Analysis and Visualization of H7 Influenza Using Genomic, Evolutionary and Geographic Information in a Modular Web Service

Overview

Journal Cladistics

Specialty Biology

Date 2020 Apr 22

PMID 32313365

Citations 1

Authors

Daniel A Janies

Laura W Pomeroy

Jacob M Aaronson

Samuel Handelman

Jori Hardman

Kevin Kawalec

Thomas Bitterman

Ward C Wheeler

Affiliations

Soon will be listed here.

Abstract

We have reported previously on use of a web-based application, Supramap (http://supramap.org) for the study of biogeographic, genotypic, and phenotypic evolution. Using Supramap we have developed maps of the spread of drug-resistant influenza and host shifts in H1N1 and H5N1 influenza and coronaviruses such as SARS. Here we report on another zoonotic pathogen, H7 influenza, and provide an update on the implementation of Supramap as a web service. We find that the emergence of pathogenic strains of H7 is labile with many transitions from high to low pathogenicity, and from low to high pathogenicity. We use Supramap to put these events in a temporal and geospatial context. We identify several lineages of H7 influenza with biomarkers of high pathogenicity in regions that have not been reported in the scientific literature. The original implementation of Supramap was built with tightly coupled client and server software. Now we have decoupled the components to provide a modular web service for POY (http://poyws.org) that can be consumed by a data provider to create a novel application. To demonstrate the web service, we have produced an application, Geogenes (http://geogenes.org). Unlike in Supramap, in which the user is required to create and upload data files, in Geogenes the user works from a graphical interface to query an underlying dataset. Geogenes demonstrates how the web service can provide underlying processing for any sequence and metadata database. © The Willi Hennig Society 2012.

Citing Articles

Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions.

Jacob Machado D, White 3rd R, Kofsky J, Janies D Antimicrob Steward Healthc Epidemiol. 2022; 1(1):e60.

PMID: 36168505 PMC: 9495640. DOI: 10.1017/ash.2021.222.

References

Rohm C, Suss J, Pohle V, Webster R . Different hemagglutinin cleavage site variants of H7N7 in an influenza outbreak in chickens in Leipzig, Germany. Virology. 1996; 218(1):253-7. DOI: 10.1006/viro.1996.0187. View

Janies D, Treseder T, Alexandrov B, Habib F, Chen J, Ferreira R . The Supramap project: linking pathogen genomes with geography to fight emergent infectious diseases. Cladistics. 2020; 27(1):61-66. PMC: 7162175. DOI: 10.1111/j.1096-0031.2010.00314.x. View

Nguyen-Van-Tam J, Nair P, Acheson P, Baker A, Barker M, Bracebridge S . Outbreak of low pathogenicity H7N3 avian influenza in UK, including associated case of human conjunctivitis. Euro Surveill. 2006; 11(5):E060504.2. DOI: 10.2807/esw.11.18.02952-en. View

Belser J, Bridges C, Katz J, Tumpey T . Past, present, and possible future human infection with influenza virus A subtype H7. Emerg Infect Dis. 2009; 15(6):859-65. PMC: 2727350. DOI: 10.3201/eid1506.090072. View

Bulach D, Halpin R, Spiro D, Pomeroy L, Janies D, Boyle D . Molecular analysis of H7 avian influenza viruses from Australia and New Zealand: genetic diversity and relationships from 1976 to 2007. J Virol. 2010; 84(19):9957-66. PMC: 2937813. DOI: 10.1128/JVI.00930-10. View

Spackman E, McCracken K, Winker K, Swayne D . H7N3 avian influenza virus found in a South American wild duck is related to the Chilean 2002 poultry outbreak, contains genes from equine and North American wild bird lineages, and is adapted to domestic turkeys. J Virol. 2006; 80(15):7760-4. PMC: 1563721. DOI: 10.1128/JVI.00445-06. View

Horimoto T, Kawaoka Y . Influenza: lessons from past pandemics, warnings from current incidents. Nat Rev Microbiol. 2005; 3(8):591-600. DOI: 10.1038/nrmicro1208. View

Berhane Y, Hisanaga T, Kehler H, Neufeld J, Manning L, Argue C . Highly pathogenic avian influenza virus A (H7N3) in domestic poultry, Saskatchewan, Canada, 2007. Emerg Infect Dis. 2009; 15(9):1492-5. PMC: 2819867. DOI: 10.3201/eid1509.080231. View

Hirst M, Astell C, Griffith M, Coughlin S, Moksa M, Zeng T . Novel avian influenza H7N3 strain outbreak, British Columbia. Emerg Infect Dis. 2005; 10(12):2192-5. PMC: 3323367. DOI: 10.3201/eid1012.040743. View

10.

Sloan C, Duell E, Shi X, Irwin R, Andrew A, Williams S . Ecogeographic genetic epidemiology. Genet Epidemiol. 2008; 33(4):281-9. PMC: 2672969. DOI: 10.1002/gepi.20386. View

11.

Stech O, Veits J, Weber S, Deckers D, Schroer D, Vahlenkamp T . Acquisition of a polybasic hemagglutinin cleavage site by a low-pathogenic avian influenza virus is not sufficient for immediate transformation into a highly pathogenic strain. J Virol. 2009; 83(11):5864-8. PMC: 2681970. DOI: 10.1128/JVI.02649-08. View

12.

Vey M, Orlich M, Adler S, Klenk H, Rott R, Garten W . Hemagglutinin activation of pathogenic avian influenza viruses of serotype H7 requires the protease recognition motif R-X-K/R-R. Virology. 1992; 188(1):408-13. PMC: 7172898. DOI: 10.1016/0042-6822(92)90775-k. View

13.

Gibson C, Daniels R, Oxford J, McCauley J . Sequence analysis of the equine H7 influenza virus haemagglutinin gene. Virus Res. 1992; 22(2):93-106. DOI: 10.1016/0168-1702(92)90037-a. View

14.

LARKIN M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H . Clustal W and Clustal X version 2.0. Bioinformatics. 2007; 23(21):2947-8. DOI: 10.1093/bioinformatics/btm404. View

15.

Spackman E, Senne D, Davison S, Suarez D . Sequence analysis of recent H7 avian influenza viruses associated with three different outbreaks in commercial poultry in the United States. J Virol. 2003; 77(24):13399-402. PMC: 296076. DOI: 10.1128/jvi.77.24.13399-13402.2003. View

16.

Suarez D, Garcia M, Latimer J, Senne D, PERDUE M . Phylogenetic analysis of H7 avian influenza viruses isolated from the live bird markets of the Northeast United States. J Virol. 1999; 73(5):3567-73. PMC: 104129. DOI: 10.1128/JVI.73.5.3567-3573.1999. View

17.

Fouchier R, Schneeberger P, Rozendaal F, Broekman J, Kemink S, Munster V . Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome. Proc Natl Acad Sci U S A. 2004; 101(5):1356-61. PMC: 337057. DOI: 10.1073/pnas.0308352100. View

18.

Janies D, Voronkin I, Das M, Hardman J, Treseder T, Studer J . Genome informatics of influenza A: from data sharing to shared analytical capabilities. Anim Health Res Rev. 2010; 11(1):73-9. DOI: 10.1017/S1466252310000083. View

19.

Lokossou A, Rietman H, Wang M, Krenek P, Van Der Schoot H, Henken B . Diversity, distribution, and evolution of Solanum bulbocastanum late blight resistance genes. Mol Plant Microbe Interact. 2010; 23(9):1206-16. DOI: 10.1094/MPMI-23-9-1206. View

20.

Li Y, Li C, Liu L, Wang H, Wang C, Tian G . Characterization of an avian influenza virus of subtype H7N2 isolated from chickens in northern China. Virus Genes. 2006; 33(1):117-22. DOI: 10.1007/s11262-005-0042-8. View