BACKGROUND Previous studies highlight viral shedding using cycle threshold (Ct) with the RT-PCT for epidemic trajectories of SARS-CoV-2 infection, but assessing Ct values transition kinetics before recovery for surveillance using individual repeated Ct values data is rare. OBJECTIVE We propose a new Ct-enshrined compartment model for understanding viral shedding kinetics in susceptible, pre-symptomatic, and symptomatic compartments before recovery or death. METHODS A series of useful recovery indices are developed to quantify the kinetic movement of Ct-up-down viral shedding toward recovery and are demonstrated with two scenarios, one is small-scale community-acquired Alpha VOC infection under the “zero-COVID-19” policy without available vaccine in May 2021, and the other is large-scale community-acquired Omicron infection with high booster vaccination but lifting the “zero-COVID-19” policy in April 2022 in Taiwan. RESULTS Kinetic indicators revealed Alpha's increased Ct-up transitions, indicative of reduced viral loads, especially among asymptomatic infections. In contrast, Omicron displayed swifter viral shedding and a higher asymptomatic recovery rate. Vaccination showed discernible effects; non-boosted individuals had a 19% higher pre-symptomatic incidence. Sensitivity analysis affirmed the chosen Ct values of 18 and 25, ensuring robust results across recovery phases. CONCLUSIONS The study provides a new insight into the dynamic CT transitions with the notable finding that Ct-up transitions toward recovery outpace Ct-down and symptom-surfacing transitions during the pre-symptomatic phase. The Ct-up against Ct-down transition varies with variants and vaccination status. The proposed Ct-enshrined compartment model is useful for the surveillance of emerging infectious diseases in the future to prevent community-acquired outbreaks.
As COVID-19 has become a pandemic emerging infectious disease it is important to examine whether there was a spatiotemporal clustering phenomenon in the globe during the rapid spread after the first outbreak reported from southern China. The open data on the number of COVID-19 cases reported at daily basis form the globe were used to assess the evolution of outbreaks with international air link on the same latitude and also including Taiwan. The dynamic Susceptible-Infected-Recovered model was used to evaluate continental transmission from December 2019 to March 2020 before the declaration of COVID-19 pandemic with basic reproductive number and effective reproductive number before and after containment measurements. For the initial COVID-19 outbreak in China, the estimated reproductive number was reduced from 2.84 during the overwhelming outbreaks in early January to 0.43 after the strict lockdown policy. It is very surprising to find there were three countries (including South Korea, Iran, and Italy) and the Washington state of the USA on the 38° North Latitude involved with large-scale community-acquired outbreaks since the first imported COVID-19 cases from China. The propagation of continental transmission was augmented from hotspot to hotspot with higher reproductive number immediately before the declaration of pandemic. By contrast, there was not any large community-acquired outbreak in Taiwan. The propagated spatiotemporal transmission from China to other hotspots may explain the emerging pandemic that can only be exempted by timely border control and preparedness of containment measurements according to Taiwan experience.
There are few studies demonstrating how the effectiveness of various extents of non-pharmaceutical interventions (NPIs) before and after vaccination periods. The study aimed to demonstrate such an effectiveness in the alteration of the epidemic curves from theory to practice.The empirical data on the daily reported COVID-19 cases were extracted from open source. A computer simulation design in conjunction with the susceptible-exposed-infected-recovered (SEIR) type model was applied to evaluating confinement measures in Italy with adjustment for underreported cases; isolation and quarantine in Taiwan; and NPIs and vaccination in Israel.In Italy scenario, the extents of confinement measures were 34% before the end of March and then scaled up to 70% after then. Both figures were reduced to 22-69% after adjusting for underreported cases. Approximately 44% of confinement measures were implemented in the second surge of pandemic in Italy. Fitting the observational data on Taiwan assuming the initial outbreak similar to Wuhan, China, 44% of isolation and quarantine were estimated before March 23rd, 2020. Isolation and quarantine were scaled up to 90% and at least 60% to contain community-acquired outbreaks from March 24th, 2020 onwards. Given 15% monthly vaccination rate from December 2020 in Israel, the effectiveness estimates of reducing the infected toll were 36%, 56%, and 85% for NPIs alone, vaccination alone, and both combined, respectively.We demonstrated how various NPIs stamp out and delay the epidemic curve of COVID-19. The optimal implementation of these NPIs has to be planned before wide vaccine uptake worldwide.
The reported cases with varicella have not decreased and outbreaks of varicella among vaccinated children continue to be reported 9 years after the public vaccination program in Taipei. We investigated an outbreak to determine varicella vaccine coverage and effectiveness.An outbreak occurred in an elementary school which located in southern Taipei from April 2007 through May 2007. A retrospect cohort study was performed by using a self-administered questionnaire for parents.Ten out of sixteen varicella cases were vaccinated. Overall vaccine coverage was 71.2%. The common reasons for not receiving varicella vaccine were that varicella vaccine was unavailable because the student didn't live in Taipei (29.4%) or the children could not be vaccinated due to certain illnesses (23.5%). The sensitivity and specificity of self-reported vaccination status was 0.900 (95% CI: 0.864, 0.935) and 0.611 (95% CI: 0.514, 0.701).The vaccine effectiveness was 69.3%-100.0% against any disease severity of varicella. Overall vaccine effectiveness against moderate or severe varicella was 85.5%. Attending cram school was associated with the risk of developing the varicella illness (RR: 13.39; 95% CI: 5.38, 33.31). Unvaccinated students tended to show moderate to severe (>50 lesions) afflictions of the disease (RR: 4.17; 95% CI: 1.15, 15.14).Because of the low vaccination coverage, varicella outbreaks continue to be reported in Taipei. Increasing vaccine coverage and second dose vaccination for increasing vaccine effectiveness may be considered.
The spread of the emerging pathogen, named as SARS-CoV-2, has led to an unprecedented COVID-19 pandemic since 1918 influenza pandemic. This review first sheds light on the similarity on global transmission, surges of pandemics, and the disparity of prevention between two pandemics. Such a brief comparison also provides an insight into the potential sequelae of COVID-19 based on the inference drawn from the fact that a cascade of successive influenza pandemic occurred after 1918 and also the previous experience on the epidemic of SARS and MERS occurring in 2003 and 2015, respectively. We then propose a systematic framework for elucidating emerging infectious disease (EID) such as COVID-19 with a panorama viewpoint from natural infection and disease process, public health interventions (non-pharmaceutical interventions (NPIs) and vaccine), clinical treatments and therapies (antivirals), until global aspects of health and economic loss, and economic evaluation of interventions with emphasis on mass vaccination. This review not only concisely delves for evidence-based scientific literatures from the origin of outbreak, the spread of SARS-CoV-2 to three surges of pandemic, and NPIs and vaccine uptakes but also provides a new insight into how to apply big data analytics to identify unprecedented discoveries through COVID-19 pandemic scenario embracing from biomedical to economic viewpoints.
Background: Accurate prediction of one-year mortality in emergency departments (EDs) is critical for guiding palliative care and end-of-life decisions. Current screening tools have limitations, prompting the development of a new risk score model tailored to predict one-year mortality and potential hospice needs in EDs.Methods: We adopted a large retrospective cohort (n=43,656) in conjunction with in-time (the trained and the holdout validation cohort) for the development of the model and out-of-time validation sample for external validation and model robustness to variation with the calendar year in EDs.Findings: The enrolled study subjects consisted of 10,474 patients aged 15 and older from the in-time variation cohort between June 2015 and December 2017 and 33,182 patients from the out-of-time validation cohort between 2017 and 2020. Significant risk scores included age (0·05 per year), qSOFA ≥ 2 (4), Cancer (5), Eastern Cooperative Oncology Group Performance Status score ≥ 2 (2), and Do-Not-Resuscitate status (DNR) (2). The AUROC curve for the in-time validation sample was 0·76 (0·74-0·78). However, the corresponding figure was slightly shrunk to 0·69 (0·69-0·70) based on out-of-time validation. The accuracy with our newly developed A-qCPR model was better than those existing tools including 0·57 (0·56–0·57) by using SQ, 0·54 (0·54-0·54) by using qSOFA, and 0·59 (0·59-0·59) by using ECOG performance status score.Applying the model to ED since 2017 has led to a year-on-year increase in the proportion of patients or their families signing DNR documents, which had not been affected by the COVID-19 pandemic.Interpretation: The model is not only effective in predicting one-year mortality but also in identifying hospice needs. Advancing the screening tool that has been widely used for hospice in various scenarios is particularly helpful for facilitating the end-of-life decision-making process in the ED.Funding: None.Declaration of Interest: The authors have no conflicts of interest to declare.Ethical Approval: De-identified participant data were collected after approval from the research ethics committee of Taipei City Hospital (TCHIRB-10703107, 13 April 2018 and TCHIRB-11008011-E, 25 August 2021). The committee approved a request to waive the documentation of informed consent.
Background: The reported cases with varicella have not decreased and outbreaks of varicella among vaccinated children continue to be reported 9 years after the public vaccination program in Taipei. We investigated an outbreak to determine varicella vaccine coverage and effectiveness. Methods: An outbreak occurred in an elementary school which located in southern Taipei from April 2007 through May 2007. A retrospect cohort study was performed by using a self-administered questionnaire for parents. Results: Ten out of sixteen varicella cases were vaccinated. Overall vaccine coverage was 71.2%. The common reasons for not receiving varicella vaccine were that varicella vaccine was unavailable because the student didn’t live in Taipei (29.4%) or the children could not be vaccinated due to certain illnesses (23.5%). The sensitivity and specificity of self-reported vaccination status was 0.900 (95% CI: 0.864, 0.935) and 0.611 (95% CI: 0.514, 0.701). The vaccine effectiveness was 69.3%-100.0% against any disease severity of varicella. Overall vaccine effectiveness against moderate or severe varicella was 85.5%. Attending cram school was associated with the risk of developing the varicella illness (RR: 13.39; 95% CI: 5.38, 33.31). Unvaccinated students tended to show moderate to severe (>50 lesions) afflictions of the disease (RR: 4.17; 95% CI: 1.15, 15.14). Conclusions: Because of the low vaccination coverage, varicella outbreaks continue to be reported in Taipei. Increasing vaccine coverage and second dose vaccination for increasing vaccine effectiveness may be considered.
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