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1.
biorxiv; 2024.
Preprint in English | bioRxiv | ID: ppzbmed-10.1101.2024.01.30.577909

ABSTRACT

Many complex natural systems undergo shifts in dynamics at particular points in time. Examples include phase transitions in gene expression during the cell cycle, introduced species affecting predator-prey interactions, and disease outbreaks responding to intervention measures. Such changepoints partition timeseries into different dynamical regimes characterized by distinct parameter sets, and inference on both the changepoints and regime-specific dynamical parameters is of primary interest. Conventional approaches to analyzing switching dynamical systems first estimate changepoints, and then estimate dynamical parameters assuming the changepoints are fixed and known. Such two-stage approaches are ad-hoc, can introduce biases in the analysis, and do not fully account for uncertainty. Here, we introduce a rigorous, simulation-based inference framework that simultaneously estimates changepoints and model parameters from noisy data while admitting full uncertainty. We use simulation studies of oscillatory predator-prey dynamics and stochastic gene expression to demonstrate that our method yields accurate estimates of changepoints and model parameters together with appropriate uncertainty bounds. We then apply our approach to a real-world case study of COVID-19 intervention effects, and show that our inferred changepoints aligned closely with the actual dates of intervention implementation. Taken together, these results suggest that our framework will have broad utility in diverse scientific domains.


Subject(s)
COVID-19
2.
Int J Antimicrob Agents ; 62(1): 106834, 2023 Jul.
Article in English | MEDLINE | ID: covidwho-2313529

ABSTRACT

BACKGROUND: Molnupiravir is an essential oral antiviral agent against coronavirus disease 2019 (COVID-19); however, its real-world effectiveness has not been evaluated in patients undergoing haemodialysis (HD). METHODS: This multi-centre retrospective study, involving 225 patients undergoing HD with initially mild or asymptomatic COVID-19, was conducted to compare the risks of 30-day COVID-19-related acute care visits between patients receiving and not receiving molnupiravir. Patients who received molnupiravir were stratified by rapid antigen detection (RAD) test results on day 7 after disease onset to assess whether rapid molnupiravir introduction accelerated viral clearance. RESULTS: Thirty-day COVID-19-related acute care visits were reported in 9.41% and 21.74% of the molnupiravir and control groups, respectively, and use of molnupiravir markedly reduced the risk of acute care visits after adjusting for baseline characteristics via propensity score weighting [hazard ratio 0.218, 95% confidence interval (CI) 0.074-0.642; P=0.006]. The tolerability of molnupiravir in the enrolled patients was generally acceptable, with only 11.88% of molnupiravir users reporting mild adverse events. Moreover, rapid initiation of molnupiravir within 1 day of COVID-19 onset was an independent predictor of conversion to a negative RAD test result on day 7 after disease onset (odds ratio 6.207, 95% CI 2.509-15.358; P<0.001). CONCLUSIONS: Molnupiravir is well tolerated and decreases the medical needs in patients with COVID-19 undergoing HD. Furthermore, the rapid initiation of molnupiravir accelerates viral clearance in patients with COVID-19 undergoing HD. These findings highlight the therapeutic role of molnupiravir for this vulnerable population.


Subject(s)
COVID-19 , Humans , Retrospective Studies , Renal Dialysis , Treatment Outcome , Antiviral Agents/therapeutic use
3.
Viruses ; 15(2)2023 02 16.
Article in English | MEDLINE | ID: covidwho-2239719

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine booster is one of the most essential strategies against coronavirus disease 2019 (COVID-19) in the era of emerging variants. However, the effectiveness of SARS-CoV-2 vaccine boosters has not much been investigated in hemodialysis (HD) patients receiving oral antiviral agents. In this retrospective study involving 258 HD patients with COVID-19 receiving molnupiravir, we stratified the study cohort according to vaccination status and compared the baseline characteristics and risks of 30-day composite events (COVID-19-related acute care visits, hospitalization, or mortality) among groups. Our analysis demonstrated that the SARS-CoV-2 vaccine boosters markedly decreased the risk of composite events in HD patients (hazard ratio (95% confidence interval), 0.163 (0.063-0.423) for three vs. ≤ two doses of vaccination, p < 0.001; 0.309 (0.115-0.830) for four vs. ≤ two doses of vaccination, p = 0.020). The benefits of vaccine boosters were similar between patients receiving mRNA-based and protein-based boosters and between those with post-booster intervals of ≤ 120 and > 120 days. In conclusion, for HD patients with initially mild or asymptomatic COVID-19 receiving molnupiravir, the benefits of SARS-CoV-2 vaccine boosters are prominent, irrespective of booster vaccine types.


Subject(s)
COVID-19 Vaccines , COVID-19 , Humans , COVID-19/prevention & control , Retrospective Studies , SARS-CoV-2 , Renal Dialysis
4.
Vaccines (Basel) ; 10(9)2022 Sep 15.
Article in English | MEDLINE | ID: covidwho-2044012

ABSTRACT

Hemodialysis (HD) patients are vulnerable to coronavirus disease 2019 (COVID-19) and have a high mortality rate. We evaluated the anti-SARS-CoV-2 spike protein antibody (ACOV2S) levels in 385 HD patients before and 4 and 8 weeks after the second dose of vector-based ChAdOx1 nCoV-19 vaccine. For study control, week 4 ACOV2S levels after the second vaccination dose were measured in 66 healthcare workers (HCWs). The seroconversion rate of HD patients was 98.96% 4 weeks after the second vaccination. Despite low antibody levels before the second dose (week 0), week 4 ACOV2S levels after the second vaccine dose in HD patients increased prominently and were compatible with those in HCWs (p = 0.814 for HCWs vs. HD patients). The ACOV2S levels in HD patients waned significantly 8 weeks after the second vaccination dose (p < 0.001 at week 8 vs. 4). Older age and immunosuppressant use were negative predictors, while higher C-reactive protein (CRP) levels were positive predictors of ACOV2S waxing after the second vaccine dose in HD patients. Higher CRP levels and platelet counts were independently associated with decreased ACOV2S waning. The ChAdOx1 nCoV-19 vaccine is effective and safe for primary vaccination in HD patients and a booster dose is necessary.

5.
arxiv; 2022.
Preprint in English | PREPRINT-ARXIV | ID: ppzbmed-2208.12928v1

ABSTRACT

Throughout the coronavirus disease 2019 (COVID-19) pandemic, decision makers have relied on forecasting models to determine and implement non-pharmaceutical interventions (NPI). In building the forecasting models, continuously updated datasets from various stakeholders including developers, analysts, and testers are required to provide precise predictions. Here we report the design of a scalable pipeline which serves as a data synchronization to support inter-country top-down spatiotemporal observations and forecasting models of COVID-19, named the where2test, for Germany, Czechia and Poland. We have built an operational data store (ODS) using PostgreSQL to continuously consolidate datasets from multiple data sources, perform collaborative work, facilitate high performance data analysis, and trace changes. The ODS has been built not only to store the COVID-19 data from Germany, Czechia, and Poland but also other areas. Employing the dimensional fact model, a schema of metadata is capable of synchronizing the various structures of data from those regions, and is scalable to the entire world. Next, the ODS is populated using batch Extract, Transfer, and Load (ETL) jobs. The SQL queries are subsequently created to reduce the need for pre-processing data for users. The data can then support not only forecasting using a version-controlled Arima-Holt model and other analyses to support decision making, but also risk calculator and optimisation apps. The data synchronization runs at a daily interval, which is displayed at https://www.where2test.de.


Subject(s)
COVID-19
6.
medrxiv; 2020.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2020.02.22.20026617

ABSTRACT

A respiratory illness has been spreading rapidly in China, since its outbreak in Wuhan city, Hubei province in December 2019. The illness was caused by a novel coronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Clinical manifestations related to SARS-CoV-2 infection ranged from no symptom to fatal pneumonia. World Health Organization (WHO) named the diseases associated with SARS-CoV-2 infection as COVID-19. Real time RT-PCR is the only laboratory test available till now to confirm the infection. However, the accuracy of real time RT-PCR depends on many factors, including sampling location and of methods, quality of RNA extraction and training of operators etc. Variations in these factors might significantly lower the sensitivity of the detection. We developed a peptide-based luminescent immunoassay to detect IgG and IgM. Cut-off value of this assay was determined by the detection of 200 healthy sera and 167 sera from patients infected with other pathogens than SARS-CoV-2. To evaluate the performance of this assay, we detected IgG and IgM in the 276 sera from confirmed patients. The positive rate of IgG and IgM were 71.4% (197/276) and 57.2% (158/276) respectively. By combining with real time RT-PCR detection, this assay might help to enhance the accuracy of diagnosis of SARS-CoV-2 infection.


Subject(s)
COVID-19 , Pneumonia
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