Development and external evaluation of predictions models for mortality of COVID-19 patients using machine learning method.

To predict the mortality of patients with coronavirus disease 2019 (COVID-19). We collected clinical data of COVID-19 patients between January 18 and March 29 2020 in Wuhan, China . Gradient boosting decision tree (GBDT), logistic regression (LR) model, and simplified LR were built to predict the mortality of COVID-19. We also evaluated different models by computing area under curve (AUC), accuracy, positive predictive value (PPV), and negative predictive value (NPV) under fivefold cross-validation. A total of 2924 patients were included in our evaluation, with 257 (8.8%) died and 2667 (91.2%) survived during hospitalization. Upon admission, there were 21 (0.7%) mild cases, 2051 (70.1%) moderate case, 779 (26.6%) severe cases, and 73 (2.5%) critically severe cases. The GBDT model exhibited the highest fivefold AUC, which was 0.941, followed by LR (0.928) and LR-5 (0.913). The diagnostic accuracies of GBDT, LR, and LR-5 were 0.889, 0.868, and 0.887, respectively. In particular, the GBDT model demonstrated the highest sensitivity (0.899) and specificity (0.889). The NPV of all three models exceeded 97%, while their PPV values were relatively low, resulting in 0.381 for LR, 0.402 for LR-5, and 0.432 for GBDT. Regarding severe and critically severe cases, the GBDT model also performed the best with a fivefold AUC of 0.918. In the external validation test of the LR-5 model using 72 cases of COVID-19 from Brunei, leukomonocyte (%) turned to show the highest fivefold AUC (0.917), followed by urea (0.867), age (0.826), and SPO2 (0.704). The findings confirm that the mortality prediction performance of the GBDT is better than the LR models in confirmed cases of COVID-19. The performance comparison seems independent of disease severity. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at(10.1007/s00521-020-05592-1).

Effectiveness of vero cell inactivated vaccine against severe acute respiratory infections (SARI) in Sibu, Malaysia: A retrospective test-negative design.

The effectiveness of the vero cell inactivated vaccine (CoronaVac®) against severe acute respiratory infection ( SARI) caused by SARS-CoV-2 in the real world was assessed. A matched test-negative case-control design was employed using the web-based national information system, as well as the hospitalization dataset in Sibu Hospital. Vaccine effectiveness was measured by conditional logistic regression with adjustment for gender, underlying comorbidity, smoking status, and education level. Between 15 March and 30 September 2021, 838 eligible SARI patients were identified from the hospitalization records. Vaccine effectiveness was 42.4% (95% confidence interval [CI]: -28.3 to 74.1) for partial vaccination (after receiving the first dose to 14 days after receiving the second dose), and 76.5% (95% CI: 45.6 to 89.8) for complete vaccination (at 15 days or more after receiving the second dose). This analysis indicated that two doses of CoronaVac® vaccine provided efficacious protection against SARI caused by SARS-CoV-2 in the short term. However, the duration of protection, and performance against new variants need to be studied continuously.

Immunogenicity of COVID-19 vaccines and levels of SARS-CoV-2 neutralising antibody in the Bruneian population: Protocol for a national longitudinal study.

INTRODUCTION: Neutralising antibodies (NAbs) have been shown to be correlative of immune protection against SARS-CoV-2. We report the protocol for a national longitudinal study to assess and compare the level of NAbs generated in response to COVID-19 vaccines in Brunei Darussalam in adults 2-6 weeks post primary series (BBIBP-CorV, AZD1222, or mRNA-1273 vaccines) and their subsequent follow-up after administration of a third (booster-1) dose (BBIBP-CorV, mRNA-1273, or BNT162b2). METHODS AND ANALYSIS: Participant data will be extracted and processed from the national electronic health record system (Bru-HIMS) and the national mobile health application (BruHealth) into a research data platform. Eligible adults who have received their primary or booster vaccine will be invited using a stratified random sampling strategy based on age, gender and vaccine type (baseline target population, n=3000; 2-6 weeks post last dose). Blood serum will be isolated, and NAb levels assessed using the cPass surrogate virus neutralisation test. Baseline participants will then be screened for eligibility for subsequent longitudinal analysis. Those who have received a third dose will be followed up at 1, 3, 6, 9 and up to 12 months. NAb levels will be evaluated across the participant population according to vaccine platform/booster type, time since the last dose and correlated with demographic data. The study period is from December 2021 to January 2023 and aims to evaluate how NAb levels wane following a third vaccine dose across different vaccine platforms and determine the impact and rate of breakthrough infections. ETHICS AND DISSEMINATION: This study has been approved by the Medical and Ethical Research Committee of Ministry of Health, Brunei Darussalam. Individual NAb test results will be shared with each participant by text message. The findings from this study will help policy-makers in Brunei develop future vaccination strategies and establish regulations across multiple agencies.

Technology-assisted adaptive recruitment strategy for a large nation-wide COVID-19 vaccine immunogenicity study in Brunei.

A national study was conducted in Brunei to assess and compare the immunogenicity of the various brands of COVID-19 vaccines administered to the population as part of the National COVID-19 Vaccination Programme. Most of the population have had received at least 2 doses of BBIBP-CorV, AZD1222 or MRNA-1273 vaccines. Neutralising antibodies against SARS-CoV-2 induced by these vaccines will be analysed to infer population-level immune protection against COVID-19. During the 5-week recruitment period, 24,260 eligible individuals were invited to the study via SMS, out of which 2,712 participants were enrolled into the study. This paper describes the novel adaptive strategy used to recruit the study participants. Digital technology was leveraged to perform targeted online recruitment to circumvent the limitations of traditional recruitment methods. Technology also enabled stratified random selection of these eligible individuals who were stratified based on age, gender and vaccine brand. Data was extracted from the electronic health records, the national mobile health application and a third-party survey platform and integrated into a dedicated research platform called EVYDResearch. The instant availability and access to up-to-date data on EVYDResearch enabled the study team to meet weekly and adopt an adaptive recruitment strategy informed by behavioural science, where interventions could be quickly implemented to improve response rates. Some examples of these include incorporating nudge messaging into SMS invitations, involving the Minister of Health to make press announcements on this study, media coverage, setting up an enquiries hotline and reaching out to foreign language speaking expatriates of a local multinational company to participate in this study. Data integration from various data sources, real time information sharing and a strong teamwork led to good outcomes adaptable to the progress of recruitment, compared to the more time-consuming and static traditional recruitment methods.

Posttraumatic stress disorders and influencing factors during the COVID-19 pandemic: A cross-sectional study of frontline nurses.

AIMS: To assess the extent of posttraumatic stress disorder (PTSD) symptoms and severity, factors motivating work continuation, and factors influencing PTSD development among frontline nurses caring for patients with COVID-19. BACKGROUND: The COVID-19 pandemic has an emotional toll on nurses. Exposure to traumatic events associated with the pandemic places frontline nurses at risk for developing PTSD. DESIGN: Cross-sectional study. METHODS: Frontline nurses (n = 370) who cared for COVID-19 patients in three governmental hospitals in the United Arab Emirates were recruited from November 2020 to January 2021. The self-reported Posttraumatic Diagnostic Scale (PDS) was used to assess PTSD. The motivational factors for work continuation explored were: work-related factors (e.g., availability of personal protective equipment and management recognition), family support, and obligation to care. We used correlation and multiple regression analyses to investigate factors that influenced PDS score, including sociodemographic characteristics (e.g., gender, age, exercising status, and general health status), work factors (e.g., hospital type [COVID vs non-COVID], prior work experience, and encountering deaths), and factors motivating work continuation. The reporting of this study was consistent with STROBE guidelines. RESULTS: In total, 36.2% participants had a probable PTSD diagnosis (PDS score ≥28) with most reporting unwanted memories. Family support (95.9%) and management recognition (90.8%) were the most frequently reported motivating factors. Factors significantly associated with higher PDS score were smoking, lack of management recognition, not exercising, and encountering COVID-19 deaths; the correlation and regression coefficients (b) were significant (p < 0.05). CONCLUSIONS AND IMPLICATIONS FOR NURSING/HEALTH POLICY: Policy makers must expand healthcare policies to address frontline nurses' mental health as a priority during the pandemic. Nurse leaders must be involved in health policy development to protect nurses in anticipation of and during global health emergencies.

Academic experiences, physical and mental health impact of COVID-19 pandemic on students and lecturers in health care education.

BACKGROUND: In keeping with nation-wide efforts to contain the spread of COVID-19, Universiti Brunei Darussalam (UBD) transformed fully its pedagogical delivery to online mode, where we investigated teaching and learning experiences, physical and mental health of undergraduate students and lecturers during the COVID-19 pandemic. METHODS: We conducted a cross-sectional study on undergraduate students and lecturers in a health science faculty using a self-developed pretested questionnaire through anonymous online data collection method. RESULTS: Fifty-six lecturers (100% response rate) and 279 students (93.3% response rate) participated. The positive experiences reported by students include becoming independent (72.8%) and adapting to online learning (67.4%), while lecturers learned new teaching techniques (50.0%) and became more innovative (50.0%) by learning new tools (48.2%). However, studying at home caused students to feel more distracted (72.0%) with a feeling of uncertainty towards examinations (66.7%), while lecturers felt that students' laboratory skills were compromised (44.6%). Even though online delivery of assessments enabled lecturers to explore all options (50.0%), they found it difficult to maintain appropriate questions (41.1%) and fair assessments (37.5%). Majority of students missed eating out (68.8%) and felt a lack of participation in extracurricular activities (64.9%), while lecturers reported more time for exercise (51.8%), despite having more screen time (50.0%) and computer-related physical stress (44.6%). In terms of mental health, increased stress in students was reported (64.9%), though they had more time for self-reflection (54.8%). Although lecturers reported a closer relationship with family (44.6%), they also felt more stressed due to deadlines, unexpected disruptions and higher workloads (44.6%) as well as concerns related to work, family and self (39.3%). CONCLUSION: In this abrupt shift to online teaching, students and lecturers in our study identified both positive and negative experiences including the impact on their physical and mental health. Our findings are important to provide the evidence for online pedagogical benefits and can serve to promote the enhancement and adaptation of digital technology in education. Our findings also aim to promote the importance of addressing physical and mental health issues of the university community's well-being through provision of emotional and mental health support and appropriate programs.

New norms and opportunities from the COVID-19 pandemic crisis in a higher education setting: perspectives from Universiti Brunei Darussalam

Purpose This paper aims to share how it was possible to change the way business was conducted in a short period in order to continue the academic semester and seek alternatives to manage the day-to-day university affairs in the midst of a pandemic crisis at a higher education setting. As a result, the authors' experiences have created new norms and opportunities for the university. Design/methodology/approach The coronavirus disease 2019 (COVID-19) pandemic in Brunei Darussalam is an evolving situation with extraordinary challenges for staff and students of the university. Although the campus remains open and essential services were continuously provided, the university had to implement and adapt to new norms instinctively to minimise the potential pathways for community spread of the coronavirus and at the same time minimise interruption in teaching and learning. Findings Firstly, structured blended learning will be the basis of teaching and learning, alongside ensuring the highest quality of online education and successful achievement of the intended learning objectives. Secondly, blended learning will open more opportunities to offer programmes in a more flexible, personalised, student-centric and lifelong learning manner, with the option of taking a study hiatus at students' convenience. Thirdly, there will be more global classrooms and the exchange of online modules with international partner universities. Fourthly, short programmes such as the Global Discovery Programmes will be modified and improvised to become an online learning experience. And finally, there will also be the opportunity to understand and consider the physical and mental well-being and durability of the university community in overcoming a national crisis situation. Originality/value This paper is intended to be a conceptual paper where the authors describe novel experiences during the pandemic. The authors' views, interventions and experiences may result into a new model for higher education that will reposition students to the new global markets and economy.

Is online assessment in higher education institutions during COVID-19 pandemic reliable?

The online learning helps to minimise disruptions on teaching and compromising students' learning outcomes;however there is limited evidence on effective online assessment methods used at Higher Education Institutions during pandemics. This paper aimed to summarise online assessment methods and recommend reliable as well as practical approaches used at HEIs during COVID-19 pandemic. We performed a scoping literature review to identify original papers, review and reports that examine the online assessment methods used in higher education before and during COVID-19 pandemic. We identified common themes in data analysis. The psychometric theory is useful when designing valid and reliable online assessment methods for online learning, particularly in medical education. The typical online assessment methods used at HEIs include online quizzes, continuous feedback, multiple-choice questions and automated assessment for essays. The online tools for formative assessment in higher education include feedback, self-test quiz and discussion forums. The critical strategies recommended managing online examination involve setting up online questions using freely available software and utilising free video conferencing tool as CCTV on mobile phones for invigilation purposes. Educators must consider readiness among students and teachers, cheating practices and student diversity when employing online assessment at HEIs. They can benefit from training for online learning and the assessment methods to prepare them better when facing global uncertainties such as COVID-19 pandemic. Furthermore, educators must evaluate the methods and their impact on students' learning outcomes.

Estimating the impact of physical distancing measures in containing COVID-19: an empirical analysis.

BACKGROUND: Epidemic modelling studies predict that physical distancing is critical in containing COVID-19. However, few empirical studies have validated this finding. Our study evaluates the effectiveness of different physical distancing measures in controlling viral transmission. METHODS: We identified three distinct physical distancing measures with varying intensity and implemented at different times-international travel controls, restrictions on mass gatherings, and lockdown-type measures-based on the Oxford COVID-19 Government Response Tracker. We also estimated the time-varying reproduction number (Rt) for 142 countries and tracked Rt temporally for two weeks following the 100th reported case in each country. We regressed Rt on the physical distancing measures and other control variables (income, population density, age structure, and temperature) and performed several robustness checks to validate our findings. FINDINGS: Complete travel bans and all forms of lockdown-type measures have been effective in reducing average Rt over the 14 days following the 100th case. Recommended stay-at-home advisories and partial lockdowns are as effective as complete lockdowns in outbreak control. However, these measures have to be implemented early to be effective. Based on the observed median timing across countries worldwide, lockdown-type measures are considered early if they were instituted about two weeks before the 100th case and travel bans a week before detection of the first case. INTERPRETATION: A combination of physical distancing measures, if implemented early, can be effective in containing COVID-19-tight border controls to limit importation of cases, encouraging physical distancing, moderately stringent measures such as working from home, and a full lockdown in the case of a probable uncontrolled outbreak.

Probable causes and risk factors for positive SARS-CoV-2 test in recovered patients: Evidence from Brunei Darussalam.

Case reports of patients with coronavirus disease-2019 (COVID-19) who have been discharged and subsequently report positive reverse transcription-polymerase chain reaction again (hereafter referred as "re-positive") do not fully describe the magnitude and significance of this issue. To determine the re-positive rate (proportion) and review probable causes and outcomes, we conduct a retrospective study of all 119 discharged patients in Brunei Darussalam up till April 23. Patients who were discharged are required to self-isolate at home for 14 days and undergo nasopharyngeal specimen collection postdischarge. Discharged patients found to be re-positive were readmitted. We reviewed the clinical and epidemiological records of all discharged patients and apply log-binomial models to obtain risk ratios for re-positive status. One in five recovered patients subsequently test positive again for severe acute respiratory syndrome coronavirus 2-this risk is more than six times higher in persons aged 60 years and above. The average Ct value of re-positive patients was lower predischarge compared with their readmission Ct value. Out of 111 close contacts tested, none were found to be positive as a result of exposure to a re-positive patient. Our findings support prolonged but intermittent viral shedding as the probable cause for this phenomenon. We did not observe infectivity potential in these patients.

Analysis of SARS-CoV-2 Transmission in Different Settings, Brunei.

We report the transmission dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) across different settings in Brunei. An initial cluster of SARS-CoV-2 cases arose from 19 persons who had attended the Tablighi Jama'at gathering in Malaysia, resulting in 52 locally transmitted cases. The highest nonprimary attack rates (14.8%) were observed from a subsequent religious gathering in Brunei and in households of attendees (10.6%). Household attack rates from symptomatic case-patients were higher (14.4%) than from asymptomatic (4.4%) or presymptomatic (6.1%) case-patients. Workplace and social settings had attack rates of <1%. Our analyses highlight that transmission of SARS-CoV-2 varies depending on environmental, behavioral, and host factors. We identify red flags for potential superspreading events, specifically densely populated gatherings with prolonged exposure in enclosed settings, persons with recent travel history to areas with active SARS-CoV-2 infections, and group behaviors. We propose differentiated testing strategies to account for differing transmission risk.

What do we know about SARS-CoV-2 transmission? A systematic review and meta-analysis of the secondary attack rate and associated risk factors.

INTRODUCTION: Current SARS-CoV-2 containment measures rely on controlling viral transmission. Effective prioritization can be determined by understanding SARS-CoV-2 transmission dynamics. We conducted a systematic review and meta-analyses of the secondary attack rate (SAR) in household and healthcare settings. We also examined whether household transmission differed by symptom status of index case, adult and children, and relationship to index case. METHODS: We searched PubMed, medRxiv, and bioRxiv databases between January 1 and July 25, 2020. High-quality studies presenting original data for calculating point estimates and 95% confidence intervals (CI) were included. Random effects models were constructed to pool SAR in household and healthcare settings. Publication bias was assessed by funnel plots and Egger's meta-regression test. RESULTS: 43 studies met the inclusion criteria for household SAR, 18 for healthcare SAR, and 17 for other settings. The pooled household SAR was 18.1% (95% CI: 15.7%, 20.6%), with significant heterogeneity across studies ranging from 3.9% to 54.9%. SAR of symptomatic index cases was higher than asymptomatic cases (RR: 3.23; 95% CI: 1.46, 7.14). Adults showed higher susceptibility to infection than children (RR: 1.71; 95% CI: 1.35, 2.17). Spouses of index cases were more likely to be infected compared to other household contacts (RR: 2.39; 95% CI: 1.79, 3.19). In healthcare settings, SAR was estimated at 0.7% (95% CI: 0.4%, 1.0%). DISCUSSION: While aggressive contact tracing strategies may be appropriate early in an outbreak, as it progresses, measures should transition to account for setting-specific transmission risk. Quarantine may need to cover entire communities while tracing shifts to identifying transmission hotspots and vulnerable populations. Where possible, confirmed cases should be isolated away from the household.

Epidemiological Investigation of the First 135 COVID-19 Cases in Brunei: Implications for Surveillance, Control, and Travel Restrictions.

Studies on the early introduction of SARS-CoV-2 in a naive population have important epidemic control implications. We report findings from the epidemiological investigation of the initial 135 COVID-19 cases in Brunei and describe the impact of control measures and travel restrictions. Epidemiological and clinical information was obtained for all confirmed COVID-19 cases, whose symptom onset was from March 9 to April 5, 2020. The basic reproduction number (R0), incubation period, and serial interval (SI) were calculated. Time-varying R was estimated to assess the effectiveness of control measures. Of the 135 cases detected, 53 (39.3%) were imported. The median age was 36 (range = 0.5-72) years. Forty-one (30.4%) and 13 (9.6%) were presymptomatic and asymptomatic cases, respectively. The median incubation period was 5 days (interquartile range [IQR] = 5, range = 1-11), and the mean SI was 5.4 days (SD = 4.5; 95% CI: 4.3, 6.5). The reproduction number was between 3.9 and 6.0, and the doubling time was 1.3 days. The time-varying reproduction number (Rt) was below one (Rt = 0.91; 95% credible interval: 0.62, 1.32) by the 13th day of the epidemic. Epidemic control was achieved through a combination of public health measures, with emphasis on a test-isolate-trace approach supplemented by travel restrictions and moderate physical distancing measures but no actual lockdown. Regular and ongoing testing of high-risk groups to supplement the existing surveillance program and a phased easing of physical distancing measures has helped maintain suppression of the COVID-19 outbreak in Brunei, as evidenced by the identification of only six additional cases from April 5 to August 5, 2020.