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Influenza Viruses

Our group

The Influenza Viruses group was formerly led Dr Holly Shelton and is currently under review.

The group’s research is specifically interested in understanding how changes in genetic information encoded by different strains of influenza A virus alters transmission, host response to infection and the pathology of disease caused. Check The Pirbright Institute job vacancies page to see opportunities to join the group.

Our aims

  1. To increase our understanding about transmission of virus between birds; what factors influence transmission, what type of transmission is important, how does transmission alter virus diversity?
  2. To investigate adaptation of avian influenza viruses to mammalian hosts. What changes are required and why? How quickly can adaptation occur and how can we predict/ risk assess which strains are of greatest pandemic potential?
  3. To deliver information about host virus interactions that can be exploited to mitigate infection and spread of virus in populations.

Our research

Rapid mammalian adaptation of influenza viruses. In the recent human infections by avian influenza of the subtype H7N9 in China up to two thirds of infected patients had virus samples that contained mammalian adaptation signatures in the viral polymerase genes. We are investigating, using animal models, which viral strains can rapidly adapt in mammals and whether adaptation can occur quickly enough for transmission to a naïve mammalian host.

Microbiome and influenza. The microbiome of a host can influence basal innate immune responses following initial challenge by a pathogen. Dysregulation of the microbiome can exacerbate clinical outcomes following pathogen infection. We are mapping the changes in the chicken respiratory and gastrointestinal microbiome following influenza infection and assessing whether application of probiotics (“good bacteria”) can module viral shedding or transmission.

Anti-viral resistant avian influenza viruses. We have limited anti-influenza virus treatments for use in humans. The most widely used treatment is the neuraminidase inhibitor drugs that prevents spread of the virus to new cells. Neuraminidase inhibitor drugs target the NA of influenza A virus. There is limited information about the motifs that confer functional resistance to these drug in NA genes of avian influenza strains. We are mapping functional resistance motif to enhance surveillance programs. Our research also assesses whether drug resistance alters viral fitness in poultry and thus the likelihood of drug resistance strains becoming the prevalent circulating strain and whether concurrent changes to other viral genes occur along the drug resistance motifs and what effects they might have.

Impact of coinfections of influenza viruses and other viral pathogens.  Avian influenza virus infection of poultry does not occur in a sterile environment in real settings, there are abundant other poultry pathogens, both viral, bacterial and parasites that cocirculate. We are working to understand the impact of coinfection of avian influenza and other poultry pathogens on viral replication, disease pathogenesis and immune legacy in poultry. Important coinfection pathogens we are examining include infectious bronchitis virus (IBV), infectious bursal disease virus (IBDV) and Newcastle disease virus (NDV).

Our impact

Influenza A viruses can infect multiple host species including farmed poultry and humans causing economic problems for farmers and potential human health threats through zoonosis.  We are studying influenza genes that may contribute to pathogenicity and transmissibility in poultry hosts and how changes in the genes may change the potential zoonotic risk of strains. By understanding the role of these viral genes and the mechanisms through which they work we can design new vaccine and therapeutic targets for both animals and humans. Such new tools would increase the effectiveness of control strategies for influenza viruses in poultry which will reduce the economic losses caused by influenza viruses for the poultry industry, enhancing food security and also protecting human health.

*Image by Cynthia Goldsmith, courtesy of the Public Health Image Library

Chrzastek K, Tennakoon C, Bialy D, Freimanis G, Flannery J, Shelton H (2022)

BMC Genomics 23 (1) , 406
Bhat S, James J, Sadeyen J-R, Mahmood S, Everest H J, Chang P, Walsh S K, Byrne A M P, Mollett B, Lean F, Sealy J E, Shelton H, Slomka M J, Brookes S M, Iqbal M (2022)

Journal of Virology 96 (5) , e0185621
Chrzastek K, Leng J, Zakaria M K, Bialy D, La Ragione R, Shelton H (2021)

Animal Microbiome 3 (1) , 64
Everest H, Billington E, Daines R, Burman A, Iqbal M (2021)

mBio 12 (5) , e0178521
Conceicao C, Thakur N, Human S, Kelly J T, Logan L, Bialy D, Bhat S, Stevenson-Leggett P, Zagrajek A K, Hollinghurst P, Varga M, Tsirigoti C, Hammond J A, Maier H J, Bickerton E, Shelton H, Dietrich I, Graham S C, Bailey D (2020)

PLOS Biology 18 (12) , e3001016


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