Discovery and characterization of swine host factors required to support swine influenza virus replication.

Lead Research Organisation: Imperial College London
Department Name: Infectious Disease


Infection of pigs with influenza viruses is a problem both for animal and human health. Swine influenza virus infections cause production losses and can predispose to more serious complications leading to loss of stock. Moreover infections of pigs by avian influenza viruses can pre-empt the emergence of a novel influenza virus that infects humans. Indeed the last influenza pandemic in 2009 had its most recent origin in pigs. Pork is an important protein source for the developed and developing world. China is a major pig producer, where pigs are reared in large holdings under sometimes crowded conditions; a perfect breeding ground for the evolution and emergence of new strains of virus. The high population in China, its geography and its climate make it a hotspot for emergence of influenza viruses. One future solution to these threats is to employ recent developments in gene editing to make a pig that is resistant to infection with influenza viruses. This is not so far-fetched; indeed, pigs resistant to another pig virus called PRRS were recently generated. However, in order to apply the breakthrough to the influenza problem we need to identify which genes in the pigs should be altered to stop the virus from being able to infect, and then define precisely how to alter them so that there is as little disruption to the meat production and breeding capacity in the edited animals.
We will identify the pig genes that are co-opted by swine influenza viruses to support their replication using a novel screening method, in pig cells with authentic swine influenza viruses typical of those circulating in China today. Then we will employ another novel screening method to work out the least changes we can make in the pig gene in order to stop the virus from infecting, because we reason this minimalistic and precise editing strategy will be the most acceptable to consumers and farmers alike.

Planned Impact

The threat of an influenza pandemic is scored as the greatest natural-origin risk to the UK on the 2015 UK government risk register. Indeed, in a global era, the next influenza pandemic will be devastating for both developed and developing countries. Pigs are thought to be the origin or to have contributed to the origin of 3 of the 4 recent influenza pandemics. Abrogating infection of domesticated pigs by influenza viruses would alleviate this risk and thus have huge consequence on human health and economic stability around the globe.
China produces around half of the world's pigs, almost one billion animals, many farmed in large holdings. Infection of pigs with swine influenza virus causes a mild respiratory disease associated with some loss in production. But influenza infection is well known to predispose to more serious secondary infections, in pigs examples would be porcine circovirus and PRRS that lead to morbidity and mortality. The economic, agricultural and human health benefits of having pigs that cannot support influenza virus replication are obvious.
But gene editing is in its infancy, and to avoid any catastrophic unpredicted negative outcomes that could halt the advance of this exciting approach, an intelligent and well informed precise editing strategy is essential. Thus we propose to generate intelligently designed editing for pigs that could be combined with the strategy already described for PRRS to create animals resistant to two of the most prevalent swine virus diseases in China and elsewhere.


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Description We have investigated, in detail, the role ANP32 proteins play in the adaptation and evolution of avian influenza viruses in different mammalian hosts. We have shown how the balance between ANP32A and ANP32B influences the profile of adaptive polymerase mutations in different hosts and how this may affect the zoonotic potential of different mammalian influenza viruses. For example, our data imply that equine and canine influenza viruses likely pose a lesser zoonotic due to ANP32 incompatabilities.

Furthermore, we have shown that due to their ANP32 proteins, swine have a unique property amongst common influenza hosts of allowing avian influenza viruses to replicate with minimal adaptation. Swine have often been described as influenza virus mixing vessels - allowing reassortant between human, swine and avian influenza viruses - and our work helps explain this property. We are further able to map the exact amino acid changes that guide this property. In addition we have been able to show how swine adapted viruses - such as the pandemic 2009 swine influenza virus - were able to further adapt to human ANP32 proteins in the year following the start of the pandemic.

Finally we have described a minimal set of substitutions in swine ANP32 proteins that would allow the creation of a gene-edited pig that we predict would be resistant to swine influenza virus infection.
Exploitation Route We propose that the generation of gene edited farmed animals is a way to prevent future outbreaks of influenza viruses.
We explain the role of pigs in supporting generation of pandemic influenza viruses.
Sectors Agriculture, Food and Drink,Healthcare,Pharmaceuticals and Medical Biotechnology

Description Barclay Zhou Newton fund collaboration 
Organisation Huazhong Agricultural University
Department College of Veterinary Medicine
Country China 
Sector Academic/University 
PI Contribution Our team is developing an 'all mutagenesis' approach to investigate how host proteins are used by influenza virus, in an unbiased approach. This method will allow us to probe both proteins of with characterised pro-viral functions as well as novel, uncharacterised proteins. We will develop this technique and then share this protocol and associated reagents with our Chinese collaborators. So far we are still in the early stages of this development.
Collaborator Contribution Our Chinese collaborators are performing a genome-wide CRISPR screen on pig cells to try and find novel pro-viral host factors. These results will be fed back to us whereby we will perform the aforementioned 'all mutagenesis' to identify regions of the protein important for function. Furthermore our Chinese collaborators will provide us with viruses and viral reagents representative of circulating viruses in China. So far our Chinese collaborators have sent us some viral reagents which have proven extremely useful for part of our work. Furthermore our collaborators have performed some preliminary screens and sent us the data.
Impact none so far
Start Year 2018
Description Roslin collaboration 
Organisation University of Edinburgh
Department The Roslin Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution We have collaborated with this group and are publishing a paper together, we have shared pertinent unpublished data together as well as laboratory reagents
Collaborator Contribution We have collaborated with this group and are publishing a paper together, we have shared pertinent unpublished data together as well as laboratory reagents
Impact A paper is currently in revisions and should be published soon in Journal of Virology.
Start Year 2019
Description 10th edition of Options for the Control of Influenza. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Gave oral presentation titled: ANP32 proteins from different mammalian species act as host range barriers and shape influenza polymerase adaptation.
Year(s) Of Engagement Activity 2019