Spatial transmission of H5N2 highly pathogenic avian influenza between Minnesota poultry premises during the 2015 outbreak

Bonney, Peter J.; Malladi, Sasidhar; Boender, Gert Jan; Weaver, James H.; Ssematimba, Amos; Halvorson, David A.; Cardona, Carol J.

doi:10.1371/journal.pone.0204262

Cited by 23 publications

(41 citation statements)

References 30 publications

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“…When such phylogeographic methods are applied to the North American HPAI outbreak among commercial poultry farms, distance is estimated to be a key factor that influenced the geographic spread of HPAI H5N2 among midwestern counties in the spring of 2015. A recent spatial modeling analysis revealed that HPAI spread among Minnesota poultry premises was heavily distance-dependent during the 2015 outbreak [13]. Our results support this claim by providing evidence that the frequency of viral transition between two locations increases as the distance between locations decreases.…”

Section: Discussionsupporting

confidence: 83%

“…Risk of infection due to proximity can also be observed in our discrete trait diffusion model in which withinstate HPAI spread was much more frequent than inter-state spread. HPAI movement between states may explain Bonney, et al's finding that distance-independent transmissions significantly improved the fit of their transmission kernel model [13].…”

Section: Discussionmentioning

confidence: 97%

“…Despite frequent reports of wild birds on the grounds and within barns of HPAIpositive turkey premises [10], a case-control study found no significant difference in exposure to wild birds between positive turkey premises and matched controls [11]. Similarly, one phylodynamic analysis found no evidence of continued HPAI introductions into the midwestern poultry industries [12], but others have suggested multiple introductions [13,14]. Geographic and environmental variables, such as human population, agricultural, climatological, and ecological measures, may help explain farm-to-farm transmission observed within the poultry industries.…”

Section: Introductionmentioning

confidence: 99%

“…Geographic and environmental variables, such as human population, agricultural, climatological, and ecological measures, may help explain farm-to-farm transmission observed within the poultry industries. For example, proximity between midwestern poultry premises has been implicated as an important risk factor for HPAI infection [11,13]. Although it has been suggested that poultry production type did not affect outbreak transmission [12], this has not been formally tested.…”

Section: Introductionmentioning

confidence: 99%

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Agricultural and geographic factors shaped the North American 2015 highly pathogenic avian influenza H5N2 outbreak

et al. 2020

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The 2014-2015 highly pathogenic avian influenza (HPAI) H5NX outbreak represents the largest and most expensive HPAI outbreak in the United States to date. Despite extensive traditional and molecular epidemiological studies, factors associated with the spread of HPAI among midwestern poultry premises remain unclear. To better understand the dynamics of this outbreak, 182 full genome HPAI H5N2 sequences isolated from commercial layer chicken and turkey production premises were analyzed using evolutionary models able to accommodate epidemiological and geographic information. Epidemiological compartmental models embedded in a phylogenetic framework provided evidence that poultry type acted as a barrier to the transmission of virus among midwestern poultry farms. Furthermore, after initial introduction, the propagation of HPAI cases was self-sustainable within the commercial poultry industries. Discrete trait diffusion models indicated that within state viral transitions occurred more frequently than inter-state transitions. Distance and sample size were very strongly supported as associated with viral transition between county groups (Bayes Factor > 30.0). Together these findings indicate that the different types of midwestern poultry industries were not a single homogenous population, but rather, the outbreak was shaped by poultry industries and geographic factors.chances of viral movement between two locations. While many theories have been proposed to explain the transmission of virus among poultry farms, presented evidence suggests human-mediated viral transportation played a key role in the spread of the highly pathogenic H5N2 outbreak in North America.Agricultural and geographic factors of the 2015 HPAI US outbreak PLOS Pathogens | https://doi.org/10.

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Section: Discussionsupporting

confidence: 83%

Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Agricultural and geographic factors shaped the North American 2015 highly pathogenic avian influenza H5N2 outbreak

et al. 2020

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“…Despite frequent reports of wild birds on the grounds and within barns of HPAI-positive turkey premises (10), a case-control study found no significant difference in exposure to wild birds between positive turkey premises and matched controls (11). Similarly, one phylodynamic analysis found no evidence of continued HPAI introductions into the Midwestern poultry industries (12), but other models have suggested multiple introductions (13,14). Geographic and environmental variables, such as human population, agricultural, climatological, and ecological measures, may help explain farm-to-farm transmission observed within the poultry industries.…”

Section: Introductionmentioning

confidence: 99%

Agricultural and geographic factors shaped the North American 2015 highly pathogenic avian influenza H5N2 outbreak

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Lee

Duvuuri

et al. 2019

Preprint

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16 KEYWORDS: highly pathogenic avian influenza, phylogenetics, phylodynamcs, avian disease, 17 Bayesian inference, coalescent models, discrete trait evolution, generalized linear model 18 2 19 ABSTRACT 20 The 2014 -2015 highly pathogenic avian influenza (HPAI) H5NX outbreak represents the 21 largest and most expensive HPAI outbreak in the United States to date. Despite extensive 22 traditional and molecular epidemiological studies, factors associated with the spread of HPAI 23 among midwestern poultry premises remain unclear. To better understand the dynamics of this 24 outbreak, 182 full genome HPAI H5N2 sequences isolated from commercial layer chicken and 25 turkey production premises were analyzed using evolutionary models modified to incorporate 26 epidemiological and geographic information. Epidemiological compartmental models 27 constructed in a phylogenetic framework provided evidence that poultry type acted as a barrier to 28 the transmission of virus among midwestern poultry farms. Furthermore, after initial 29 introduction, a continuous external source of virus was not needed to explain the propagation of 30 HPAI cases within the commercial poultry industries. Discrete trait diffusion models indicated 31 that within state viral transitions occurred more frequently than inter-state transitions. Distance, 32 road density and proportion of water coverage were all supported as associated with viral 33 transition between county groups (Bayes Factor > 3.0). Together these findings indicate that the 34 midwestern poultry industries were not a single homogenous population, but rather, the outbreak 35 was shaped by poultry sectors and geographic factors.

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Big data, data privacy, and plant and animal disease research using GEMS

et al. 2021

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One of the major challenges in ensuring global food security is the ever-changing biotic risk affecting the productivity and efficiency of the global food supply system. Biotic risks that threaten food security include pests and diseases that affect pre-and postharvest terrestrial agriculture and aquaculture. Strategies to minimize this risk depend heavily on plant and animal disease research. As data collected at high spatial and temporal resolutions become increasingly available, epidemiological models used to assess and predict biotic risks have become more accurate and, thus, more useful. However, with the advent of Big Data opportunities, a number of challenges have arisen that limit researchers' access to complex, multi-sourced, multi-scaled data collected on pathogens, and their associated environments and hosts. Among these challenges, one of the most limiting factors is data privacy concerns from data owners and collectors. While solutions, such as the use of de-identifying and anonymizing tools that protect sensitive information are recognized as effective practices for use by plant and animal disease researchers, there are comparatively few platforms that include data privacy by design that are accessible to researchers. We describe how the general thinking and design used for data sharing and analysis platforms can intrinsically address a number of these data privacy-related challenges that are a barrier to researchers wanting to access data. We also describe how some of the data privacy concerns confronting plant and animal disease researchers are addressed by way of the GEMS informatics platform.

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Spatial transmission of H5N2 highly pathogenic avian influenza between Minnesota poultry premises during the 2015 outbreak

Cited by 23 publications

References 30 publications

Agricultural and geographic factors shaped the North American 2015 highly pathogenic avian influenza H5N2 outbreak

Agricultural and geographic factors shaped the North American 2015 highly pathogenic avian influenza H5N2 outbreak

Agricultural and geographic factors shaped the North American 2015 highly pathogenic avian influenza H5N2 outbreak

Big data, data privacy, and plant and animal disease research using GEMS

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