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  1. Abstract Background No versatile web app exists that allows epidemiologists and managers around the world to comprehensively analyze the impacts of COVID-19 mitigation. The web app presented here fills this gap. Methods Our web app uses a model that explicitly identifies susceptible, contact, latent, asymptomatic, symptomatic and recovered classes of individuals, and a parallel set of response classes, subject to lower pathogen-contact rates. The user inputs a CSV file of incidence and, if of interest, mortality rate data. A default set of parameters is available that can be overwritten through input or online entry, and a user-selected subset ofmore »these can be fitted to the model using maximum-likelihood estimation (MLE). Model fitting and forecasting intervals are specifiable and changes to parameters allow counterfactual and forecasting scenarios. Confidence or credible intervals can be generated using stochastic simulations, based on MLE values, or on an inputted CSV file containing Markov chain Monte Carlo (MCMC) estimates of one or more parameters. Results We illustrate the use of our web app in extracting social distancing, social relaxation, surveillance or virulence switching functions (i.e., time varying drivers) from the incidence and mortality rates of COVID-19 epidemics in Israel, South Africa, and England. The Israeli outbreak exhibits four distinct phases: initial outbreak, social distancing, social relaxation, and a second wave mitigation phase. An MCMC projection of this latter phase suggests the Israeli epidemic will continue to produce into late November an average of around 1500 new case per day, unless the population practices social-relaxation measures at least 5-fold below the level in August, which itself is 4-fold below the level at the start of July. Our analysis of the relatively late South African outbreak that became the world’s fifth largest COVID-19 epidemic in July revealed that the decline through late July and early August was characterised by a social distancing driver operating at more than twice the per-capita applicable-disease-class (pc-adc) rate of the social relaxation driver. Our analysis of the relatively early English outbreak, identified a more than 2-fold improvement in surveillance over the course of the epidemic. It also identified a pc-adc social distancing rate in early August that, though nearly four times the pc-adc social relaxation rate, appeared to barely contain a second wave that would break out if social distancing was further relaxed. Conclusion Our web app provides policy makers and health officers who have no epidemiological modelling or computer coding expertise with an invaluable tool for assessing the impacts of different outbreak mitigation policies and measures. This includes an ability to generate an epidemic-suppression or curve-flattening index that measures the intensity with which behavioural responses suppress or flatten the epidemic curve in the region under consideration.« less
    Free, publicly-accessible full text available December 1, 2022
  2. Free, publicly-accessible full text available October 1, 2022
  3. When a transmission hotspot for an environmentally persistent pathogen establishes in otherwise high-quality habitat, the disease may exert a strong impact on a host population. However, fluctuating environmental conditions lead to heterogeneity in habitat quality and animal habitat preference, which may interrupt the overlap between selected and risky habitats. We evaluated spatio-temporal patterns in anthrax mortalities in a plains zebra ( Equus quagga ) population in Etosha National Park, Namibia, incorporating remote-sensing and host telemetry data. A higher proportion of anthrax mortalities of herbivores was detected in open habitats than in other habitat types. Resource selection functions showed that themore »zebra population shifted habitat selection in response to changes in rainfall and vegetation productivity. Average to high rainfall years supported larger anthrax outbreaks, with animals congregating in preferred open habitats, while a severe drought forced animals into otherwise less preferred habitats, leading to few anthrax mortalities. Thus, the timing of anthrax outbreaks was congruent with preference for open plains habitats and a corresponding increase in pathogen exposure. Given shifts in habitat preference, the overlap in high-quality habitat and high-risk habitat is intermittent, reducing the adverse consequences for the population.« less
    Free, publicly-accessible full text available June 9, 2022
  4. Abstract

    Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to the spread of modern humans into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. Here, we propose that infectious-disease dynamics can explain the localization and persistence of the inter-species boundary. We further propose, and support with dynamical-systems models, that introgression-based transmission of alleles related to the immune system would have gradually diminished this barrier to pervasive inter-species interaction, leadingmore »to the eventual release of the inter-species boundary from its geographic localization. Asymmetries between the species in the characteristics of their associated ‘pathogen packages’ could have generated feedback that allowed modern humans to overcome disease burden earlier than Neanderthals, giving them an advantage in their subsequent spread into Eurasia.

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  5. Free, publicly-accessible full text available July 1, 2022
  6. Abstract

    Over the last 100 years, boundary layer meteorology grew from the subject of mostly near-surface observations to a field encompassing diverse atmospheric boundary layers (ABLs) around the world. From the start, researchers drew from an ever-expanding set of disciplines—thermodynamics, soil and plant studies, fluid dynamics and turbulence, cloud microphysics, and aerosol studies. Research expanded upward to include the entire ABL in response to the need to know how particles and trace gases dispersed, and later how to represent the ABL in numerical models of weather and climate (starting in the 1970s–80s); taking advantage of the opportunities afforded by themore »development of large-eddy simulations (1970s), direct numerical simulations (1990s), and a host of instruments to sample the boundary layer in situ and remotely from the surface, the air, and space. Near-surface flux-profile relationships were developed rapidly between the 1940s and 1970s, when rapid progress shifted to the fair-weather convective boundary layer (CBL), though tropical CBL studies date back to the 1940s. In the 1980s, ABL research began to include the interaction of the ABL with the surface and clouds, the first ABL parameterization schemes emerged; and land surface and ocean surface model development blossomed. Research in subsequent decades has focused on more complex ABLs, often identified by shortcomings or uncertainties in weather and climate models, including the stable boundary layer, the Arctic boundary layer, cloudy boundary layers, and ABLs over heterogeneous surfaces (including cities). The paper closes with a brief summary, some lessons learned, and a look to the future.

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