During the early part of the genomics era, there was rapid technological growth with lots of sequencing of genomes from different organisms like the dog, the chicken and even Neanderthals. Some companies such as AncestryDNA and 23&Me started to provide ‘spit tests’ - cheap, carry out at home DNA tests to let people get their genomes sequenced. While these tests have let us learn more about ourselves and undoubtedly gained the most attention, importantly the same techniques can be used to track and analyse diseases and the Covid pandemic has demonstrated how crucial this capability is.
This pandemic has shown us how much diagnostic tests for infectious diseases are now an essential part of healthcare. As we have seen over the last two years, accuracy, cost-efficiency, and turnaround times are vital criteria to adopt new technologies that promise improvements in the performance of diagnostic tests.
Introducing sequencing into diagnostic and public health laboratories has already improved patient care, for example it has been used to detect existing and emerging drug resistance for the human immunodeficiency virus (HIV), a vital part of making sure that patients are receiving the right treatment. During the last two years, the public have learnt a lot about viruses. We now all know that viruses evolve rapidly, and we have all heard reports in the news of different variants of the Sars-Cov-2 virus – the Kent (or British) variant, the Brazilian variant and the South African variant. Genomic sequencing allows the detection of this variation and allows us to track the different mutations that arise as the virus reproduces.
In the UK, the Covid-19 Genomics UK consortium (Cog-UK) is leading the effort to sequence the virus. The Welcome Sanger Institute in Hinxton, a vital part of the human genome project all those years ago is the co-ordinating hub. Other members are the UK’s four public health agencies and a range of academic, NHS and public health organisations including the University of Edinburgh, the University of Glasgow and their associated NHS Boards. Using this UK wide network of 16 hubs, consortium members sequence positive samples from people with Covid-19. Since its launch, the consortium has sequenced a massive 459,143 virus samples, more than any other country, except the USA. It is an important part of the viral genome monitoring, which has informed government strategy and provided vital information for the companies developing vaccines.
Although Cog-UK’s work on the pandemic is far from complete, it has already delivered so much. In principle, what has been done with Covid can be applied to any virus. As with many bacterial and viral pathogens, multidrug resistance is becoming an issue. By sequencing samples, we can predict if the pathogen is resistant to a particular drug, making it much quicker to identify the right drug and get the patient started on the most effective treatment.
Genome sequencing still has a long way to go but the claims of it being able to ‘revolutionise the diagnosis, prevention and treatment of most, if not all, human diseases’ are fast becoming a reality. And for that, we are all truly grateful.
Dr Diane Harbison is Co-Founder and CEO at Decipher Analytics