Genomic surveillance in action

Here are three short case histories, each demonstrating genomic surveillance in action. They each, in different ways, show you how our ability to sequence genomes and track the variants of pathogens is revolutionising the way we understand and manage outbreaks of serious disease.

1. Covid-19

Genomic surveillance is only as good as the number of samples analysed and the width of the area surveyed.

While it is debatable whether viruses are ‘alive’, they do possess genetic material in the form of DNA or RNA, which behaves like that of living creatures during its reproduction. As a result, genomic surveillance works extremely well in tracking virus outbreaks.

In the case of SARS-CoV-2, genomic surveillance allows us to monitor how the virus changes over time and evolves into the different variants we hear about on the news. It also allows us to see whether similar changes occur across variants – such as the E484K mutation seen several times in different variants.

The Covid-19 pandemic has dramatically accelerated the use of genomic surveillance to a scale never seen before. It allows scientists and governments to determine which variants are present in their country. It also helps determine how infectious or lethal new variants are, by monitoring how quickly they spread, and how often they are found in people who require hospitalization or who die.

By monitoring the genome of SARS-CoV-2, we can also see if any new variants are able to evade the protection provided by previous infections or vaccines. This shows us if people become infected a second time and, if so, by which variant. If the same variant is constantly able to infect people who are fully vaccinated, or have had a previous confirmed infection, then it would be classed as an escape variant.

Presently, genomic surveillance for SARS-CoV-2 is patchy around the world, with some countries able to carry out a lot of it, and others with fewer facilities. This means there may be many more variants than we presently realize. While the pandemic has showcased the power and potential of genomic surveillance as a tool, it has also displayed its biggest weakness. It is only as good as the number of samples analysed and the width of the area surveyed.

2. Ebola

90% of people infected with the Ebola virus will die within days.

Ebola is a deadly disease caused by the Ebola virus. It spreads rapidly through contact with body fluids, and up to 90% of people infected with the virus will die within days. It springs up sporadically across Africa with little warning. Genomic surveillance has proved of great help in tracking and halting outbreaks. Knowing how closely related new cases of Ebola were to those already sequenced, helped to determine patterns of transmission.

If the viral genome from a new patient was very similar to others, then that patient was probably exposed in a known outbreak, or from a common source. If, however, the viral genome showed many differences, it indicated a new outbreak. This was especially important when someone fell ill in an area outside of the main epidemic. Were they the first in a new outbreak? Or could their virus be traced back to the main epidemic?

Additionally, the genomic surveillance performed during the 2013-16 West African Ebola epidemic became unexpectedly useful in 2021, when a new cluster of cases emerged in Guinea. Their genetic sequence? Almost identical to that of the earlier epidemic. This has led to speculation the Ebola virus lay dormant in a survivor for several years before becoming infectious once more, opening up new areas of research on how the virus behaves.

3. MRSA

Genomic surveillance can also provide vital information for outbreaks on a far smaller scale.

Epidemics and pandemics aren’t the only areas where genomic surveillance is useful. It can provide vital information for outbreaks on a far smaller scale, as one English hospital found out.

During an outbreak of the superbug MRSA (Methicillin-Resistant Staphylococcus aureus) in the maternity unit, sequencing determined that most cases came from a common source. Despite proper actions to deep-clean the wards and implement changes, a second outbreak occurred – and this was linked to the first by sequencing.

This led to further investigations, and 3 members of staff were found to be colonized with symptomless MRSA. Sequencing data linked the genome from one of them to the MRSA found on the babies. Treating and decolonising the affected staff member broke the transmission pathway, ending the cycle of outbreaks and making the maternity ward safe again. Learn more about this story in ‘Tracking superbugs’.

What about the future? As we become able to sequence genomes faster and cheaper than ever before, the potential for genomic surveillance only grows. The greater the number of genomes we can sequence and compare, the more closely we will be able to monitor outbreaks of disease and understand how they spread, mutate and respond to medicines or vaccines.

Article written by Valerie Vancollie, Scientist and Product Lead for the COVID-19 Genomic Surveillance team” at the Wellcome Sanger Institute.