Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations.
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ABSTRACT:
SUBMITTER: Douglas J
PROVIDER: S-EPMC8344840 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Phylodynamic models are widely used in infectious disease epidemiology to infer the dynamics and structure of pathogen populations. However, these models generally assume that individual hosts contact one another at random, ignoring the fact that many pathogens spread through highly structured contact networks. We present a new framework for phylodynamics on local contact networks based on pairwise epidemiological models that track the status of pairs of nodes in the network rather than just individuals. Shifting our focus from individuals to pairs leads naturally to coalescent models that describe how lineages move through networks and the rate at which lineages coalesce. These pairwise coalescent models not only consider how network structure directly shapes pathogen phylogenies, but also how the relationship between phylogenies and contact networks changes depending on epidemic dynamics and the fraction of infected hosts sampled. By considering pathogen phylogenies in a probabilistic framework, these coalescent models can also be used to estimate the statistical properties of contact networks directly from phylogenies using likelihood-based inference. We use this framework to explore how much information phylogenies retain about the underlying structure of contact networks and to infer the structure of a sexual contact network underlying a large HIV-1 sub-epidemic in Switzerland.
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Project description:BackgroundHospital-based contact tracing aims to limit spread of COVID-19 within healthcare facilities. In large outbreaks, this can stretch resources and workforce due to quarantine of uninfected staff. We analysed the performance of a manual contact tracing system for healthcare workers (HCW) at a multi-site healthcare facility in Melbourne, Australia, from June-September 2020, during an epidemic of COVID-19.MethodsAll HCW close contacts were quarantined for 14 days, and tested around day 11, if not already diagnosed with COVID-19. We examined the prevalence and timing of symptoms in cases detected during quarantine, described this group as proportions of all close contacts and of all cases, and used logistic regression to assess factors associated with infection.ResultsCOVID-19 was diagnosed during quarantine in 52 furloughed HCWs, from 483 quarantine episodes (11%), accounting for 19% (52/270) of total HCW cases. In 361 exposures to a clear index case, odds of infection were higher after contact with an infectious patient compared to an infectious HCW (aOR: 4.69, 95% CI: 1.98-12.14). Contact with cases outside the workplace increased odds of infection compared to workplace contact only (aOR: 7.70, 95% CI: 2.63-23.05). We estimated 30%, 78% and 95% of symptomatic cases would develop symptoms by days 3, 7, and 11 of quarantine, respectively.ConclusionIn our setting, hospital-based contact tracing detected and contained a significant proportion of HCW cases, without excessive quarantine of uninfected staff. Effectiveness of contact tracing is determined by a range of dynamic factors, so system performance should be monitored in real-time.
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Project description:Contact tracing is currently one of the most effective measures to contain the COVID-19 pandemic. In order to identify persons that would otherwise not be known or remembered and to keep the time delay when reporting an infection and when contacting people as short as possible, digital contact tracing using smartphones seems to be a reasonable measure additional to manual contact tracing. Although first modelling studies predicted a positive effect in terms of prompt contact tracing, no empirically reliable data are as yet available, neither on the population-wide benefit nor on the potential risks of contact tracing apps. Risk-benefit assessment of such an app includes investigating whether such an app fulfils its purpose, as also research on the effectiveness, risks and side effects, and implementation processes (e.?g. planning and inclusion of different participants). The aim of this article was to give an overview of possible public health benefits as well as technical, social, legal and ethical aspects of a contact-tracing app in the context of the COVID-19 pandemic. Furthermore, conditions for the widest possible use of the app are presented.
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Project description:Emerging evidence suggests that contact tracing has had limited success in the UK in reducing the R number across the COVID-19 pandemic. We investigate potential pitfalls and areas for improvement by extending an existing branching process contact tracing model, adding diagnostic testing and refining parameter estimates. Our results demonstrate that reporting and adherence are the most important predictors of programme impact but tracing coverage and speed plus diagnostic sensitivity also play an important role. We conclude that well-implemented contact tracing could bring small but potentially important benefits to controlling and preventing outbreaks, providing up to a 15% reduction in R. We reaffirm that contact tracing is not currently appropriate as the sole control measure.
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Project description:Background and objectivesCompared with non-First Nations, First Nations People with diabetes experience higher rates of kidney failure and death, which may be related to disparities in care. This study examined First Nations and non-First Nations People with diabetes for differences in quality indicators and their association with kidney failure and death.Design, setting, participants, & measurementsAdults with diabetes and an outpatient creatinine in Alberta from 2005 to 2008 were identified. Logistic regression was used to determine the likelihood of process of care indicators (measurement of urine albumin/creatinine ratio [ACR], LDL, and hemoglobin A1C [A1C]) and surrogate outcome indicators (achievement of LDL and A1C targets). Cox regression was used to determine the association between lack of achievement of indicator targets and each of kidney failure and death.ResultsThis study identified 140,709 non-First Nations and 6574 First Nations People with diabetes. There was a significant interaction between First Nations status and CKD for the outcomes (P<0.01); therefore, results are stratified by CKD. Among participants without CKD, First Nations People were less likely to receive process of care indicators and achieve target A1C compared with non-First Nations People. For those with CKD, First Nations People were as likely to receive these indicators (other than LDL) and achieve LDL and A1C targets. Lack of LDL and A1C assessment and achievement of targets were associated with increased risk of kidney failure and death similarly for both groups.ConclusionsCompared with non-First Nations, First Nations People with diabetes but without CKD experience disparities in assessment of quality indicators and achievement of A1C target.
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Project description:Tumor evolution is driven by the progressive acquisition of genetic and epigenetic alterations that enable uncontrolled growth and expansion to neighboring and distal tissues. The study of phylogenetic relationships between cancer cells provides key insights into these processes. Here, we introduced an evolving lineage-tracing system with a single-cell RNA-seq readout into a mouse model of Kras;Trp53(KP)-driven lung adenocarcinoma and tracked tumor evolution from single-transformed cells to metastatic tumors at unprecedented resolution. We found that the loss of the initial, stable alveolar-type2-like state was accompanied by a transient increase in plasticity. This was followed by the adoption of distinct transcriptional programs that enable rapid expansion and, ultimately, clonal sweep of stable subclones capable of metastasizing. Finally, tumors develop through stereotypical evolutionary trajectories, and perturbing additional tumor suppressors accelerates progression by creating novel trajectories. Our study elucidates the hierarchical nature of tumor evolution and, more broadly, enables in-depth studies of tumor progression.
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Project description:To date, research on social capital in Indigenous contexts has been scarce. In this quantitative study, our objectives were to (1): Describe bonding social capital within four distinct First Nations communities in Canada, and (2) Explore the associations between bonding social capital and self-rated health in these communities. With community permission, cross-sectional data were drawn from the Canadian Alliance for Healthy Hearts and Minds study. Four reserve-based First Nations communities were included in the analysis, totaling 591 participants. Descriptive statistics were computed to examine levels of social capital among communities and logistic regression analyses were performed to identify social capital predictors of good self-rated health. Age, sex, education level, and community were controlled for in all models. Across the four communities in this study, areas of common social capital included frequent socialization among friends and large and interconnected family networks. Positive self-rated health was associated with civic engagement at federal or provincial levels (OR=1.65, p<0.05) and organizational membership (OR=1.60, p<0.05), but overall, sociodemographic variables were more significantly associated with self-rated health than social capital variables. Significant differences in social capital were found across the four communities and community of residence was a significant health outcomes predictor in all logistic regression models. In conclusion, this study represents one of the first efforts to quantitatively study First Nations social capital with respect to health in Canada. The results reflect significant differences in the social capital landscape across different First Nations communities and suggest the need for social capital measurement tools that may be adapted to unique Indigenous contexts. Further, the impact of social capital on health may be better explored and interpreted with more community-specific instruments and with supplementary qualitative inquiry.
| S-EPMC8599144 | biostudies-literature
Project description:Traditional contact tracing relies on knowledge of the interpersonal network of physical interactions, where contagious outbreaks propagate. However, due to privacy constraints and noisy data assimilation, this network is generally difficult to reconstruct accurately. Communication traces obtained by mobile phones are known to be good proxies for the physical interaction network, and they may provide a valuable tool for contact tracing. Motivated by this assumption, we propose a model for contact tracing, where an infection is spreading in the physical interpersonal network, which can never be fully recovered; and contact tracing is occurring in a communication network which acts as a proxy for the first. We apply this dual model to a dataset covering 72 students over a 9 month period, for which both the physical interactions as well as the mobile communication traces are known. Our results suggest that a wide range of contact tracing strategies may significantly reduce the final size of the epidemic, by mainly affecting its peak of incidence. However, we find that for low overlap between the face-to-face and communication interaction network, contact tracing is only efficient at the beginning of the outbreak, due to rapidly increasing costs as the epidemic evolves. Overall, contact tracing via mobile phone communication traces may be a viable option to arrest contagious outbreaks.
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Project description:As over 1000 new cases of HIV/AIDS occur in Korea annually, preventive health programs against HIV/AIDS are urgently needed. Since phylodynamic studies have been suggested as a way to understand how infectious diseases are transmitted and evolve, phylodynamic inferences can be a useful tool for HIV/AIDS research. In particular, phylodynamic models are helpful for dating the origins of an epidemic and estimating its basic reproduction number. Thus, the introduction of phylodynamics would be a highly valuable step towards controlling the HIV/AIDS epidemic in Korea.
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Project description:BackgroundCanada's Aboriginal population faces significantly higher rates of stillbirth and neonatal and postnatal death than those seen in the general population. The objective of this study was to compare indicators of obstetric care quality and use of obstetric interventions between First Nations and non-First Nations mothers in British Columbia, Canada.MethodsWe linked obstetrical medical records with the First Nations Client File for all nulliparous women who delivered single infants in British Columbia from 1999 to 2011. Using logistic regression models, we examined differences in the proportion of women who received services aligned with best practice guidelines, as well as the overall use of obstetric interventions among First Nations mothers compared with the general population, controlling for geographic barriers (distance to hospital) and other relevant confounders.ResultsDuring the study period, 215,993 single births occurred in nulliparous women in British Columbia, 9152 of which were to members of our First Nations cohort. First Nations mothers were less likely to have early ultrasonography (adjusted risk difference = 10.2 fewer women per 100 deliveries [95% confidence interval {CI} -11.3 to -9.3]), to have at least 4 antenatal care visits (3.6 fewer women per 100 deliveries [95% CI -4.6 to -2.6]), and to undergo labour induction after prolonged (> 24 hours) prelabour rupture of membranes (-5.9 [95% CI -11.8 to 0.1]) or at post-dates gestation (-10.6 [95% CI -13.8 to -7.5]). Obstetric interventions including epidural, labour induction, instrumental delivery and cesarean delivery were used less often in First Nations mothers.InterpretationWe identified differences in the obstetric care received by First Nations mothers compared with the general population. Such differences warrant further investigation, given increases in perinatal mortality that are consistently shown and that may be a downstream consequence of differences in care.
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