Orthomyxoviridae Influenzavirus A
The Orthomyxoviridae family of viruses are segmented (8 segments, in the case of influenza A virus), negative-sense, enveloped RNA viruses, which infect vertebrate hosts. (see ICTVdB - The Universal Virus Database, version 4).
Of the viruses belonging to the family Orthomyxoviridae, influenza A virus is the most predominant cause of morbidity and mortality in humans, in which it causes respiratory illness. The natural hosts of all influenza A subtypes are wild birds, primarily those belonging to the family Anatidae (ducks, geese, and swans). Transmission of numerous subtypes to humans and other animals have been documented, but establishment of persistent infection of new subtypes in humans is rare. Apart from waterfowl and humans, transmission of influenza A is known to persist in birds of the order Galliformes, pigs, horses, and dogs.
Influenza A viruses are classified into subtypes based on the antigenic relationships of their two major surface proteins: haemagglutinin (HA), which binds to sialic acid residues on surface proteins of host cells, and induces fusion of the virus membrane with that of the host cell; and neuraminidase (NA), which cleaves sialic acid residues from surface proteins, enabling release of virus particles from host cells.
Until recently, two influenza A subtypes - H1N1 and H3N2 - persisted in humans, and caused seasonal epidemics of influenza in temperate countries, and year-round infections in humans in tropical regions. In 2009, a new variant of H1N1, distantly related to seasonal H1N1, emerged in the human population, and caused the first influenza pandemic of the 21st century - this virus is now referred to as pandemic (H1N1) 2009.
The Wellcome Trust Sanger Institute is committed to two facets of influenza A virus sequencing: whole genome sequencing; and deep amplicon sequencing.
Our influenza whole genome sequencing is funded by the Wellcome Trust, and involves collaboration with researchers at the Health Protection Agency (HPA), National Institute for Medical Research, London (NIMR), and the Veterinary Laboratories Agency (VLA). We have developed robust approaches to sequencing influenza A genomes using capillary, 454, and Illumina sequencing platforms. The role of these projects is to supplement the sequences of subgenomic genes/segments, which are rapidly generated by our collaborators, with whole genome consensus sequences.
Our deep amplicon sequencing projects are also funded by the Wellcome Trust, and involve collaborations with the Cambridge Infectious Disease Consortium (CIDC) and the Animal Health Trust, Newmarket (AHT). Rather than generating consensus sequence for the whole genome, these projects involve deep sequencing of some genes (usually HA1), to investigate changes in frequency of rare variants over time during infection, both within the period of infection of an individual and through chains of transmission.
Published Genome Data
Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans.
Science (New York, N.Y.) 2009;325;5937;197-201
Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic.
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution.
This project is ongoing and data for this organism will be made available in due course.
Data Use Statement
This sequencing centre plans on publishing the completed and annotated sequences in a peer-reviewed journal as soon as possible. Permission of the principal investigator should be obtained before publishing analyses of the sequence/open reading frames/genes on a chromosome or genome scale. See our data sharing policy.
Please address all sequencing enquiries to: firstname.lastname@example.org