Molecular epidemiology of H9N2 avian influenza viruses in Pakistan
Lead Research Organisation:
Royal Veterinary College
Abstract
Avian influenza viruses (AIV) of the H9N2 subtype are causing devastating losses in poultry in many countries throughout Asia, the Middle East and North Africa including Pakistan. Recent evidence suggests that H9N2 viruses have a particularly high tendency for donating internal genes by reassortment to other co-circulating AIV, and these internal genes may contain molecular markers associated with mammalian transmissibility, thus posing a risk for pandemic emergence of novel human-transmissible genotypes. To reduce the impact of H9N2 in poultry, several countries employ vaccination, however the efficacy of these programs is compromised by continued rapid adaptive evolution of the virus, and the emergence of variants that are not covered by current vaccine formulations.
This project will investigate the epidemiology of H9N2 in Pakistan, a country that has experienced severe outbreaks of H9N2 avian influenza in poultry. The aims include (i) characterising diversity of H9 viruses among poultry productions systems at varying levels of industrialisation; (ii) examining the role of live bird markets in H9 transmission; and (iii) evaluating the extent of antigenic diversity and implications for vaccine effectiveness. The project will involve surveillance activities in Pakistan; field trials of novel diagnostics tools; and phylogenetic analysis of H9 sequences. The project will be conducted within the larger framework of a ZELS project to develop novel avian influenza vaccines, with the goal of understanding how vaccine intervention strategies impact viral diversity and industrialisation of poultry production. There will be opportunities for comparative analysis of AIV and H9 epidemiology across different countries.
This project will investigate the epidemiology of H9N2 in Pakistan, a country that has experienced severe outbreaks of H9N2 avian influenza in poultry. The aims include (i) characterising diversity of H9 viruses among poultry productions systems at varying levels of industrialisation; (ii) examining the role of live bird markets in H9 transmission; and (iii) evaluating the extent of antigenic diversity and implications for vaccine effectiveness. The project will involve surveillance activities in Pakistan; field trials of novel diagnostics tools; and phylogenetic analysis of H9 sequences. The project will be conducted within the larger framework of a ZELS project to develop novel avian influenza vaccines, with the goal of understanding how vaccine intervention strategies impact viral diversity and industrialisation of poultry production. There will be opportunities for comparative analysis of AIV and H9 epidemiology across different countries.
Publications
Peacock THP
(2019)
A Global Perspective on H9N2 Avian Influenza Virus.
in Viruses
Chang P
(2019)
Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity.
in Journal of virology
Sealy JE
(2018)
Association of Increased Receptor-Binding Avidity of Influenza A(H9N2) Viruses with Escape from Antibody-Based Immunity and Enhanced Zoonotic Potential.
in Emerging infectious diseases
Bayraktar E
(2018)
First Molecular Characterization of Avian Metapneumovirus (aMPV) in Turkish Broiler Flocks.
in Avian diseases
Rodriguez L
(2018)
Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30.
in Frontiers in microbiology
Sealy JE
(2019)
Poultry trading behaviours in Vietnamese live bird markets as risk factors for avian influenza infection in chickens.
in Transboundary and emerging diseases
Dalby A
(2017)
Rapid lineage assignment for the influenza A internal genes
Dalby A
(2017)
Rapid lineage assignment for the influenza A internal genes
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/N503563/1 | 01/10/2015 | 30/09/2019 | |||
| 1811252 | Studentship | BB/N503563/1 | 05/10/2015 | 04/04/2019 | Joshua Sealy |
| Description | Through characterizing the antigenic diversity of H9N2 avian influenza viruses form Pakistan we have identified a subset of circulating viruses with antigenic diversity compared to previous H9N2 strains from Pakistan. The immediate implication is the potential for vaccine failure if current vaccines are poorly matched to the diverse H9N2 strains infecting poultry in Pakistan. Further, the causative mutation for this antigenic divergence is in the haeamagglutinin glycoprotein with the added effect of facilitating receptor binding to mammalian cellular receptors. The implications are therefore two-fold; there are circulating H9N2 avian influenza viruses in Pakistan which can escape vaccine-induced immunity and they also have enhanced zoonotic potential. This information can be used in future vaccine design and can provide impetus to active surveillance efforts. This work has now been published in the journal Emerging Infectious Diseases. A field study in Vietnamese live bird markets was completed were risk factors for infection of chickens with influenza A virus were identified. These risk factors include poultry trading practices of poultry traders working in live bird markets. The data generated from this study can be used to identify certain types of poultry trader e.g. middlemen, who may present an increased risk of having influenza A infected chickens. This work has been published in the journal Transboundary and Emerging Diseases in 2019. |
| Exploitation Route | Regarding the antigenic diversity of circulating strains of H9N2 in Pakistan, vaccines that are cross-protective can be developed. Regarding the identified risk factors for influenza A infection of chickens in Vietnam, improved surveillance strategies and plans to mitigate the circulation of influenza can be through the understanding of drivers of influenza persistence in the poultry trading industry. |
| Sectors | Agriculture, Food and Drink,Communities and Social Services/Policy,Healthcare,Pharmaceuticals and Medical Biotechnology |
| URL | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302589/ |
| Description | PhD training funds |
| Amount | £500 (GBP) |
| Organisation | The Pirbright Institute |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 05/2018 |
| End | 05/2018 |
| Description | Pirbright Institute Flexible Talent Mobility Account |
| Amount | £180,000 (GBP) |
| Funding ID | BB/S507945/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2018 |
| End | 03/2021 |
| Description | Society Conference Grant |
| Amount | £300 (GBP) |
| Organisation | Microbiology Society |
| Sector | Learned Society |
| Country | United Kingdom |
| Start | 04/2017 |
| End | 04/2017 |
| Title | Sequencing data generated for public access |
| Description | H9N2 avian influenza viruses were isolated from poultry in Pakistan, and H9N2 and H5N6 avian influenza viruses were isolated from poultry in Vietnam. Viruses were sequenced and sequencing data submitted to a public access database (NCBI). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Analysis of sequencing data was followed by publication in a peer-reviewed journal. |
| Description | BBSRC - Oxford University iCASE Studentship (October 2019- September 2023). Production and assessment of antiviral prophylactic properties of natural biomolecules against avian influenza and Newcastle disease viruses affecting poultry production |
| Organisation | University of Oxford |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This collaboration between The Pirbright Institute (UK), Oxford University (UK) and industrial partners in Italy. This project will conceived and developed bu MI. The PhD student (Holly Everest) in my group is investigating the antiviral prophylactic properties of natural biomolecules against avian influenza and Newcastle disease viruses affecting poultry production. |
| Collaborator Contribution | The partners in Italy will produce and purify natural antiviral molecules effective against avian influenza and other poultry viruses. |
| Impact | This project started in January 2020. |
| Start Year | 2020 |
| Description | Collaboration with University of Veterinary and Animals Sciences, Lahore, Pakistan for poultry surveillance against H9N2 aviain influenza. |
| Organisation | University of Veterinary & Animal Sciences |
| Country | Pakistan |
| Sector | Academic/University |
| PI Contribution | Provide reagents for the PCR amplification of viral RNA extracted from isolated H9N2 avian influenza viruses from poultry farms in Pakistan. This PCR work was done by myself during a trip to UVAS, Pakistan. The samples being amplified were generated from surveillance activities carried out by staff at UVAS between 2014 and 2016. |
| Collaborator Contribution | Surveillance of poultry farms in Pakistan was carried out against avian influenza viruses infecting poultry. This surveillance was carried out by staff and students enrolled at UVAS supervised by one of the co-supervisors of this project. This work was conducted between 2014 and 2016 and involved swabbing poultry, screening samples and isolating viruses for subsequent PCR amplification by myself. Further characterization of Pakistan H9N2 viruses was conducted at Pirbright by myself. |
| Impact | A research article was published in Emerging Infectious Diseases in 2019 as a result of collaboration between UVAS in Pakistan, CRICK in the UK and the Pirbright Institute in the UK. This research article characterised H9N2 avian influenza viruses isolated from chickens in Pakistan. |
| Start Year | 2014 |
| Description | Field research in northern Vietnam, partnership with Oxford University Clinical Research Unit, Hanoi and National Centre for Veterinary Diagnosis, Hanoi |
| Organisation | University of Oxford |
| Department | Oxford University Clinical Research Unit Vietnam (OUCRU) |
| Country | Viet Nam |
| Sector | Academic/University |
| PI Contribution | I conducted field studies on avian influenza in live bird markets in northern Vietnam for six months. During this time I generated data on prevalence of influenza among chickens in northern Vietnam, and will aim to generate risk assessment of poultry trade behaviors for avian influenza infection in chickens. This contributes to diseases estimates in northern Vietnam and will contribute to understanding poultry trade behaviors which may enhance infection rate of chickens. Samples containing influenza viruses are now stored at NCVD for use in further virus characterization if required. |
| Collaborator Contribution | The two partnering institutes hosted me in their laboratories and offices, supplying me with space to work and facilities to receive research consumables which were paid for by our common budget. They helped with getting the government-level approval and permissions to conduct the studies and provided supervision when necessary. |
| Impact | Influenza prevalence data in chickens have been generated, analysis of questionnaires linked to trade behaviors and influenza infection has been carried out. Sequencing data for virus isolates has been generated. A peer reviewed research article based on this work was published in Transboundary and Emerging Diseases in 2019. The potential impact for this work is economic and policy & public services by facilitating more targeted influenza surveillance activities in the future and understanding trade behaviors that enhance risk of chicken infection. |
| Start Year | 2017 |
| Description | Investigating antigenic determinants inducing stronger and broader cross-protective immunity among H5 avian influenza viruses. |
| Organisation | Royal Veterinary College (RVC) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We developed research programme to characterise diversity of antigenic epitopes induce protective immunity in chickens against H5 subtypes of avian influenza viruses. |
| Collaborator Contribution | Collaborating partner Dr Nicola Lewis at Royal Veterinary College provide advise to on cartography programme to visualize the antigenic similarity or difference among different strains of influenza viruses. |
| Impact | The work under this collaborative determined the antigenic differences among different clades of H5 avian influenza viruses circulating in birds. This project is multi-disciplinary. our laboratory mainly work on virology and immunology part of the project and we seek help on computer modeling part from the collaborating partner Dr Nicola Lewis. |
| Start Year | 2019 |
| Description | Next generation sequencing at the Crick Worldwide Influenza Centre |
| Organisation | Francis Crick Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Provided PCR products to Crick-WIC for next generation sequencing |
| Collaborator Contribution | Crick-WIC conducted NGS on influenza PCR products which were generated from surveillance activities in poultry farms in Pakistan. The raw data was assembled and analysed at Pirbright by myself. |
| Impact | A peer-reviewed research article was published in Emerging Infectious Diseases in 2019 that investigates the current genetic and antigenic composition of H9N2 avian influenza viruses in Pakistan. This research highlights an important method of immune escape that has potential to impact the risk of zoonotic infection. Collaboration with the CRICK-WIC, London enabled the sequencing of viruses from Pakistan that were later characterised in this research. |
| Start Year | 2015 |
| Description | The Pirbright "Livestock Antibody Hub" funded by Bill & Melinda Gates Foundation |
| Organisation | The Pirbright Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Me and my team established collaboration in the "Livestock Antibody Hub" funded ($5.5 million) by the from Bill & Melinda Gates Foundation. Focus of our partnership is to develop techniques and capacity to analyse immune cells (B cells) of cattle, poultry and pigs that produce virus neutralizing antibodies. This research will support rational development of next generation of vaccines and to explore antibody-based passive immunization approaches for treatment and prophylaxis of infectious viral diseases affecting livestock and humans. Our initial focus is to target major animal viral pathogens that cause severe losses within Low and Middle-Income Countries (LMIC) animal production systems including avian influenza virus (AIV), Newcastle disease virus (NDV), infectious bursal disease virus (IBDV), infectious bronchitis virus (IBV) and foot-and-mouth disease virus (FMDV). |
| Collaborator Contribution | This is a collaborative project and partners are providing help in provision of reagents and techniques for analysis of diversity of B cells repertoire that produce infleunza virus-specific antibodies, single cell sequencing and bioinformatic analysis. This project will further strengthen our on-going research collaborations with many research groups in academia as well as with animal health industry (Zoetis, Boehringer Ingelheim Animal Health, Merck, CEVA, Jovac, YeBio, ILRI, Galvmed, The Roslin Institute, HuMabs, AbCellera and Distributed Bio) to take the research outputs from laboratory to the field. The outputs of research will be improved vaccines and diagnostics enabling to reduce the impact of infectious diseases on farm animals, which offer substantial direct and indirect economic, public health, environmental and social benefits to the UK and rest of the world. |
| Impact | Development of passive immunization approaches against avian influenza viruses affecting poultry (project incited in January 2020). |
| Start Year | 2020 |
| Description | Determinants of antigenicity of H9 Avian Influenza Viruses. UK-China Swine and Poultry Workshop.17-18 June 2019, The Pirbright Institute, UK. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The talk and the discussion on the improvement of disease control systems (vaccines and diagnostics) to prevent avian influenza viruses infection in poultry and zoonotic infections in humans. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Flu fighters |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Greater than 200 people attended the Guildford Live facility that hosted an exhibition on a wide variety of companies, technologies and entertainment. The Pirbright institute maintained a stall at this event and I represented the institute. This involved public engagement on research conducted at the institute, including influenza research and research into other animal viruses and vaccines. |
| Year(s) Of Engagement Activity | 2016,2017 |
| Description | Improving vaccines and diagnostics for Avian influenza viruses affecting poultry. Presented at the International Poultry Expo "Poultry Science Conference", Lahore, Pakistan, 13-15 September 2019. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The talk and the discussion was the best practices to improve control systems (vaccines and diagnostics) for prevention of avian influenza viruses infection in poultry and zoonotic infections in humans. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Influenza update meeting at the CRICK institute, London. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | A specialist annual meeting attended by researchers from the influenza field. Oral and poster presentations were given by postgraduates, postdocs and group leaders. The latest findings on "hot topic" areas of influenza research were disseminated and discussed. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Participation in the Young Entrepreneur Scheme 2018 competition |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Participation in this event was not linked to my PhD research work. In this competition,myself and three other postgraduate students/employees competed against other postgraduate students/employees from UK academic institutions for the chance to win a cash prize. This competition was the Young Entrepreneur Scheme (YES) 2018 competition where scientists with no business background are tasked with formulating a business plan that relies on a biotechnological achievement for the purpose of commercialization. |
| Year(s) Of Engagement Activity | 2018 |
| Description | The Centenary Influenza Meeting held at the CRICK institute, London. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A meeting of academics, physicians, industry researchers, postgraduates and postdocs to mark 100 years since the 1918 'spanish' influenza pandemic. This meeting was attended by world leading researchers from the influenza field. Oral and poster presentations were given that documented 100 years of development in our understanding of the influenza virus, including epidemiology, virology and immunology. |
| Year(s) Of Engagement Activity | 2018 |