waiting time for consultation, and the time from pre-examination to virus screening has been shortened from 18 to 8 hours, from 2 hours to 10 minutes, and from 34 to 3 hours, respectively; (IV) the transfer distance has been shortened from 450 to 20 m, and the observation time has been shortened from 72 to 26 hours. The median waiting time for image examination has been reduced from 40 to 3 minutes, and the moving distance has been shortened from 800 to 10 m; (V) the diagnosis and treatment process is facilitated by 5G, achieving zero contact between doctors and patients. CONCLUSIONS: Through the implantation of information technology, the local transformation of the site, the rational allocation of medical teams and the planned distribution of protective equipment, in a short period of time, individual medical institutions can set up a safe FUO emergency department to provide 24-hour screening and detention services. Establishing an FUO emergency department with lean management and realizing the management approach of combining daily operation with prevention and control could help China and other countries to handle the outbreak of fulminant infectious diseases.

Spread and Impact of COVID-19 in China: A Systematic Review and Synthesis of Predictions From Transmission-Dynamic Models.

Background: Coronavirus disease 2019 (COVID-19) was first identified in Wuhan, China, in December 2019 and quickly spread throughout China and the rest of the world. Many mathematical models have been developed to understand and predict the infectiousness of COVID-19. We aim to summarize these models to inform efforts to manage the current outbreak. Methods: We searched PubMed, Web of science, EMBASE, bioRxiv, medRxiv, arXiv, Preprints, and National Knowledge Infrastructure (Chinese database) for relevant studies published between 1 December 2019 and 21 February 2020. References were screened for additional publications. Crucial indicators were extracted and analysed. We also built a mathematical model for the evolution of the epidemic in Wuhan that synthesised extracted indicators. Results: Fifty-two articles involving 75 mathematical or statistical models were included in our systematic review. The overall median basic reproduction number (R0) was 3.77 [interquartile range (IQR) 2.78-5.13], which dropped to a controlled reproduction number (Rc) of 1.88 (IQR 1.41-2.24) after city lockdown. The median incubation and infectious periods were 5.90 (IQR 4.78-6.25) and 9.94 (IQR 3.93-13.50) days, respectively. The median case-fatality rate (CFR) was 2.9% (IQR 2.3-5.4%). Our mathematical model showed that, in Wuhan, the peak time of infection is likely to be March 2020 with a median size of 98,333 infected cases (range 55,225-188,284). The earliest elimination of ongoing transmission is likely to be achieved around 7 May 2020. Conclusions: Our analysis found a sustained Rc and prolonged incubation/ infectious periods, suggesting COVID-19 is highly infectious. Although interventions in China have been effective in controlling secondary transmission, sustained global efforts are needed to contain an emerging pandemic. Alternative interventions can be explored using modelling studies to better inform policymaking as the outbreak continues.

Clinical characteristics of coronavirus disease 2019 (COVID-19) in China: A systematic review and meta-analysis.

OBJECTIVE: To better inform efforts to treat and control the current outbreak with a comprehensive characterization of COVID-19. METHODS: We searched PubMed, EMBASE, Web of Science, and CNKI (Chinese Database) for studies published as of March 2, 2020, and we searched references of identified articles. Studies were reviewed for methodological quality. A random-effects model was used to pool results. Heterogeneity was assessed using I2. Publication bias was assessed using Egger's test. RESULTS: 43 studies involving 3600 patients were included. Among COVID-19 patients, fever (83.3% [95% CI 78.4-87.7]), cough (60.3% [54.2-66.3]), and fatigue (38.0% [29.8-46.5]) were the most common clinical symptoms. The most common laboratory abnormalities were elevated C-reactive protein (68.6% [58.2-78.2]), decreased lymphocyte count (57.4% [44.8-69.5]) and increased lactate dehydrogenase (51.6% [31.4-71.6]). Ground-glass opacities (80.0% [67.3-90.4]) and bilateral pneumonia (73.2% [63.4-82.1]) were the most frequently reported findings on computed tomography. The overall estimated proportion of severe cases and case-fatality rate (CFR) was 25.6% (17.4-34.9) and 3.6% (1.1-7.2), respectively. CFR and laboratory abnormalities were higher in severe cases, patients from Wuhan, and older patients, but CFR did not differ by gender. CONCLUSIONS: The majority of COVID-19 cases are symptomatic with a moderate CFR. Patients living in Wuhan, older patients, and those with medical comorbidities tend to have more severe clinical symptoms and higher CFR.