At the Intersection of Public-health Informatics and Bioinformatics

Scotch, Matthew; Mei, Changjiang; Brandt, Cynthia; Sarkar, Indra Neil; Cheung, Kei Hoi

doi:10.1097/ede.0b013e3181f534dd

Cited by 13 publications

(10 citation statements)

References 13 publications

(12 reference statements)

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“…We submitted the FASTA files to ZooPhy, a phylogeography system developed by one of the authors (Scotch et al, 2010). ZooPhy acts as a pipeline for automatically connecting a series of bioinformatics applications including ClustalW (Larkin et al, 2007) for nucleotide alignment, jModeltest (Posada, 2008) for evaluation of substitution models, and BEAST (Drummond et al, 2012) for generation of Bayesian discrete phylogeographic trees.…”

Section: Methodsmentioning

confidence: 99%

Diffusion of influenza viruses among migratory birds with a focus on the Southwest United States

Scotch

Lam

Pabilonia

et al. 2014

Infection, Genetics and Evolution

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The Southwest United States, including Arizona and New Mexico, has a diverse climate and is home to many different avian species. We sequenced the hemagglutinin (HA) gene of twenty influenza specimens for the years 2007–2009. This included four from Arizona, and sixteen from New Mexico. We analyzed the sequences and determined the following HA subtypes: H3, H4, H6, H8, and H11. For each subtype, we combined our virus sequences with those from a public database, and inferred phylogeographic models of influenza diffusion. Statistical phylogeography indicated that overall evolutionary diffusion of avian influenza viruses is geographically structured (p < 0.05). In addition, we found that diffusion to the Southwest was often from nearby states including California. For H3, H4 and H6, the intra-flyway gene flow rates were significantly (p < 0.001) higher than those of inter-flyway. Such rate difference was also observed in H8 and H11, yet, without statistical significance (p=0.132, p=0.190 respectively). Excluding any one flyway from the calculation generated similar results, suggesting that such barrier effect on gene flow rates is not exclusively produced by any single flyway. We also calculated the Bayes factor test for the significant non-zero rates between states and identified significant routes both within and across flyways. Such inter-flyway spread of influenza was probably the result of birds from four flyways co-mingling on breeding grounds in northern regions or marshaling on staging areas post breeding in Canada or Alaska, before moving south each fall. This study provides an initial analysis of evolutionary diffusion of avian influenza virus to and from the Southwest United States. However, more sequences from this region need to be generated to determine the role of host migration and other factors on influenza diffusion.

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Section: Methodsmentioning

confidence: 99%

Diffusion of influenza viruses among migratory birds with a focus on the Southwest United States

Scotch

Lam

Pabilonia

et al. 2014

Infection, Genetics and Evolution

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“…Both sets of sequences were preprocessed then submitted as FASTA files to ZooPhy (Scotch et al, 2010), a bioinformatics framework for zoonotic phylogeography developed at Arizona State University (ASU). ZooPhy integrates separate bioinformatics software into a single framework including: ClustalW (Higgins and Sharp, 1988; Thompson et al, 1994) for sequence alignment, jModeltest (Posada, 2009; Posada, 2011) for analysis of substitution models, and BEAST (2011; Drummond and Rambaut, 2007) for molecular evolution and phylogeography using a Bayesian approach.…”

Section: Methodsmentioning

confidence: 99%

Phylogeography of swine influenza H3N2 in the United States: Translational public health for zoonotic disease surveillance

Scotch

Mei

2013

Infection, Genetics and Evolution

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The field of phylogeography has received a lot of attention for its application to molecular evolution and geographic migration of species. More recent work has included infectious diseases especially zoonotic RNA viruses like influenza and rabies. Phylogeography of viruses has the potential to advance surveillance at agencies such as public health departments, agriculture departments, and wildlife agencies. However, little is known about how these agencies could use phylogeography for applied surveillance and the integration of animal and human sequence data. Here, we highlight its potential to support ‘translational public health’ that could bring sequence data to the forefront of surveillance. We focus on swine influenza H3N2 because of the recent link to a variant form in humans. We discuss the implications to applied surveillance and the need for an integrated biomedical informatics approach for adoption at agencies of animal and public health.

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“…Other GIS tools of interest to phylogeographers are Z oo P hy (Scotch et al. 2010) and geophylobuilder (Kidd & Liu 2008).…”

Section: Integration With Google Earth: a Powerful Tool For Exploratomentioning

confidence: 99%

“…2010) and geophylobuilder (Kidd & Liu 2008). Z oo P hy is a more comprehensive phylogeography visualization tool that takes Genbank sequence information, constructs phylogenies, then geolocates the data to follow the evolution of zoonotic diseases (Scotch et al. 2010).…”

Section: Integration With Google Earth: a Powerful Tool For Exploratomentioning

confidence: 99%

PhyloGeoViz: a web‐based program that visualizes genetic data on maps

Tsai

2010

Molecular Ecology Resources

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The first step of many population genetic studies is the simple visualization of allele frequencies on a landscape. This basic data exploration can be challenging without proprietary software, and the manual plotting of data is cumbersome and unfeasible at large sample sizes. I present an open source, web-based program that plots any kind of frequency or count data as pie charts in Google Maps (Google Inc., Mountain View, CA). Pie polygons are then exportable to Google Earth (Google Inc.), a free Geographic Information Systems platform. Import of genetic data into Google Earth allows phylogeographers access to a wealth of spatial information layers integral to forming hypotheses and understanding patterns in the data.

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At the Intersection of Public-health Informatics and Bioinformatics

Cited by 13 publications

References 13 publications

Diffusion of influenza viruses among migratory birds with a focus on the Southwest United States

Diffusion of influenza viruses among migratory birds with a focus on the Southwest United States

Phylogeography of swine influenza H3N2 in the United States: Translational public health for zoonotic disease surveillance

PhyloGeoViz: a web‐based program that visualizes genetic data on maps

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