publication . Article . 2017

Inferring epidemiologic dynamics from viral evolution: 2014–2015 Eurasian/North American highly pathogenic avian influenza viruses exceed transmission threshold, R0 = 1, in wild birds and poultry in North America

Daniel A. Grear; Jeffrey S. Hall; Robert J. Dusek; Hon S. Ip;
Open Access English
  • Published: 01 Dec 2017 Journal: Evolutionary Applications, volume 11, issue 4, pages 547-557 (eissn: 1752-4571, Copyright policy)
  • Publisher: John Wiley and Sons Inc.
Abstract
Highly pathogenic avian influenza virus (HPAIV) is a multi-host pathogen with lineages that pose health risks for domestic birds, wild birds, and humans. One mechanism of intercontinental HPAIV spread is through wild bird reservoirs and wild birds were the likely sources of a Eurasian (EA) lineage HPAIV into North America in 2014. The introduction resulted in several reassortment events with North American (NA) lineage low pathogenic avian influenza viruses and the reassortant EA/NA H5N2 went on to cause one of the largest HPAIV poultry outbreaks in North America. We evaluated three hypotheses about novel HPAIV introduced into wild and domestic bird hosts: (i) t...
Subjects
Medical Subject Headings: virus diseasesanimal diseases
free text keywords: Original Article, basic pathogen reproductive number, highly pathogenic avian influenza, phylodynamics, phylogeny, poultry, R 0, whole‐genome sequence, wild birds, Virology, Basic reproduction number, Ecology, Viral evolution, Reassortment, Population, education.field_of_study, education, Viral phylodynamics, Phylogenetics, Transmission (mechanics), law.invention, law, Biology, Outbreak
Related Organizations
52 references, page 1 of 4

Aldous, E. W., Seekings, J. M., McNally, A., Nili, H., Fuller, C. M., Irvine, R. M., … Brown, I. (2010). Infection dynamics of highly pathogenic avian influenza and virulent avian paramyxovirus type 1 viruses in chickens, turkeys and ducks. Avian Pathology, 39(4), 265–273. https://doi.org/10.1080/03079457.2010.492825 20706882 [PubMed]

Baele, G., Suchard, M. A., Rambaut, A., & Lemey, P. (2017). Emerging concepts of data integration in pathogen phylodynamics. Systematic Biology, 1(1), e47–e65. https://doi.org/10.1093/sysbio/syw054 [OpenAIRE]

Bevins, S., Dusek, R. J., White, C. L., Gidlewski, T., Bodenstein, B., Mansfield, K. G., … Deliberto, T. J. (2016). Widespread detection of highly pathogenic H5 influenza viruses in wild birds from the Pacific Flyway of the United States. Scientific Reports, 6, 28980 https://doi.org/10.1038/srep28980 27381241 [OpenAIRE] [PubMed]

Blanchong, J. A., Robinson, S. J., Samuel, M. D., & Foster, J. T. (2016). Application of genetics and genomics to wildlife epidemiology. Journal of Wildlife Management, 80(4), 593–608. https://doi.org/10.1002/jwmg.1064

Boskova, V., Bonhoeffer, S., & Stadler, T. (2014). Inference of epidemiological dynamics based on simulated phylogenies using birth‐death and coalescent models. PLoS Computational Biology, 10(11), https://doi.org/10.1371/journal.pcbi.1003913

Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C. H., Xie, D., … Drummond, A. J. (2014). BEAST 2: A software platform for bayesian evolutionary analysis. PLoS Computational Biology, 10(4), 1–6. https://doi.org/10.1371/journal.pcbi.1003537

Brown, J. D., Goekjian, G., Poulson, R., Valeika, S., & Stallknecht, D. E. (2009). Avian influenza virus in water: Infectivity is dependent on pH, salinity and temperature. Veterinary Microbiology, 136(1–2), 20–26. https://doi.org/10.1016/j.vetmic.2008.10.027 19081209 [PubMed]

Buhnerkempe, M. G., Roberts, M. G., Dobson, A. P., Heesterbeek, H., Hudson, P. J., & Lloyd‐Smith, J. O. (2015). Eight challenges in modelling disease ecology in multi‐host, multi‐agent systems. Epidemics, 10, 26–30. https://doi.org/10.1016/j.epidem.2014.10.001 25843378 [OpenAIRE] [PubMed]

Buhnerkempe, M. G., Webb, C. T., Merton, A. A., Buhnerkempe, J. E., Givens, G. H., Miller, R. S., & Hoeting, J. A. (2016). Identification of migratory bird flyways in North America using community detection on biological networks. Ecological Applications, 26(3), 740–751. https://doi.org/10.1890/15-0934 27411247 [PubMed]

Chen, R., & Holmes, E. C. (2006). Avian influenza virus exhibits rapid evolutionary dynamics. Molecular Biology and Evolution, 23(12), 2336–2341. https://doi.org/10.1093/molbev/msl102 16945980 [PubMed]

Chen, H., Smith, G. J. D., Li, K. S., Wang, J., Fan, X. H., Rayner, J. M., … Guan, Y. (2006). Establishment of multiple sublineages of H5N1 influenza virus in Asia: Implications for pandemic control. Proceedings of the National Academy of Sciences, 103(8), 2845–2850. https://doi.org/10.1073/pnas.0511120103

De Maio, N., Wu, C. H., O'Reilly, K. M., & Wilson, D. (2015). New routes to phylogeography: A Bayesian structured coalescent approximation. PLoS Genetics, 11(8), 1–22. https://doi.org/10.1371/journal.pgen.1005421

Farnsworth, M. L., Miller, R. S., Pedersen, K., Lutman, M. W., Swafford, S. R., Riggs, P. D., & Webb, C. T. (2012). Environmental and demographic determinants of avian influenza viruses in waterfowl across the contiguous United States. PLoS ONE, 7(3), 1–11. https://doi.org/10.1371/journal.pone.0032729

Fraser, C., Donnelly, C. A., Cauchemez, S., Hanage, W. P., Van Kerkhove, M. D., Hollingsworth, T. D., … Roth, C. (2009). Pandemic potential of a strain of influenza A (H1N1): Early findings. Science, 324(5934), 1557–1561. https://doi.org/10.1126/science.1176062 19433588 [OpenAIRE] [PubMed]

Frost, S. D., & Volz, E. M. (2010). Viral phylodynamics and the search for an “effective number of infections”. Philosophical Transactions of the Royal Society of London. Series B, Biological sciences, 365(1548), 1879–1890. https://doi.org/365/1548/1879 20478883 [OpenAIRE] [PubMed]

52 references, page 1 of 4
Abstract
Highly pathogenic avian influenza virus (HPAIV) is a multi-host pathogen with lineages that pose health risks for domestic birds, wild birds, and humans. One mechanism of intercontinental HPAIV spread is through wild bird reservoirs and wild birds were the likely sources of a Eurasian (EA) lineage HPAIV into North America in 2014. The introduction resulted in several reassortment events with North American (NA) lineage low pathogenic avian influenza viruses and the reassortant EA/NA H5N2 went on to cause one of the largest HPAIV poultry outbreaks in North America. We evaluated three hypotheses about novel HPAIV introduced into wild and domestic bird hosts: (i) t...
Subjects
Medical Subject Headings: virus diseasesanimal diseases
free text keywords: Original Article, basic pathogen reproductive number, highly pathogenic avian influenza, phylodynamics, phylogeny, poultry, R 0, whole‐genome sequence, wild birds, Virology, Basic reproduction number, Ecology, Viral evolution, Reassortment, Population, education.field_of_study, education, Viral phylodynamics, Phylogenetics, Transmission (mechanics), law.invention, law, Biology, Outbreak
Related Organizations
52 references, page 1 of 4

Aldous, E. W., Seekings, J. M., McNally, A., Nili, H., Fuller, C. M., Irvine, R. M., … Brown, I. (2010). Infection dynamics of highly pathogenic avian influenza and virulent avian paramyxovirus type 1 viruses in chickens, turkeys and ducks. Avian Pathology, 39(4), 265–273. https://doi.org/10.1080/03079457.2010.492825 20706882 [PubMed]

Baele, G., Suchard, M. A., Rambaut, A., & Lemey, P. (2017). Emerging concepts of data integration in pathogen phylodynamics. Systematic Biology, 1(1), e47–e65. https://doi.org/10.1093/sysbio/syw054 [OpenAIRE]

Bevins, S., Dusek, R. J., White, C. L., Gidlewski, T., Bodenstein, B., Mansfield, K. G., … Deliberto, T. J. (2016). Widespread detection of highly pathogenic H5 influenza viruses in wild birds from the Pacific Flyway of the United States. Scientific Reports, 6, 28980 https://doi.org/10.1038/srep28980 27381241 [OpenAIRE] [PubMed]

Blanchong, J. A., Robinson, S. J., Samuel, M. D., & Foster, J. T. (2016). Application of genetics and genomics to wildlife epidemiology. Journal of Wildlife Management, 80(4), 593–608. https://doi.org/10.1002/jwmg.1064

Boskova, V., Bonhoeffer, S., & Stadler, T. (2014). Inference of epidemiological dynamics based on simulated phylogenies using birth‐death and coalescent models. PLoS Computational Biology, 10(11), https://doi.org/10.1371/journal.pcbi.1003913

Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C. H., Xie, D., … Drummond, A. J. (2014). BEAST 2: A software platform for bayesian evolutionary analysis. PLoS Computational Biology, 10(4), 1–6. https://doi.org/10.1371/journal.pcbi.1003537

Brown, J. D., Goekjian, G., Poulson, R., Valeika, S., & Stallknecht, D. E. (2009). Avian influenza virus in water: Infectivity is dependent on pH, salinity and temperature. Veterinary Microbiology, 136(1–2), 20–26. https://doi.org/10.1016/j.vetmic.2008.10.027 19081209 [PubMed]

Buhnerkempe, M. G., Roberts, M. G., Dobson, A. P., Heesterbeek, H., Hudson, P. J., & Lloyd‐Smith, J. O. (2015). Eight challenges in modelling disease ecology in multi‐host, multi‐agent systems. Epidemics, 10, 26–30. https://doi.org/10.1016/j.epidem.2014.10.001 25843378 [OpenAIRE] [PubMed]

Buhnerkempe, M. G., Webb, C. T., Merton, A. A., Buhnerkempe, J. E., Givens, G. H., Miller, R. S., & Hoeting, J. A. (2016). Identification of migratory bird flyways in North America using community detection on biological networks. Ecological Applications, 26(3), 740–751. https://doi.org/10.1890/15-0934 27411247 [PubMed]

Chen, R., & Holmes, E. C. (2006). Avian influenza virus exhibits rapid evolutionary dynamics. Molecular Biology and Evolution, 23(12), 2336–2341. https://doi.org/10.1093/molbev/msl102 16945980 [PubMed]

Chen, H., Smith, G. J. D., Li, K. S., Wang, J., Fan, X. H., Rayner, J. M., … Guan, Y. (2006). Establishment of multiple sublineages of H5N1 influenza virus in Asia: Implications for pandemic control. Proceedings of the National Academy of Sciences, 103(8), 2845–2850. https://doi.org/10.1073/pnas.0511120103

De Maio, N., Wu, C. H., O'Reilly, K. M., & Wilson, D. (2015). New routes to phylogeography: A Bayesian structured coalescent approximation. PLoS Genetics, 11(8), 1–22. https://doi.org/10.1371/journal.pgen.1005421

Farnsworth, M. L., Miller, R. S., Pedersen, K., Lutman, M. W., Swafford, S. R., Riggs, P. D., & Webb, C. T. (2012). Environmental and demographic determinants of avian influenza viruses in waterfowl across the contiguous United States. PLoS ONE, 7(3), 1–11. https://doi.org/10.1371/journal.pone.0032729

Fraser, C., Donnelly, C. A., Cauchemez, S., Hanage, W. P., Van Kerkhove, M. D., Hollingsworth, T. D., … Roth, C. (2009). Pandemic potential of a strain of influenza A (H1N1): Early findings. Science, 324(5934), 1557–1561. https://doi.org/10.1126/science.1176062 19433588 [OpenAIRE] [PubMed]

Frost, S. D., & Volz, E. M. (2010). Viral phylodynamics and the search for an “effective number of infections”. Philosophical Transactions of the Royal Society of London. Series B, Biological sciences, 365(1548), 1879–1890. https://doi.org/365/1548/1879 20478883 [OpenAIRE] [PubMed]

52 references, page 1 of 4
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publication . Article . 2017

Inferring epidemiologic dynamics from viral evolution: 2014–2015 Eurasian/North American highly pathogenic avian influenza viruses exceed transmission threshold, R0 = 1, in wild birds and poultry in North America

Daniel A. Grear; Jeffrey S. Hall; Robert J. Dusek; Hon S. Ip;