Enhancing phylogeography by improving geographical information from GenBank

Scotch, Matthew; Sarkar, Indra Neil; Mei, Changjiang; Leaman, Robert; Cheung, Kei‐Hoi; Ortiz, Pierina; Singraur, Ashutosh; González, Graciela

doi:10.1016/j.jbi.2011.06.005

Cited by 33 publications

(45 citation statements)

References 16 publications

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“…We utilized the centroid latitude and longitude for each state and this likely does not reflect the true location of each swine host that was represented in the sequences. Our previous work highlights the lack of sufficient geographical metadata in GenBank and the need for biomedical informatics approaches to enhance the quality of this key element of phylogeography (Scotch et al, 2011). This is especially important if a state (likely a large area such as Texas, Alaska, or California) needs to focus on internal spread from one part of the state to another.…”

Section: Discussionmentioning

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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Section: Discussionmentioning

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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“…Unfortunately, even if 624I had been reported and sequenced in Italy since 60's (Taddei et al, 2012), JQ901492 is the oldest public available 624I sequence. Such scarcity of data makes it impossible to confidently support or refute this hypothesis, highlighting the importance of the need for further sequence data availability (Brister et al, 2010;Scotch et al, 2011).…”

Section: Gene 1abmentioning

confidence: 99%

Molecular investigation of a full-length genome of a Q1-like IBV strain isolated in Italy in 2013

et al. 2015

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Since 1996 a new Infectious Bronchitis virus (IBV) genotype, referred to as Q1, circulated in China and was reported for the first time in Italy in 2011, associated with an increase of mortality, kidney lesions and proventriculitis. During northern Italian outbreak of respiratory disease in a broiler flock in 2013, an IBV strain was detected by RT-PCR and characterized as Q1-like based on partial S1 sequence. The virus was isolated and named γCoV/Ck/Italy/I2022/13. All coding regions of the isolate were sequenced and compared with 130 complete genome sequences of IBV and TCoV, downloaded from ViPR. This showed the highest identity with a Chinese strain CK/CH/LDL/97I (p-distance=0.044). To identify potential recombination events a complete genome SimPlot analysis was carried out which revealed the presence of possible multiple recombination events, but the minor parent strains remained unknown. A phylogenetic analysis of the complete S1 gene was performed using all complete S1 sequences available on ViPR and showed the isolate clustered with an Q1-like strain isolated in Italy in 2011 (p-distance=0.004) and a group of Chinese Q1-like strains isolated from the mid 90's (p-distance equal or higher than 0.001). It could be hypothesized that the isolate descended from the Italian 2011 Q1-like strain or was the result of a separate introduction from China through commercial trade or migratory birds; but the data currently available does not distinguish between these possibilities.

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“…For example, GenBank (8) and the Influenza Virus Sequence Database (9) have sparse or nonexistent geographic data. An analysis of GenBank sequences showed that only about 20% of records had "sufficient" geographic data (e.g., below the state/provincial level) to conduct spatial analyses (10). Records that did have a geographic indicator were not standardized, so that the contributor could list any type of geographic identifier for their gene sequence.…”

Section: Introductionmentioning

confidence: 99%

Evolution of respiratory syncytial virus (RSV) over space and time in rural Filipino children

Root

Gaensbauer

Nohynek

et al. 2012

Proceedings of the First ACM SIGSPATIAL International Workshop on Use of GIS in Public Health

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Very little is known about how spatial distance influences viral evolution or what local spatio-temporal patterns of evolution look like. In this study, we use data from a randomized controlled efficacy trial of an 11-valent pneumococcal vaccine (PCV) undertaken in the Bohol province of the Philippines from July 2000 to December 2004. Viral culture and multiplex PCR were done on nasal wash specimens, collected from a sample of infants visiting the regional hospital or outpatient clinics during the vaccine trial. We performed a nested phylogeographic analysis of respiratory syncytial virus (RSV) positive samples and classified virus samples into distinct subgroups. The geographic coordinates of household of residence were obtained for study participants using GPS and used to link phylogenetic results to the geographic location of each patient. We then performed a retrospective spacetime scan statistic to identify the spatial location and temporal extent of clusters of each subgroup and visualized geographic patterns using GIS. The spatio-temporal scan statistic identified several unique space-time clusters of RSV-A and RSV-B subgroups. The results show that RSV subgroups evolve in distinct localized areas at different points in time, suggesting that spatial distance a population factors play an important role in viral evolution. Spatial analysis and geovisualization is the first step in exploring the effects of distance on viral evolution and potential ecological pressures that contribute to evolutionary pressures.

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Enhancing phylogeography by improving geographical information from GenBank

Cited by 33 publications

References 16 publications

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

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

Molecular investigation of a full-length genome of a Q1-like IBV strain isolated in Italy in 2013

Evolution of respiratory syncytial virus (RSV) over space and time in rural Filipino children

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