Dear all,
I am Marion Delphin, a postdoctoral fellow in Philippa Matthews’ group at the Francis Crick Institute (London UK). I am happy to share with you the latest research from our lab, and I have added links to scientific articles for those of you who can/wish to get into more details, and I am happy to reply to any questions!
Have a good read.
Sequencing HBV: How reading the HBV genome can help fight liver disease
In Philippa Matthews’ group at the Francis Crick Institute in London, we are working to understand Hepatitis B Virus (HBV) by studying its genetic code through sequencing technologies. But HBV doesn’t make it easy.
- First of all, why does this matter?
You might ask, “What does sequencing actually tell me?”. Medical test results are often confusing enough, so why add another one? But here’s what makes sequencing different.
Genotype matters. HBV is extremely genetically diverse. It comes in different strains which we call ‘genotypes’ that have a bigger genetic difference than between us, humans, and gorillas. Some genotypes may be associated with different outcomes, for example being more likely to cause liver inflammation, or with a higher risk of transmission.
Understanding responses to antivirals. Responses to antiviral treatment are quite variable depending on individuals, and the reasons are not fully characterised yet. However, one reason could be small differences in the viral genetic code. Sequencing can show us exactly what these changes are and understand why/how people have different outcomes. It also enables us to inform and improve current monitoring or treatment strategies.
Anticipating risks of liver diseases. In collaboration with others, we helped identify specific mutations in the HBV genome that are linked to liver cancer potentially paving the way for new diagnostic tools in the future read more here.
Transmission patterns. By comparing the genetic code of different individuals, we can better understand how the virus is transmitted in populations. This insight is especially valuable in settings where a lot of people are living with HBV, helping to target vaccination campaigns, tailor screening strategies and prioritize interventions.
- The challenges we had
Low DNA quantities Unlike viruses such as HIV or SARS-CoV-2, HBV is often present in very low amounts in the blood. In nearly half of individuals, the virus is so scarce that it becomes incredibly hard to detect with standard laboratory methods. To make things even harder, there is always a lot of human DNA in blood samples and HBV DNA ends up being like a needle in a haystack.
Viral diversity As mentioned, HBV is very diverse, and we need tools that can work across all genotypes, which is technically very difficult.
Genome structure And as if that weren’t enough, HBV has a uniquely odd genome. Its structure is full of loops, gaps and quirks that must be untangled or filled in before we can sequence it.
Sequencing availability and affordability: While sequencing parts of the HBV genome is already available in some clinics, it remains a costly, complex and resource-heavy process, requiring trained staff and expensive equipment. We wanted to make it simpler, cheaper and more accessible so more people and more labs can benefit from it.
- Our solution: Sequencing for all
After several years of trial and error (and a fair amount of sweat and a few tears), our team developed two complementary ways to sequence the entire HBV genome:
Capture-based sequencing. where we use short ‘bait’ strands of DNA (called probes) to ‘fish out’ HBV from a blood sample. The virus sticks to the bait, allowing us to isolate and read its genome.
Amplicon-based sequencing: where we use primers to amplify specific segments of the HBV genome and then stitch them together using bioinformatic tools, like a puzzle.
Both methods required careful design to ensure they would work across all genotypes. To do this, we built on tools and approaches originally developed during the COVID-19 pandemic, including: PrimalScheme for amplicon probe design (https://primalscheme.com) and the ARTIC protocols and pipelines, which helped standardise viral sequencing globally.
We’ve now shown that these methods work well on a range of sequencing platforms. However, the Oxford Nanopore’s MinION, a compact sequencer the size of a USB stick, makes sequencing more portable and accessible in low-resource settings.
See our full article here: Whole genome sequencing of hepatitis B virus using tiled amplicon (HEPTILE) and probe based enrichment on Illumina and Nanopore platforms | Scientific Reports
- Towards accessible genomics for HBV
We are at an exciting moment in the field where sequencing whole HBV genomes from patient samples is finally possible and becoming more accessible. We hope this work will pave the way for HBV sequencing to become part of routine care, giving people living with HBV more answers, personalised treatment and ultimately greater control over their health.