FluGenome: a web tool for genotyping influenza A virus

Influenza A viruses are hosted by numerous avian and mammalian species, which have shaped their evolution into distinct lineages worldwide. The viral genome consists of eight RNA segments that are frequently exchanged between different viruses via a process known as genetic reassortment. A complete genotype nomenclature is essential to describe gene segment reassortment. Specialized bioinformatic tools to analyze reassortment are not available, which hampers progress in understanding its role in host range, virulence and transmissibility of influenza viruses. To meet this need, we have developed a nomenclature to name influenza A genotypes and implemented a web server, FluGenome (http://www.flugenome.org/), for the assignment of lineages and genotypes. FluGenome provides functions for the user to interrogate the database in different modalities and get detailed reports on lineages and genotypes. These features make FluGenome unique in its ability to automatically detect genotype differences attributable to reassortment events in influenza A virus evolution.

[1]  A. Karasin,et al.  Characterization of Avian H3N3 and H1N1 Influenza A Viruses Isolated from Pigs in Canada , 2004, Journal of Clinical Microbiology.

[2]  A. Osterhaus,et al.  Global Patterns of Influenza A Virus in Wild Birds , 2006, Science.

[3]  R. Webster,et al.  Multiple lineages of antigenically and genetically diverse influenza A virus co-circulate in the United States swine population. , 2004, Virus research.

[4]  W. Fitch,et al.  Biological and genetic evolution of the nucleoprotein gene of human influenza A viruses. , 1989, The Journal of general virology.

[5]  T. Kuiken,et al.  Newer respiratory virus infections: human metapneumovirus, avian influenza virus, and human coronaviruses , 2005, Current opinion in infectious diseases.

[6]  Thomas M. Keane,et al.  DPRml: distributed phylogeny reconstruction by maximum likelihood , 2005, Bioinform..

[7]  A. Douglas,et al.  The evolution of human influenza viruses. , 2001, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[8]  R. Lamb,et al.  The gene structure and replication of influenza virus. , 1983, Annual review of biochemistry.

[9]  Paul Kellam,et al.  Genotyping Hepatitis B virus from whole- and sub-genomic fragments using position-specific scoring matrices in HBV STAR. , 2006, The Journal of general virology.

[10]  R. Webster,et al.  Matrix Gene of Influenza A Viruses Isolated from Wild Aquatic Birds: Ecology and Emergence of Influenza A Viruses , 2004, Journal of Virology.

[11]  C. N. Brorn,et al.  WHO? , 1896 .

[12]  V. A. Isachenko,et al.  A new avian influenza virus from feral birds in the USSR: recombination in nature? , 1974, Bulletin of the World Health Organization.

[13]  Wenjun Ma,et al.  Isolation and Genetic Characterization of New Reassortant H3N1 Swine Influenza Virus from Pigs in the Midwestern United States , 2006, Journal of Virology.

[14]  W. J. Bean,et al.  Evolutionary analysis of the influenza A virus M gene with comparison of the M1 and M2 proteins , 1991, Journal of virology.

[15]  R. Webster,et al.  The Surface Glycoproteins of H5 Influenza Viruses Isolated from Humans, Chickens, and Wild Aquatic Birds Have Distinguishable Properties , 1999, Journal of Virology.

[16]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[17]  F. Pedersen,et al.  Biochemical evidence that "new" influenza virus strains in nature may arise by recombination (reassortment). , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[18]  R. Webster,et al.  Emergence of H3N2 reassortant influenza A viruses in North American pigs. , 2000, Veterinary microbiology.

[19]  R. Webster,et al.  Evolution of influenza A virus PB2 genes: implications for evolution of the ribonucleoprotein complex and origin of human influenza A virus , 1990, Journal of virology.

[20]  Etsuko N. Moriyama,et al.  GenomeBlast: a web tool for small genome comparison , 2006, First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06).

[21]  R. Webster,et al.  Evolutionary pathways of the PA genes of influenza A viruses. , 1989, Virology.

[22]  F. Burnet.  Portraits of viruses: influenza virus A. , 1979, Intervirology.

[23]  Keiji Fukuda,et al.  Mortality associated with influenza and respiratory syncytial virus in the United States. , 2003, JAMA.

[24]  Sudhir Kumar,et al.  MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment , 2004, Briefings Bioinform..

[25]  S. Goyal,et al.  Genetic Characterization of H1N2 Influenza A Viruses Isolated from Pigs throughout the United States , 2002, Journal of Clinical Microbiology.

[26]  J. Drake.  Rates of spontaneous mutation among RNA viruses. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[27]  K. D. Patterson,et al.  The geography and mortality of the 1918 influenza pandemic. , 1991, Bulletin of the history of medicine.

[28]  Niall Johnson,et al.  Updating the Accounts: Global Mortality of the 1918-1920 "Spanish" Influenza Pandemic , 2002, Bulletin of the history of medicine.

[29]  W. Fitch,et al.  Evolution of human influenza A viruses over 50 years: rapid, uniform rate of change in NS gene. , 1986, Science.

[30]  K. Subbarao,et al.  Genetic characterization of H3N2 influenza viruses isolated from pigs in North America, 1977-1999: evidence for wholly human and reassortant virus genotypes. , 2000, Virus research.