The virtual biobank

Understanding how pathogens, whether viruses, bacteria or others, are behaving in a population is necessary prerequisite to their control.

• Is a pathogen becoming more common?
• Is there a new variant that escapes vaccines?
• Have we imported something new into the UK?
• Does a particular dog pathogen pose a risk to humans?

To address these questions requires regular access to a wide range of samples, and the modern sequencing technologies needed to fingerprint and thereby track pathogens. Modern improvements in laboratory technology mean the sequencing is now becoming easier. The problem is getting samples, since while they're regularly collected and stored from humans and farm animals, they're not routinely available for companion animals.

That got us thinking. If we catalogued the large number of clinical samples that are being submitted, by vets from their individual patients to diagnostic laboratories, could we identify important samples and retrieve them for sequencing? These are samples where diagnostic testing, to investigate disease in the companion animal, has been completed, where the samples would be otherwise discarded once individual test results become available.

In partnership with a growing number of diagnostic laboratories across the country, the Small Animal Veterinary Surveillance Network (SAVSNET) now uses these anonymous samples to further investigate important diseases in companion animals. Using real-time signals, we'll identify and retrieve key samples for further phenotypic and genotypic analyses. We call this idea a virtual biobank.

What do we do with the samples?

By analysing samples in the laboratory we can add extra information such as the species or strain responsible, number of animals affected, and the types of animals at risk. We can then inform on potential preventative or therapeutic measures.

Sequencing and serology are the two broad methods we can use on samples we receive for the virtual biobank.

Sequencing

Sequencing is fantastic technology which allows us to “fingerprint” a pathogen and thereby see how it is moving around and evolving.

• In traditional Sanger sequencing, we sequence small parts to identify what strain or variant the pathogen is. This usually only gives us part of the pathogen’s sequence, but it is relatively cheap allowing many samples to be sequenced
• A newer technology is next-generation (or whole genome) sequencing. This is sequencing on massive scale. It sequences more of the pathogen’s genome than Sanger sequencing so that we can characterise individual pathogens in much more detail. It can also spot new pathogens. However, next-generation sequencing is more expensive and therefore restricted to fewer samples.

Thanks to a collaboration with IDEXX Laboratories, we have used sequencing of virtual biobank samples to characterise parvoviruses in UK cats and dogs. With IDEXX Laboratories and Nationwide Laboratories, we have also identified new variants of Escherichia coli (known as E. coli) that are both resistant to important antibiotics and potentially transmissible between pets and people.

Serology

In contrast to sequencing, that looks at a pathogen's genetic fingerprint, serology looks at antibodies to specific pathogens. If an animal has antibodies then it means they have either been infected, or if a vaccine is available, then they may also have had a vaccine. Young animals may also have antibodies they acquired from their mum.

With IDEXX Laboratories, we have used sera from the virtual biobank to look for infection in cats and dogs by severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2).

Ongoing projects

We have an ongoing project on antimicrobial resistance using samples from the virtual biobank.

Calls for samples

We can’t do our work without those UK veterinary diagnostic laboratories that collaborate with SAVSNET and provide samples for the virtual biobank. We are immensely grateful.

We are currently looking for samples from canine distemper virus sequencing (UK and Europe) and rabbit viral haemorrhagic disease virus.

If you would like to know more about the virtual biobank, or you work at a diagnostic laboratory and think you have left-over samples from animals that have tested positive for these pathogens, then please do get in touch.