tetano
Editor, Senior Moderator
Bioinformatics. 2019 Dec 2. pii: btz882. doi: 10.1093/bioinformatics/btz882. [Epub ahead of print] [h=1]Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - application to H5N1 spread in the Mekong region.[/h]
Dellicour S[SUP]1,[/SUP][SUP]2[/SUP], Lemey P[SUP]1[/SUP], Artois J[SUP]2[/SUP], Lam TT[SUP]3[/SUP], Fusaro A[SUP]4[/SUP], Monne I[SUP]4[/SUP], Cattoli G[SUP]4,[/SUP][SUP]5[/SUP], Kuznetsov D[SUP]6[/SUP], Xenarios I[SUP]7[/SUP], Dauphin G[SUP]8[/SUP], Kalpravidh W[SUP]9[/SUP], Von Dobschuetz S[SUP]10[/SUP], Claes F[SUP]9[/SUP], Newman SH[SUP]11[/SUP], Suchard MA[SUP]12,[/SUP][SUP]13,[/SUP][SUP]14[/SUP], Baele G[SUP]1[/SUP], Gilbert M[SUP]2[/SUP].
[h=3]Author information[/h] 1 Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, Leuven, Belgium. 2 Spatial Epidemiology Lab (SpELL), Universit? Libre de Bruxelles, CP160/12 50, av. FD Roosevelt, Bruxelles, Belgium. 3 State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China. 4 Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Universit? 10, Legnaro, Italy. 5 Animal Production and Health Laboratory, Joint FAO/IAEA Division, 2444 Seibersdorf, Austria. 6 SIB, Swiss Institute of Bioinformatics, Lausanne, Switzerland. 7 Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland. 8 Ceva Sant? Animale, 10 Avenue de la Ballasti?re, Libourne, France. 9 Food and Agriculture Organization of the United Nations, Regional Office for Asia and the Pacific, Emergency Center of the Transboundary Animal Diseases, Bangkok, Thailand. 10 Food and Agriculture Organization of the United Nations, Headquarters, Rome, Italy. 11 Food and Agriculture Organization of the United Nations, Regional Office for Africa, Accra, Ghana. 12 Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA. 13 Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA. 14 Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
[h=3]Abstract[/h] [h=4]MOTIVATION:[/h] The potentially low precision associated with the geographic origin of sampled sequences represents an important limitation for spatially-explicit (i.e. continuous) phylogeographic inference of fast-evolving pathogens such as RNA viruses. A substantial proportion of publicly available sequences are geo-referenced at broad spatial scale such as, for example, the administrative unit of origin rather than more exact locations (e.g. GPS coordinates). Most frequently, such sequences are either discarded prior to continuous phylogeographic inference or arbitrarily assigned to the geographic coordinates of the centroid of their administrative area of origin for lack of a better possibility.
[h=4]RESULTS:[/h] We here implement and describe a new approach that allows to incorporate heterogeneous prior sampling probabilities over a geographic area. External data, such as outbreak locations, are used to specify these prior sampling probabilities over a collection of sub-polygons. We apply this new method to the analysis of highly pathogenic avian influenza (HPAI) H5N1 clade data in the Mekong region. Our method allows to properly include, in continuous phylogeographic analyses, H5N1 sequences that are only associated with large administrative areas of origin and assign them with more accurate locations. Finally, we use continuous phylogeographic reconstructions to analyse the dispersal dynamics of different H5N1 clades and investigate the impact of environmental factors on lineage dispersal velocities.
[h=4]AVAILABILITY:[/h] Our new method allowing heterogeneous sampling priors for continuous phylogeographic inference is implemented in the open-source multi-platform software package BEAST 1.10.
[h=4]SUPPLEMENTARY INFORMATION:[/h] Supplementary data are available at Bioinformatics online and on figshare.com.
? The Author(s) (2019). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
PMID: 31790143 DOI: 10.1093/bioinformatics/btz882
Dellicour S[SUP]1,[/SUP][SUP]2[/SUP], Lemey P[SUP]1[/SUP], Artois J[SUP]2[/SUP], Lam TT[SUP]3[/SUP], Fusaro A[SUP]4[/SUP], Monne I[SUP]4[/SUP], Cattoli G[SUP]4,[/SUP][SUP]5[/SUP], Kuznetsov D[SUP]6[/SUP], Xenarios I[SUP]7[/SUP], Dauphin G[SUP]8[/SUP], Kalpravidh W[SUP]9[/SUP], Von Dobschuetz S[SUP]10[/SUP], Claes F[SUP]9[/SUP], Newman SH[SUP]11[/SUP], Suchard MA[SUP]12,[/SUP][SUP]13,[/SUP][SUP]14[/SUP], Baele G[SUP]1[/SUP], Gilbert M[SUP]2[/SUP].
[h=3]Author information[/h] 1 Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, Leuven, Belgium. 2 Spatial Epidemiology Lab (SpELL), Universit? Libre de Bruxelles, CP160/12 50, av. FD Roosevelt, Bruxelles, Belgium. 3 State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China. 4 Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Universit? 10, Legnaro, Italy. 5 Animal Production and Health Laboratory, Joint FAO/IAEA Division, 2444 Seibersdorf, Austria. 6 SIB, Swiss Institute of Bioinformatics, Lausanne, Switzerland. 7 Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland. 8 Ceva Sant? Animale, 10 Avenue de la Ballasti?re, Libourne, France. 9 Food and Agriculture Organization of the United Nations, Regional Office for Asia and the Pacific, Emergency Center of the Transboundary Animal Diseases, Bangkok, Thailand. 10 Food and Agriculture Organization of the United Nations, Headquarters, Rome, Italy. 11 Food and Agriculture Organization of the United Nations, Regional Office for Africa, Accra, Ghana. 12 Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA. 13 Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA. 14 Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
[h=3]Abstract[/h] [h=4]MOTIVATION:[/h] The potentially low precision associated with the geographic origin of sampled sequences represents an important limitation for spatially-explicit (i.e. continuous) phylogeographic inference of fast-evolving pathogens such as RNA viruses. A substantial proportion of publicly available sequences are geo-referenced at broad spatial scale such as, for example, the administrative unit of origin rather than more exact locations (e.g. GPS coordinates). Most frequently, such sequences are either discarded prior to continuous phylogeographic inference or arbitrarily assigned to the geographic coordinates of the centroid of their administrative area of origin for lack of a better possibility.
[h=4]RESULTS:[/h] We here implement and describe a new approach that allows to incorporate heterogeneous prior sampling probabilities over a geographic area. External data, such as outbreak locations, are used to specify these prior sampling probabilities over a collection of sub-polygons. We apply this new method to the analysis of highly pathogenic avian influenza (HPAI) H5N1 clade data in the Mekong region. Our method allows to properly include, in continuous phylogeographic analyses, H5N1 sequences that are only associated with large administrative areas of origin and assign them with more accurate locations. Finally, we use continuous phylogeographic reconstructions to analyse the dispersal dynamics of different H5N1 clades and investigate the impact of environmental factors on lineage dispersal velocities.
[h=4]AVAILABILITY:[/h] Our new method allowing heterogeneous sampling priors for continuous phylogeographic inference is implemented in the open-source multi-platform software package BEAST 1.10.
[h=4]SUPPLEMENTARY INFORMATION:[/h] Supplementary data are available at Bioinformatics online and on figshare.com.
? The Author(s) (2019). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
PMID: 31790143 DOI: 10.1093/bioinformatics/btz882