Use of temperature to improve West Nile virus forecasts

DeFelice, Nicholas; Schneider, Zachary; Little, Eliza A.H.; Barker, Christopher M.; Caillouët, Kevin A.; Campbell, Scott R.; Damian, Dan; Irwin, Patrick; Jones, Herff M. P.; Townsend, John; Shaman, Jeffrey

doi:10.1371/journal.pcbi.1006047

Cited by 36 publications

(45 citation statements)

References 46 publications

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“…Higher temperatures have been also associated with shorter extrinsic incubation periods, accelerating WNV transmission by the mosquito vector 54,55 . Interestingly, temperature has also been suggested as a variable that can increase the predictive power of WNV forecast models 56 . The impact of temperature that we reveal here on both dispersal velocity and viral genetic diversity is particularly important in the context of global warming.…”

Section: Discussionmentioning

confidence: 99%

Phylogeographic and phylodynamic approaches to epidemiological hypothesis testing

Dellicour

Lequime

Vrancken

et al. 2019

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Computational analyses of pathogen genomes are increasingly being used to unravel the dispersal history and transmission dynamics of epidemics. Here, we show how to go beyond historical reconstructions and use spatially-explicit phylogeographic and phylodynamic approaches to formally test epidemiological hypotheses. We focus on the spread and invasion of West Nile virus spread in North America that has been responsible for substantial impacts on public, veterinary and wildlife health. WNV isolates have been sampled at various times and locations across North America since its introduction to New York twenty years ago. We exploit this genetic data repository to demonstrate that factors hypothesised to affect viral dispersal and demography can be statistically tested. We find that WNV lineages tend to disperse faster in areas with higher temperatures and we identify temporal variation in temperature as a main predictor of viral genetic diversity through time. Finally, we compare inferred and simulated dispersal histories of lineages in order to assess the impact of migratory bird flyways on the rapid east-to-west continental spread of WNV. We find no evidence that viral lineages preferentially circulate within the same migratory flyway, suggesting a substantial role for non-migratory birds or mosquito dispersal along the longitudinal gradient. Our study demonstrates that the development and application of statistical approaches, coupled with comprehensive pathogen genomic data, can address epidemiological questions that might otherwise be difficult or unacceptably costly to answer.The evolutionary analysis of rapidly evolving pathogens, particularly RNA viruses, allows us to establish the epidemiological relatedness of cases through time and space. Such transmission information can be difficult to detect using classical epidemiological approaches. The development of spatially-explicit phylogeographic models 1, 2 , which place time-referenced phylogenies in a geographical context, can provide a detailed spatiotemporal picture of the dispersal history of virus lineages 3 . Recent advances in methodology have moved beyond simple reconstructions of epidemic history and instead attempt to analyse the impact of underlying factors on the dispersal dynamics of virus lineages 4-6 , giving rise to the concept of landscape phylogeography 7 .Similar improvements have been made to phylodynamic analyses that use flexible coalescent models to reconstruct virus demographic history 8,9 ; these methods can now provide insights into epidemiological or environmental variables that might be associated with population size change 10 . In this study we aim to go beyond historical reconstructions and formally test epidemiological hypotheses by exploiting phylodynamic and spatially-explicit phylogeographic models. We illustrate our approach by examining the spread of West Nile virus (WNV) across North America, an emergent virus lineage that is responsible for substantial impacts on public, veterinary, and wildlife health 11 .

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Section: Discussionmentioning

confidence: 99%

Phylogeographic and phylodynamic approaches to epidemiological hypothesis testing

Dellicour

Lequime

Vrancken

et al. 2019

Preprint

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“…This analysis used 2 forecasting systems, a baseline model with no temperature forcing 13 and a model that includes environmental forcing (average daily temperature [ie, climatology] for the region) by accounting for temperature modulation of the extrinsic incubation period for mosquitos. 12 Both models used a standard susceptible-infected-recovered epidemiological construct and were optimized using a data assimilation method and 2 observed data streams: mosquito infection rates and reported human WNV cases. The methodological approach and its application in real-time infectious diseases forecasting are briefly described later in this section.…”

Section: Methodsmentioning

confidence: 99%

“…For further details on the validation of the WNV model-inference forecasting systems, see the articles by DeFelice et al 12 , 13 The remainder of the Methods section describes how we used the observed reporting lags from the 2017 WNV season to evaluate the associations of reporting delays with forecast accuracy for 110 historical outbreaks. 12 We followed the Consolidated Health Economic Evaluation Reporting Standards ( CHEERS ) 21 reporting guideline to report the difference in likelihood of an accurate forecast given current reporting lags relative to ideal reporting of all data in real time. This research received institutional review board approval from Columbia University, which waived requirements for participant informed consent because the study used deidentified data.…”

Section: Methodsmentioning

confidence: 99%

“…The forecast system relies on 3 components: (1) a core compartmental epidemiological model representing the transmission dynamics of WNV among mosquitoes and birds, as well as spillover to humans 12 , 13 ; (2) WNV surveillance data, ie, vector mosquito WNV infection rates and reported human WNV cases; and (3) a data assimilation method (here, the ensemble adjustment Kalman filter 25 ). The data assimilation method uses the surveillance data to recursively inform and optimize an ensemble of model simulations and, in so doing, provide an improved, posterior estimate of the true state as well as estimates of unobserved state variables and parameters.…”

Section: Methodsmentioning

confidence: 99%

“…In a recent study, 12 , 13 we showed that accurate and reliable forecasts of WNV outbreaks can be made using WNV surveillance data and a mathematical model representing the transmission dynamics of WNV among mosquitoes and birds, as well as spillover to humans. This model system was able to retrospectively forecast mosquito infection rates prior to the week of mosquito peak infection and to forecast accurately the seasonal total number of human WNV cases prior to when the majority of cases were reported.…”

Section: Introductionmentioning

confidence: 99%

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Modeling and Surveillance of Reporting Delays of Mosquitoes and Humans Infected With West Nile Virus and Associations With Accuracy of West Nile Virus Forecasts

et al. 2019

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Key Points Question What are the operational challenges limiting effective implementation of a real-time West Nile virus (WNV) forecasting system? Findings In this modeling study of historical and real-time mosquito WNV assay results and human medical records, delays in data reporting for both infected mosquitoes and human WNV cases were associated with a reduction in average WNV forecast accuracy. Meaning For public health departments and mosquito abatement districts to integrate forecasting effectively into operational decision making, the relaying of real-time health and environmental surveillance data should be prioritized.

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