Cumulative Infection Research Articles

Estimating cumulative infection rate of COVID-19 after adjusting the dynamic zero-COVID policy in China

Estimating cumulative infection rate of COVID-19 after adjusting the dynamic zero-COVID policy in China

Strong long ties facilitate epidemic containment on mobility networks.

The analysis of connection strengths and distances in the mobility network is pivotal for delineating critical pathways, particularly in the context of epidemic propagation. Local connections that link proximate districts typically exhibit strong weights. However, ties that bridge distant regions with high levels of interaction intensity, termed strong long (SL) ties, warrant increased scrutiny due to their potential to foster satellite epidemic clusters and extend the duration of pandemics. In this study, SL ties are identified as outliers on the joint distribution of distance and flow in the mobility network of Shanghai constructed from 1 km × 1 km high-resolution mobility data. We propose a grid-joint isolation strategy alongside a reaction-diffusion transmission model to assess the impact of SL ties on epidemic propagation. The findings indicate that regions connected by SL ties exhibit a small spatial autocorrelation and display a temporal similarity pattern in disease transmission. Grid-joint isolation based on SL ties reduces cumulative infections by an average of 17.1% compared with other types of ties. This work highlights the necessity of identifying and targeting potentially infected remote areas for spatially focused interventions, thereby enriching our comprehension and management of epidemic dynamics.

Association between delayed outbreak identification and SARS-CoV-2 infection and mortality among long-term care home residents, Ontario, Canada, March to November 2020: a cohort study.

BackgroundLate outbreak identification is a common risk factor mentioned in case reports of large respiratory infection outbreaks in long-term care (LTC) homes.AimTo systematically measure the association between late SARS-CoV-2 outbreak identification and secondary SARS-CoV-2 infection and mortality in residents of LTC homes.MethodsWe studied SARS-CoV-2 outbreaks across LTC homes in Ontario, Canada from March to November 2020, before the COVID-19 vaccine rollout. Our exposure (late outbreak identification) was based on cumulative infection pressure (the number of infectious resident-days) on the outbreak identification date (early: ≤ 2 infectious resident-days, late: ≥ 3 infectious resident-days), where the infectious window was -2 to +8 days around onset. Our outcome consisted of 30-day incidence of secondary infection and mortality, based on the proportion of at-risk residents with a laboratory-confirmed SARS-CoV-2 infection with onset within 30 days of the outbreak identification date.ResultsWe identified 632 SARS-CoV-2 outbreaks across 623 LTC homes. Of these, 36.4% (230/632) outbreaks were identified late. Outbreaks identified late had more secondary infections (10.3%; 4,437/42,953) and higher mortality (3.2%; 1,374/42,953) compared with outbreaks identified early (infections: 3.3%; 2,015/61,714; p < 0.001, mortality: 0.9%; 579/61,714; p < 0.001). After adjustment for 12 LTC home covariates, the incidence of secondary infections in outbreaks identified late was 2.90-fold larger than that of outbreaks identified early (OR: 2.90; 95% CI: 2.04-4.13).ConclusionsThe timeliness of outbreak identification could be used to predict the trajectory of an outbreak, plan outbreak measures and retrospectively provide feedback for quality improvement, with the objective of reducing the impacts of respiratory infections in LTC home residents.

Effects of doxycycline post-exposure prophylaxis for prevention of sexually transmitted infections on gonorrhoea prevalence and antimicrobial resistance among men who have sex with men in the USA: a modelling study

Doxycycline post-exposure prophylaxis (PEP) has been shown to be efficacious for the prevention of bacterial sexually transmitted infections, but resistance implications for Neisseria gonorrhoeae remain unknown. We aimed to use a mathematical model to investigate the anticipated impact of doxycycline PEP on the burden of gonorrhoea and antimicrobial resistance dynamics in men who have sex with men (MSM) in the USA. Using a deterministic compartmental model, characterising gonorrhoea transmission in a US MSM population comprising three sexual activity groups defined by annual partner turnover rates, we introduced doxycycline PEP at various uptake levels (10-90%) among those with high sexual activity. Infections were stratified by symptom status and resistance profile (ie, susceptible, ceftriaxone-resistant, tetracycline-resistant, or dual-resistant), with ceftriaxone the treatment for active infection. As resistance to tetracycline, not doxycycline, is monitored and reported nationally, we used this as a proxy for doxycycline PEP resistance. We compared the 20-year prevalence, incidence rates, and cumulative incidence of gonococcal infection, resistance dynamics (time to 5% prevalence of ceftriaxone resistance, 5% prevalence of dual resistance, and 84% prevalence of tetracycline resistance), and antibiotic consumption with baseline (ie, no doxycycline PEP). Uptake of doxycycline PEP resulted in substantial reductions in the prevalence and incidence of gonorrhoea, but accelerated the spread of tetracycline resistance. The maximum reduction in prevalence over 20years compared with no uptake ranged from 40·3% (IQR 15·3-83·4) with 10% doxycycline PEP uptake to 77·4% (68·4-84·9) with 90%uptake. Similarly, the maximum reduction in the incidence rate ranged from 38·6% (14·1-83·6) with 10% uptake to 77·6% (68·1-84·7) with 90% uptake. Cumulative gonococcal infections were reduced by a median of 14·5% (IQR8·4-21·6) with 10% uptake and up to 46·2% (26·5-59·9) with 90% uptake after 5years, and by 6·5% (3·4-13·0) with 10% uptake and 8·7% (4·3-36·2) with 90% uptake by 20years. In almost all scenarios explored, doxycycline PEP lost clinical effectiveness (defined as 84% prevalence of tetracycline resistance) within the 20-year period, but itslifespan ranged from a median of 12·1years (IQR 9·9-15·7) with 10% uptake to 1·6years (1·3-1·9) with 90%uptake. Doxycycline PEP implementation had minimal impact on extending the clinical lifespan of ceftriaxone monotherapy (5·0years [IQR 4·0-6·2]), with the median time to 5% prevalence of resistance ranging from 4·8years (3·9-6·0) for 90% uptake to 5·0years (4·1-6·2) for 10% uptake. Similarly, the median time to 5%prevalence of dual resistance to ceftriaxone and tetracycline ranged from 4·8years (3·9-6·0) for 90% uptake to 5·8years (4·8-7·4) for 10% uptake. Median decrease in ceftriaxone consumption for high doxycycline PEP uptake levels compared with baseline ranged from 41·7% (27·0-54·3) for 50% uptake to 50·2% (29·3-62·7) for 90% uptake at 5years, but dropped to 11·8% (6·9-32·0) for 50% uptake and 12·1% (7·0-41·6) for 90% uptake after 20years. Notwithstanding the clear benefits of doxycycline PEP for other sexually transmitted infections, for Ngonorrhoeae, model findings suggest that doxycycline PEP is an effective but impermanent solution for reducing infection burden, given eventual selection for resistant strains. This finding presents a challenge for policy makers considering strategies for doxycycline PEP implementation and oversight: the need to balance the clear, short-term clinical benefits with the risk of harm via antimicrobial resistance. US Centers for Disease Control and Prevention, National Institute of Allergy and Infectious Diseases.

Infection Rates and Symptomatic Proportion of SARS-CoV-2 and Influenza in Pediatric Population, China, 2023.

We conducted a longitudinal cohort study of SARS-CoV-2 and influenza rates in childcare centers and schools in Wuxi, China, collecting 1,760 environmental samples and 9,214 throat swabs from 593 students (regardless of symptoms) in weekly collections during February-June 2023. We estimated a cumulative infection rate of 124.8 (74 episodes)/1,000 persons for SARS-CoV-2 and 128.2 (76 episodes)/1,000 persons for influenza. The highest SARS-CoV-2 infection rate was in persons 18 years of age, and for influenza, in children 4 years of age. The asymptomatic proportion of SARS-CoV-2 was 59.6% and 66.7% for influenza; SARS-CoV-2 symptomatic proportion was lower in 16-18-year-olds than in 4-6-year-olds. Only samples from frequently touched surface tested positive for SARS-CoV-2 (4/1,052) and influenza (1/1,052). We found asynchronous circulation patterns of SARS-CoV-2 and influenza, similar to trends in national sentinel surveillance. The results support vaccination among pediatric populations and other interventions, such as environmental disinfection in educational settings.

A model-based assessment of social isolation practices for COVID-19 outbreak response in residential care facilities

BackgroundResidential aged-care facilities (RACFs, also called long-term care facilities, aged care homes, or nursing homes) have elevated risks of respiratory infection outbreaks and associated disease burden. During the COVID-19 pandemic, social isolation policies were commonly used in these facilities to prevent and mitigate outbreaks. We refer specifically to general isolation policies that were intended to reduce contact between residents, without regard to confirmed infection status. Such policies are controversial because of their association with adverse mental and physical health indicators and there is a lack of modelling that assesses their effectiveness.MethodsIn consultation with the Australian Government Department of Health and Aged Care, we developed an agent-based model of COVID-19 transmission in a structured population, intended to represent the salient characteristics of a residential care environment. Using our model, we generated stochastic ensembles of simulated outbreaks and compared summary statistics of outbreaks simulated under different mitigation conditions. Our study focuses on the marginal impact of general isolation (reducing social contact between residents), regardless of confirmed infection. For a realistic assessment, our model included other generic interventions consistent with the Australian Government’s recommendations released during the COVID-19 pandemic: isolation of confirmed resident cases, furlough (mandatory paid leave) of staff members with confirmed infection, and deployment of personal protective equipment (PPE) after outbreak declaration.ResultsIn the absence of any asymptomatic screening, general isolation of residents to their rooms reduced median cumulative cases by approximately 27%. However, when conducted concurrently with asymptomatic screening and isolation of confirmed cases, general isolation reduced the median number of cumulative infections by only 12% in our simulations.ConclusionsUnder realistic sets of assumptions, our simulations showed that general isolation of residents did not provide substantial benefits beyond those achieved through screening, isolation of confirmed cases, and deployment of PPE. Our results also highlight the importance of effective case isolation, and indicate that asymptomatic screening of residents and staff may be warranted, especially if importation risk from the outside community is high. Our conclusions are sensitive to assumptions about the proportion of total contacts in a facility accounted for by casual interactions between residents.

Rapid and extensive SARS-CoV-2 Omicron variant infection wave revealed by wastewater surveillance in Shenzhen following the lifting of a strict COVID-19 strategy

Wastewater-based epidemiology (WBE) has emerged as a promising tool for monitoring the spread of COVID-19, as SARS-CoV-2 can be shed in the faeces of infected individuals, even in the absence of symptoms. This study aimed to optimize a prediction model for estimating COVID-19 infection rates based on SARS-CoV-2 RNA concentrations in wastewater, and reveal the infection trends and variant diversification in Shenzhen, China following the lifting of a strict COVID-19 strategy. Faecal samples (n = 4337) from 1204 SARS-CoV-2 infected individuals hospitalized in a designated hospital were analysed to obtain Omicron variant-specific faecal shedding dynamics. Wastewater samples from 6 wastewater treatment plants (WWTPs) and 9 pump stations, covering 3.55 million people, were monitored for SARS-CoV-2 RNA concentrations and variant abundance. We found that the viral load in wastewater increased rapidly in December 2022 in the two districts, demonstrating a sharp peak in COVID-19 infections in late-December 2022, mainly caused by Omicron subvariants BA.5.2.48 and BF.7.14. The prediction model, based on the mass balance between total viral load in wastewater and individual faecal viral shedding, revealed a surge in the cumulative infection rate from <0.1 % to over 70 % within three weeks after the strict COVID-19 strategy was lifted. Additionally, 39 cryptic SARS-CoV-2 variants were identified in wastewater, in addition to those detected through clinical surveillance. These findings demonstrate the effectiveness of WBE in providing comprehensive and efficient assessments of COVID-19 infection rates and identifying cryptic variants, highlighting its potential for monitoring emerging pathogens with faecal shedding.

Prenatal exposure to common infections and newborn DNA methylation: A prospective, population-based study

BackgroundInfections during pregnancy have been robustly associated with adverse mental and physical health outcomes in offspring, yet the underlying molecular pathways remain largely unknown. Here, we examined whether exposure to common infections in utero associates with DNA methylation (DNAm) patterns at birth and whether this in turn relates to offspring health outcomes in the general population. MethodsUsing data from 2,367 children from the Dutch population-based Generation R Study, we first performed an epigenome-wide association study to identify differentially methylated sites and regions at birth associated with prenatal infection exposure. We also examined the influence of infection timing by using self-reported cumulative infection scores for each trimester. Second, we sought to develop an aggregate methylation profile score (MPS) based on cord blood DNAm as an epigenetic proxy of prenatal infection exposure and tested whether this MPS prospectively associates with offspring health outcomes, including psychiatric symptoms, BMI, and asthma at ages 13–16 years. Third, we investigated whether prenatal infection exposure associates with offspring epigenetic age acceleration – a marker of biological aging. Across all analysis steps, we tested whether our findings replicate in 864 participants from an independent population-based cohort (ALSPAC, UK). ResultsWe observed no differentially methylated sites or regions in cord blood in relation to prenatal infection exposure, after multiple testing correction. 33 DNAm sites showed suggestive associations (p < 5e10 − 5; of which one was also nominally associated in ALSPAC), indicating potential links to genes associated with immune, neurodevelopmental, and cardiovascular pathways. While the MPS of prenatal infections associated with maternal reports of infections in the internal hold out sample in the Generation R Study (R2incremental = 0.049), it did not replicate in ALSPAC (R2incremental = 0.001), and it did not prospectively associate with offspring health outcomes in either cohort. Moreover, we observed no association between prenatal exposure to infections and epigenetic age acceleration across cohorts and clocks. ConclusionIn contrast to prior studies, which reported DNAm differences in offspring exposed to severe infections in utero, we do not find evidence for associations between self-reported clinically evident common infections during pregnancy and DNAm or epigenetic aging in cord blood within the general pediatric population. Future studies are needed to establish whether associations exist but are too subtle to be statistically meaningful with present sample sizes, whether they replicate in a cohort with a more similar infection score as our discovery cohort, whether they occur in different tissues than cord blood, and whether other biological pathways may be more relevant for mediating the effect of prenatal common infection exposure on downstream offspring health outcomes.

Intervention effect of targeted workplace closures may be approximated by single-layered networks in an individual-based model of COVID-19 control

Individual-based models of infectious disease dynamics commonly use network structures to represent human interactions. Network structures can vary in complexity, from single-layered with homogeneous mixing to multi-layered with clustering and layer-specific contact weights. Here we assessed policy-relevant consequences of network choice by simulating different network structures within an established individual-based model of SARS-CoV-2 dynamics. We determined the clustering coefficient of each network structure and compared this to several epidemiological outcomes, such as cumulative and peak infections. High-clustered networks estimate fewer cumulative infections and peak infections than less-clustered networks when transmission probabilities are equal. However, by altering transmission probabilities, we find that high-clustered networks can essentially recover the dynamics of low-clustered networks. We further assessed the effect of workplace closures as a layer-targeted intervention on epidemiological outcomes and found in this scenario a single-layered network provides a sufficient approximation of intervention effect relative to a multi-layered network when layer-specific contact weightings are equal. Overall, network structure choice within models should consider the knowledge of contact weights in different environments and pathogen mode of transmission to avoid over- or under-estimating disease burden and impact of interventions.

Specific and cumulative infection burden and mild cognitive impairment and dementia: A population-based study

Infection by pathogenic microbes is widely hypothesized to be a risk factor for the development of neurocognitive disorders and dementia, but evidence remains limited. We analyzed the association of seropositivity to 11 common pathogens and cumulative infection burden with neurocognitive disorder (mild cognitive impairment and dementia) in a population-based cohort of 475 older individuals (mean age = 67.6 y) followed up over 3–5 years for the risk of MCI-dementia. Specific seropositivities showed a preponderance of positive trends of association with MCI-dementia, including for Plasmodium, H. pylori, and RSV (p < 0.05), as well as Chickungunya, HSV-2, CMV and EBV (p > 0.05), while HSV-1 and HHV-6 showed equivocal or no associations, and Dengue and VZV showed negative associations (p < 0.05) with MCI-dementia. High infection burden (5 + cumulated infections) was significantly associated with an increased MCI-dementia risk in comparison with low infection burden (1–3 cumulative infections), adjusted for age, sex, and education. Intriguingly, for a majority (8 of 11) of pathogens, levels of antibody titers were significantly lower in those with MCI-dementia compared to cognitive normal individuals. Based on our observations, we postulate that individuals who are unable to mount strong immunological responses to infection by diverse microorganisms, and therefore more vulnerable to infection by greater numbers of different microbial pathogens or repeated infections to the same pathogen in the course of their lifetime are more likely to develop MCI or dementia. This hypothesis should be tested in more studies.

Vaccination for communicable endemic diseases: optimal allocation of initial and booster vaccine doses.

For some communicable endemic diseases (e.g., influenza, COVID-19), vaccination is an effective means of preventing the spread of infection and reducing mortality, but must be augmented over time with vaccine booster doses. We consider the problem of optimally allocating a limited supply of vaccines over time between different subgroups of a population and between initial versus booster vaccine doses, allowing for multiple booster doses. We first consider an SIS model with interacting population groups and four different objectives: those of minimizing cumulative infections, deaths, life years lost, or quality-adjusted life years lost due to death. We solve the problem sequentially: for each time period, we approximate the system dynamics using Taylor series expansions, and reduce the problem to a piecewise linear convex optimization problem for which we derive intuitive closed-form solutions. We then extend the analysis to the case of an SEIS model. In both cases vaccines are allocated to groups based on their priority order until the vaccine supply is exhausted. Numerical simulations show that our analytical solutions achieve results that are close to optimal with objective function values significantly better than would be obtained using simple allocation rules such as allocation proportional to population group size. In addition to being accurate and interpretable, the solutions are easy to implement in practice. Interpretable models are particularly important in public health decision making.

Systemic immune markers and infection risk in preterm infants fed human milk fortified with bovine colostrum or conventional fortifier, a secondary analysis of the FortiColos trial

BackgroundFor very preterm infants, human milk is often fortified with formula products based on processed bovine milk. Intact bovine colostrum (BC), rich in anti-inflammatory milk factors, is considered an alternative. We investigated if BC affects anti-inflammatory/TH2 immunity and infection risk in very preterm infants.MethodsFor a secondary analysis of a multicenter, randomized controlled trial (NCT03537365), very preterm infants (26–31 weeks gestation, 23% small for gestational age, SGA) were randomized to receive BC (ColoDan, Biofiber, Denmark, n = 113) or conventional fortifier (PreNAN, Nestlé, Switzerland, n = 116). Infection was defined as antibiotic treatment for five or more consecutive days and 29 cytokines/chemokines were measured in plasma before and after start of fortification.ResultsIn general, infection risk after start of fortification was associated with low gestational age, SGA status and antibiotics use prior to fortification. Adjusted for confounders, infants fortified with BC showed more infection episodes (20 vs 12%, P < 0.05) and higher cumulative infection risk (hazard ratio, HR 1.9, P = 0.06), particularly for SGA infants (HR 3.6, P < 0.05). Additionally, BC-fortified infants had higher levels of TH2-related cytokines/chemokines (IL-10, MDC, MCP4) and reduced levels of cytokines related to TH1/TH17-responses (IL-15, IL-17, GM-CSF). The differences were most pronounced in SGA infants, displaying higher levels of TH2-related IL-4, IL-6, and IL-13, and lower interferon-γ and IL-1α levels in the BC group.ConclusionInfants fortified with BC displayed a delayed shift from TH2- to TH1-biased systemic immunity, notably in SGA infants, possibly influenced by multiple confounding factors, alongside elevated antibiotic use, suggesting increased susceptibility to infection.

COVID-19 outbreaks in residential aged care facilities: an agent-based modeling study.

A disproportionate number of COVID-19 deaths occur in Residential Aged Care Facilities (RACFs), where better evidence is needed to target COVID-19 interventions to prevent mortality. This study used an agent-based model to assess the role of community prevalence, vaccination strategies, and non-pharmaceutical interventions (NPIs) on COVID-19 outcomes in RACFs in Victoria, Australia. The model simulated outbreaks in RACFs over time, and was calibrated to distributions for outbreak size, outbreak duration, and case fatality rate in Victorian RACFs over 2022. The number of incursions to RACFs per day were estimated to fit total deaths and diagnoses over time and community prevalence.Total infections, diagnoses, and deaths in RACFs were estimated over July 2023-June 2024 under scenarios of different: community epidemic wave assumptions (magnitude and frequency); RACF vaccination strategies (6-monthly, 12-monthly, no further vaccines); additional non-pharmaceutical interventions (10, 25, 50% efficacy); and reduction in incursions (30% or 60%). Total RACF outcomes were proportional to cumulative community infections and incursion rates, suggesting potential for strategic visitation/staff policies or community-based interventions to reduce deaths. Recency of vaccination when epidemic waves occurred was critical; compared with 6-monthly boosters, 12-monthly boosters had approximately 1.2 times more deaths and no further boosters had approximately 1.6 times more deaths over July 2023-June 2024. Additional NPIs, even with only 10-25% efficacy, could lead to a 13-31% reduction in deaths in RACFs. Future community epidemic wave patterns are unknown but will be major drivers of outcomes in RACFs. Maintaining high coverage of recent vaccination, minimizing incursions, and increasing NPIs can have a major impact on cumulative infections and deaths.

Patients, healthcare providers, and general population preferences for hemodialysis vascular access: a discrete choice experiment.

A patient-centered dialysis treatment option requires an understanding of patient preferences for alternative vascular accesses and nephrologists often face difficulties when recommending vascular access to end-stage kidney disease (ESKD) patients. We aimed to quantify the relative importance of various vascular access characteristics to patients, healthcare providers and general population, and how they affect acceptability for patients and healthcare providers. In a discrete choice experiment, patients with maintenance hemodialysis (MHD), healthcare providers, and individuals from the general population were invited to respond to a series of hypothetical vascular access scenarios that differed in five attributes: cumulative patency, infection rate, thrombosis rate, cost, and time to maturation. We estimated the respondents' preference heterogeneity and relative importance of the attributes with a mixed logit model (MXL) and predicted the willingness to pay (WTP) of respondents via a multinomial logit model (MNL). Healthcare providers (n = 316) and the general population (n = 268) exhibited a favorable inclination toward longer cumulative patency, lower access infection rate and lower access thrombosis rate. In contrast, the patients (n = 253) showed a preference for a 3-year cumulative patency, 8% access infection rate, 35% access thrombosis rate and 1.5 access maturity time, with only the 3-year cumulative patency reaching statistical significance. Among the three respondent groups, the general population found cumulative patency less important than healthcare providers and patients did. Patients demonstrated the highest WTP for cumulative patency, indicating a willingness to pay an extra RMB$24,720(US$3,708) for each additional year of patency time. Patients and healthcare providers had a strong preference for vascular access with superior patency. While the general population preferred vascular access with lower thrombosis rates. These results indicate that most patients prefer autogenous arteriovenous fistula (AVF) as an appropriate choice for vascular access due to its superior patency and lower complications than other vascular access types.

A Bayesian latent variable model for the optimal identification of disease incidence rates given information constraints

Abstract We present an original approach for measuring infections as a latent variable and making use of serological and expert surveys to provide ground truth identification during the early pandemic period. Compared to existing approaches, our model relies more on empirical information than strong structural forms, permitting inference with relatively few assumptions of cumulative infections. We also incorporate a range of political, economic, and social covariates to richly parameterize the relationship between epidemic spread and human behaviour. To show the utility of the model, we provide robust estimates of total infections that account for biases in COVID-19 cases and tests counts in the U.S. from March to July of 2020, a period of time when accurate data about the nature of the SARS-CoV-2 virus was of limited availability. In addition, we can show how sociopolitical factors like the Black Lives Matter protests and support for President Donald Trump are associated with the spread of the virus via changes in fear of the virus and cell phone mobility. A reproducible version of this article is available as an Rmarkdown file at https://github.com/CoronaNetDataScience/covid_model.

Survival, cumulative hospital days and infectious complications in urgent-start PD compared with urgent-start HD.

Urgent-start peritoneal dialysis (PD) carries a similar efficacy and safety profile compared to urgent-start haemodialysis (HD) but is only sparsely applied due to resource issues and concerns of complication risks. Furthermore, few data exist on adverse outcomes associated with central venous catheter (CVC) insertions in urgent-start HD patients. Thus, we sought to compare patient and dialysis-related outcomes in patients undergoing urgent-start PD or HD. All patients initiating urgent-start PD in a tertiary research hospital in 2005-2018 were included in this retrospective, single-centre, comparative study and matched with urgent-start HD patients of similar age and chronic kidney disease aetiology. All urgent-start PDs were initiated within 72 h after catheter insertion, and urgent-start HDs were performed via a CVC. All analyses were performed at 3 months and at 1 year of follow-up, respectively. Thirty-three patients who commenced urgent-start PD and 58 matched urgent-start HD control patients were included. Altogether, 26 patients (29%; PD: 36%, HD 24%) died within the 1-year follow-up, and patient survival was similar at 3 months (hazard ratio (HR): 1.15, 95% confidence interval (CI): 0.35-3.81, p = 0.82) and at 1 year of follow-up (HR: 0.64, 95% CI: 0.30-1.39, p = 0.26) between the study groups. There were no differences in the total kidney replacement therapy (KRT)-related infection rate (p = 0.66) or cumulative first-year hospital care days (p = 0.43) between the treatment groups. Altogether, 139 CVCs were inserted during the 1-year follow-up. The number of CVCs per patient was associated with the emergence of blood culture-positive bacteraemia and increased cumulative first-year hospital care days. Patient survival, cumulative first-year hospital care days and total KRT-related infection rate at 3 months and 1-year follow-up are similar between urgent-start PD and urgent-start HD patients. Furthermore, CVC insertion rate is associated with incident blood culture-positive bacteraemia and increased cumulative first-year hospital care days.

An effectiveness study of vaccination and quarantine combination strategies for containing mpox transmission on simulated college campuses

The ongoing transmission of mpox in specific countries and regions necessitates urgent action. It is essential to implement targeted containment strategies that concentrate on high-risk populations and critical locations, such as college campuses, to effectively curb the spread of mpox. This study is dedicated to evaluating the performance of various vaccination and quarantine strategies in curbing the spread of mpox and estimating the outbreak risk. To accomplish this, we constructed a stochastic, agent-based, discrete-time susceptible-latent-infectious-recovered (SLIR) model, to examine mpox transmission on a simulated college campus. Our findings reveal that relying solely on PEP is insufficient in containing mpox effectively. To bolster the population immunity and protect the vulnerable, pre-exposure vaccination among high-risk populations prior to an outbreak is imperative. Our study demonstrates that a pre-exposure vaccination rate of 50% in high-risk populations can led to a remarkable 74.2% reduction of infections. This translated to a mere 1.0% cumulative infection incidence in the overall population. In cases where the desired vaccination coverage is not attainable, enhancing case detection and isolation measures can serve as an effective emergency response to contain mpox outbreaks. For pre-exposure vaccination coverage of 20% or lower, a 40% isolation ratio is necessary to keep the cumulative number of infections in check. However, when the coverage exceeds 30%, a reduced isolation ratio of 20% becomes sufficient to manage the outbreak effectively. These insights underscore the importance of strategic pre-exposure vaccination in conjunction with robust surveillance and isolation protocols to safeguard public health and prevent the escalation of mpox outbreaks.

SARS-CoV-2 seroprevalence in Nova Scotia blood donors.

SARS-CoV-2 seroprevalence monitors cumulative infection rates irrespective of case testing protocols. We aimed to describe Nova Scotia blood donor seroprevalence in relation to public health policy and reported data over the course of the COVID-19 pandemic (May 2020 to August 2022). Monthly random Nova Scotia blood donation samples (24,258 in total) were tested for SARS-CoV-2 infection antibodies (anti-nucleocapsid) from May 2020 to August 2022, and vaccination antibodies (anti-spike) from January 2021 to August 2022. Multivariable logistic regression for infection antibodies and vaccination antibodies separately with month, age, sex, and racialization identified independent predictors. The provincial nucleic acid amplification test (NAAT)-positive case rate over the pandemic was calculated from publicly available data. Anti-N seroprevalence was 3.8% in January 2022, increasing to 50.8% in August 2022. The general population COVID-19 case rate was 3.5% in January 2022, increasing to 12.5% in August 2022. The percentage of NAAT-positive samples in public health laboratories increased from 1% in November 2021 to a peak of 30.7% in April 2022 with decreasing numbers of tests performed. Higher proportions of younger donors as well as Black, Indigenous, and racialized blood donors were more likely to have infection antibodies (p < 0.01). Vaccination antibodies increased to 100% over 2021, initially in older donors (60+ years), and followed by progressively younger age groups. SARS-CoV-2 infection rates were relatively low in Nova Scotia until the more contagious Omicron variant dominated, after which about half of Nova Scotia donors had been infected despite most adults being vaccinated (although severity was much lower in vaccinated individuals). Most COVID-19 cases were detected by NAAT until Omicron arrived. When NAAT testing priorities focused on high-risk individuals, infection rates were better reflected by seroprevalence.

A GPU-accelerated computational fluid dynamics solver for assessing shear-driven indoor airflow and virus transmission by scale-resolved simulations

We explore the applicability of MATLAB for 3D computational fluid dynamics (CFD) of shear-driven indoor airflows. A new scale-resolving, large-eddy simulation (LES) solver titled DNSLABIB is proposed for MATLAB utilizing graphics processing units (GPUs). In DNSLABIB, the finite difference method is applied for the convection and diffusion terms while a Poisson equation solver based on the fast Fourier transform (FFT) is employed for the pressure. The immersed boundary method (IBM) for Cartesian grids is proposed to model solid walls and objects, doorways, and air ducts by binary masking of the solid/fluid domains. The solver is validated in two canonical reference cases and against experimental data. Then, we demonstrate the validity of DNSLABIB in a room geometry by comparing the results against another CFD software (OpenFOAM). Next, we demonstrate the solver performance in several isothermal indoor ventilation configurations and the implications of the results are discussed in the context of airborne transmission of COVID-19. The novel numerical findings using the new CFD solver are as follows. First, a linear scaling of DNSLABIB is demonstrated and a speed-up by a factor of 3-4 is also noted in comparison to similar OpenFOAM simulations. Second, ventilation in three different indoor geometries are studied at both low (0.1 m/s) and high (1 m/s) airflow rates corresponding to Re=5000 and Re=50000. An analysis of the indoor CO2 concentration is carried out as the room is emptied from stale, high CO2 content air. We estimate the air changes per hour (ACH) values for three different room geometries and show that the numerical estimates from 3D CFD simulations differ by 80%–150% (Re=50000) and 75%–140% (Re=5000) from the theoretical ACH value based on the perfect mixing assumption. Third, the analysis of the CO2 probability distributions (PDFs) indicates a relatively non-uniform distribution of fresh air indoors. Fourth, utilizing a time-dependent Wells-Riley analysis, an example is provided on the growth of the cumulative infection risk which is shown to reduce rapidly after the ventilation is started. The average infection risk is shown to reduce by a factor of 2 for lower ventilation rates (ACH=3.4-6.3) and 10 for the higher ventilation rates (ACH=37-64). Finally, we utilize the new solver to comment on respiratory particle transport indoors. A key contribution of the paper is to provide an efficient, GPU compatible CFD solver environment enabling scale-resolved simulations (LES/DNS) of airflow in large indoor geometries on a single GPU designed for high-performance computing. The demonstrated efficacy of MATLAB for GPU computing indicates a high potential of DNSLABIB for various future developments on airflow prediction.

Global dynamics of an epidemic model with a two-threshold policy

This work proposes a non-smooth epidemic model with a two-threshold control strategy. Under the two-threshold policy, social distancing is suggested when the infection level exceeds a certain threshold, and contact tracing is implemented and isolation rate is improved when the infection level exceeds a higher threshold. The global dynamics of the non-smooth system is investigated and it reveals that the disease-free equilibrium, or one of the three endemic equilibria of the subsystems, or one of the two pseudo-equilibria may be globally asymptotically stable, which depends on the two threshold levels and the intensity of control measures. The global stability of the pseudo-equilibrium indicates that the disease could be maintained at a previously given level by choosing the two thresholds properly. It is also obtained that at low thresholds and high intensity of control measures, the peak value is low and peak time is late for the unisolated infections and daily new infections, and the number of cumulative infections is small. However, the effects of control measures are very limited both on the final trend of the epidemic and the cumulative infections if threshold levels are too high.