Predictive evolutionary modelling for influenza virus by site-based dynamics of mutations.

Influenza virus continuously evolves to escape human adaptive immunity and generates seasonal epidemics. Therefore, influenza vaccine strains need to be updated annually for the upcoming flu season to ensure vaccine effectiveness. We develop a computational approach, beth-1, to forecast virus evolution and select representative virus for influenza vaccine. The method involves modelling site-wise mutation fitness. Informed by virus genome and population sero-positivity, we calibrate transition time of mutations and project the fitness landscape to future time, based on which beth-1 selects the optimal vaccine strain. In season-to-season prediction in historical data for the influenza A pH1N1 and H3N2 viruses, beth-1 demonstrates superior genetic matching compared to existing approaches. In prospective validations, the model shows superior or non-inferior genetic matching and neutralization against circulating virus in mice immunization experiments compared to the current vaccine. The method offers a promising and ready-to-use tool to facilitate vaccine strain selection for the influenza virus through capturing heterogeneous evolutionary dynamics over genome space-time and linking molecular variants to population immune response.

Health and wellbeing among the empty nest and non-empty nest elderly in China-Results from a national cross-sectional study.

BACKGROUND: The number of empty nest elderly in China has gradually increased in recent years. There is growing concern about the physical and mental health of this population as empty nest elderly are commonly at the risk of compromising health, home safety and quality of life. This study reported the health and well-being of empty nest elderly with regards to their health status, depression and satisfaction, lifestyle as compared to non-empty nest elderly in China. METHODS: Data was collected from the 2018 follow-up interviews of China Health and Retirement Longitudinal Survey. We included 4,630 empty nest elderly and 6,188 non-empty nest elderly. Chi-square Test and Logistic Regression were used to compare the differences between these two groups. RESULTS: As compared to the non-empty nest elderly, there was higher proportion of empty nest elderly who suffered from dyslipidemia, diabetes, chronic lung diseases, heart attack (27.0% vs. 25.0%; 16.6% vs. 15.1%; 19.4% vs. 16.4%; 26.3% vs. 23.4%, P < 0.05). The empty nest elderly had higher proportion of participants who drank more than once a month (25.3% vs. 23.9%, P < 0.05), who felt satisfied with their marriage (71.6% vs. 66.2%, P < 0.001), who were satisfied with their children's relationship (85.2% vs. 83.2%, P < 0.001). However, these significances disappeared in the Logistic Regression analysis (P > 0.05). CONCLUSION: Our study showed that significant between-group difference was found between empty nest elderly and non-empty nest elderly in their health and wellbeing. However, disappearance of such difference in the multivariable analysis may indicate improved health and wellbeing among the empty nest elderly. Even though our study still suggested the importance of improving the health, lifestyles and family dynamics of the elderly and promoting the integration of health and social care for the elderly, especially among the empty nest elderly.

A Prism Vote method for individualized risk prediction of traits in genotype data of Multi-population.

Multi-population cohorts offer unprecedented opportunities for profiling disease risk in large samples, however, heterogeneous risk effects underlying complex traits across populations make integrative prediction challenging. In this study, we propose a novel Bayesian probability framework, the Prism Vote (PV), to construct risk predictions in heterogeneous genetic data. The PV views the trait of an individual as a composite risk from subpopulations, in which stratum-specific predictors can be formed in data of more homogeneous genetic structure. Since each individual is described by a composition of subpopulation memberships, the framework enables individualized risk characterization. Simulations demonstrated that the PV framework applied with alternative prediction methods significantly improved prediction accuracy in mixed and admixed populations. The advantage of PV enlarges as genetic heterogeneity and sample size increase. In two real genome-wide association data consists of multiple populations, we showed that the framework considerably enhanced prediction accuracy of the linear mixed model in five-group cross validations. The proposed method offers a new aspect to analyze individual's disease risk and improve accuracy for predicting complex traits in genotype data.

Impact of endoscopic ultrasound-guided gallbladder drainage on reducing costs of reintervention and unplanned readmission: a budget impact analysis.

Background and study aims Endoscopic ultrasound-guided gallbladder drainage (EUS-GBD) is the preferred treatment for patients with acute calculous cholecystitis who are unfit for surgery. The aim of this study was to perform a cost-effective analysis (CEA) comparing EUS-GBD with percutaneous gallbladder drainage (PT-GBD). Patients and methods CEA was performed on patients recruited for our prior randomized controlled trial. A budget impact model was developed to compare the base-case and scenario of EUS-GBD applications. The costs including peri-procedure and intra-procedure, reinterventions, expenses associated with treatment of adverse events (AEs), costs of hospital stay, subsequent clinic follow-up, and unplanned readmission were included. Results PT-GBD had a lower total procedure cost per patient (USD$4,375.00) than EUS-GBD (USD$9,397.44). For EUS-GBD, the cost of cautery-enhanced lumen-apposing stent accounted for the major part of the expense (USD$4,910.26). EUS-GBD resulted in a lower expected cost (USD$108.26 vs USD$1,601.54) for a re-procedure. The expected cost per patient in unplanned readmissions in the EUS-GBD group (USD$450.00) was lower than that in the PT-GBD group (USD$1,717.56). Based on the budget impact analysis, the net budget impact per year of introducing EUS-GBD to replace PT-GBD was higher (USD$16,424.10 vs USD$11,433.08). The net budget impact was most sensitive to the cost of stent and linear echoendoscope used in EUS-GBD. Conclusions The net budget impact per year was higher for introducing EUS-GBD. The cost of the stent accounted for the major cost difference between the two procedures. EUS-GBD saved on the cost in management of AEs, reinterventions, and unplanned readmissions but these did not offset the cost of the stent.

Rapid evaluation of COVID-19 vaccine effectiveness against symptomatic infection with SARS-CoV-2 variants by analysis of genetic distance.

Timely evaluation of the protective effects of Coronavirus Disease 2019 (COVID-19) vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is urgently needed to inform pandemic control planning. Based on 78 vaccine efficacy or effectiveness (VE) data from 49 studies and 1,984,241 SARS-CoV-2 sequences collected from 31 regions, we analyzed the relationship between genetic distance (GD) of circulating viruses against the vaccine strain and VE against symptomatic infection. We found that the GD of the receptor-binding domain of the SARS-CoV-2 spike protein is highly predictive of vaccine protection and accounted for 86.3% (P = 0.038) of the VE change in a vaccine platform-based mixed-effects model and 87.9% (P = 0.006) in a manufacturer-based model. We applied the VE-GD model to predict protection mediated by existing vaccines against new genetic variants and validated the results by published real-world and clinical trial data, finding high concordance of predicted VE with observed VE. We estimated the VE against the Delta variant to be 82.8% (95% prediction interval: 68.7-96.0) using the mRNA vaccine platform, closely matching the reported VE of 83.0% from an observational study. Among the four sublineages of Omicron, the predicted VE varied between 11.9% and 33.3%, with the highest VE predicted against BA.1 and the lowest against BA.2, using the mRNA vaccine platform. The VE-GD framework enables predictions of vaccine protection in real time and offers a rapid evaluation method against novel variants that may inform vaccine deployment and public health responses.

Superspreading and heterogeneity in transmission of SARS, MERS, and COVID-19: A systematic review.

BACKGROUND: Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and coronavirus disease 2019 (COVID-19) have caused substantial public health burdens and global health threats. Understanding the superspreading potentials of these viruses are important for characterizing transmission patterns and informing strategic decision-making in disease control. This systematic review aimed to summarize the existing evidence on superspreading features and to compare the heterogeneity in transmission within and among various betacoronavirus epidemics of SARS, MERS and COVID-19. METHODS: PubMed, MEDLINE, and Embase databases were extensively searched for original studies on the transmission heterogeneity of SARS, MERS, and COVID-19 published in English between January 1, 2003, and February 10, 2021. After screening the articles, we extracted data pertaining to the estimated dispersion parameter (k) which has been a commonly-used measurement for superspreading potential. FINDINGS: We included a total of 60 estimates of transmission heterogeneity from 26 studies on outbreaks in 22 regions. The majority (90%) of the k estimates were small, with values less than 1, indicating an over-dispersed transmission pattern. The point estimates of k for SARS and MERS ranged from 0.12 to 0.20 and from 0.06 to 2.94, respectively. Among 45 estimates of individual-level transmission heterogeneity for COVID-19 from 17 articles, 91% were derived from Asian regions. The point estimates of k for COVID-19 ranged between 0.1 and 5.0. CONCLUSIONS: We detected a substantial over-dispersed transmission pattern in all three coronaviruses, while the k estimates varied by differences in study design and public health capacity. Our findings suggested that even with a reduced R value, the epidemic still has a high resurgence potential due to transmission heterogeneity.

In silico prediction of influenza vaccine effectiveness by sequence analysis.

The effectiveness of seasonal influenza vaccines varies with the matching of vaccine strains to circulating strains. Based on the genetic distance of hemagglutinin and neuraminidase gene of the influenza viruses to vaccine strains, we statistically quantified the relationship between the genetic mismatch and vaccine effectiveness (VE) for influenza A/H1N1pdm09, A/H3N2 and B. We also proposed a systematic approach to integrate multiple genes and influenza types for overall VE estimation. Evident linear relationships were identified and validated in independent data. The modelling framework may enable in silico prediction for VE on a real-time basis and inform the influenza vaccine selection strategy.

Gender differences in quality of life among patients with myasthenia gravis in China.

BACKGROUND: Myasthenia gravis (MG), a chronic neuromuscular disorder, can adversely affect patients' health-related quality of life (HRQoL), especially in women. The study aimed to evaluate the difference in HRQoL of women and men MG patients and explore the factors that mediate the relationship between gender and HRQoL. METHODS: A cross-sectional study was conducted among 1815 patients with MG in China. The revised 15-item MG quality of life scale (MG-QOL15r) was used to access patients' HRQoL in overall, physical, social and emotional domains. Socio-demographic information, diagnosis and treatment history, comorbidities, social support, active lifestyle and the MG activities of daily living scale (MG-ADL) were recorded and compared between women and men using the Student's t-test and Pearson's Chi-square test. Multivariable regression analyses were conducted to identify independent contributors to HRQoL, especially those affecting different gender. RESULTS: On average, female patients with MG reported a lower MG-QOL15r score than the males (44.49 ± 29.10 vs 49.32 ± 29.18). The association between gender and patients' HRQoL interacted with the number of comorbidities across the overall, physical and social domains of patients. As the number of comorbidities increased, the scores of HRQoL decreased and it was faster among females than the males (p < 0.05). Moreover, unemployment, exacerbation of the disease, and active lifestyle contributed to the patients' HRQoL across all domains. Unemployment (ß = - 4.99 [95%CI, - 7.80 to - 2.18], p < 0.001) and exacerbations (ß = - 8.49 [95%CI, - 11.43 to - 5.54], p < 0.001) were correlated with poorer HRQoL; while an active lifestyle had a positive impact on HRQoL (ß = 0.28 [95%CI, 0.16 to 0.40], p < 0.001). CONCLUSIONS: The results indicate that the HRQoL of women MG patients was lower than that of men. The relationship between gender and HRQoL is modulated by the number of comorbidities. Thus, to improve the HRQoL of women MG patients, symptomatic treatments might not be enough, their comorbid conditions should be considered as well. Additionally, employment status, MG exacerbations, and an active lifestyle have been found as determining factors of the patients' HRQoL, which suggests future interventions should cope with these factors to improve their quality of life.

Genetic evolution of Human Enterovirus A71 subgenotype C4 in Shenzhen, China, 1998-2013.

BACKGROUND: Human Enterovirus A71 (EV-A71) is one of the severest enteroviruses that causes hand, foot, and mouth disease (HFMD) among children. This study identified the mutations of EV-A71 VP1 amino acid residues over a number of years and explored the possible association of identified mutations and HFMD epidemic outbreaks in Shenzhen, China. METHODS: A total of 3760 stool specimens were collected from HFMD patients by Shenzhen Centers for Disease Control and Prevention (CDC) between 1998 and 2013. In total 289 VP1 strains were sequenced in this study, and amino acids mutation frequency was calculated. There were 2040 China nationwide sequences downloaded from Genebank as replication data. RESULTS: In our samples, 1036 subjects (27.6%) were EV-A71 infected. Three amino acid positions on VP1 protein were found to have high mutation prevalence. These are Q22H, S283T, and A289H. Site 22 showed a fast mutation fixation in the year 2008, at the time of the large scale epidemic outbreak in Shenzhen. Analysis of the nationwide data replicated the same trend of mutation prevalence of the three sites. CONCLUSION: The switching from Q to H on site 22 of the EV-A71 VP1 strain might be associated with the HFMD outbreak in Shenzhen in 2008. The identified amino acid sites 22, 283 and 289 provided information for developing anti-viral drugs against EV-A71 in the future.

Cardiovascular disease risk reduction in rural China: a clustered randomized controlled trial in Zhejiang.

BACKGROUND: Cardiovascular disease (CVD) is a major cause of death in China. Despite government efforts, the majority of hypertensive and diabetic patients in China do not receive proper treatment. Reducing CVD events requires long-term care that is proactive, patient-centred, community-based, and sustainable. We have designed a package of interventions for patients at high risk of CVD to be implemented by family doctors based in township hospitals (providers of primary care) in rural Zhejiang, China. This trial aims to determine whether the systematic CVD risk reduction package results in reduced CVD events among patients at risk of CVD compared with usual care, and whether the package is cost-effective and suitable for routine implementation and scale-up. METHODS/DESIGN: This is a prospective, open-label, cluster randomized controlled trial (RCT) with blinded data analysis. The trial will randomize 67 township hospitals with 31,708 participants in three counties in Zhejiang Province. Participants will be identified from existing health records and will comprise adults aged 50 to 74 years, with a calculated 10-year CVD risk of 20% or higher, or diabetes. In the intervention arm, participants will receive a package of interventions including: 1) healthy lifestyle counseling (smoking cessation, and salt, oil, and alcohol reduction); 2) prescription of a combination of drugs (antihypertensives, aspirin, and statin); and 3) adherence support for drug compliance and healthy lifestyle change. In the control arm, participants will receive usual care for hypertension and diabetes management at individual clinicians' discretion. The primary outcome is the incidence of severe CVD events over 24 months of follow-up. All CVD events will be defined according to the World Health Organization (WHO) monitoring of trends and determinants in cardiovascular disease (MONICA) definitions, diagnosed at the county hospital or higher level, and reported by the Zhejiang surveillance system. Secondary outcomes include: mean systolic and diastolic blood pressure, blood glucose, serum total cholesterol (TC), and adherence to appointments, and drugs and lifestyle changes. DISCUSSION: This trial focuses on risk reduction of CVD rather than specific diseases. It is not designed to compare therapeutic and healthy lifestyle interventions, but rather their combined effects in primary care settings. Through the trial, we intend to understand the effectiveness of the comprehensive CVD reduction package in routine practice. We also intend to understand the barriers and facilitators to implementing the package, and thus to advise on policy and practice change. TRIAL REGISTRATION: Current Controlled Trials: ISRCTN58988083.