8 Feb 2022

“Epidemiology and genomics go hand-in-hand”: How genomics is helping us to understand transmission of COVID-19 in universities.

Universities across the world have been significantly impacted by the COVID-19 pandemic. We spoke to Dr Dinesh Aggarwal, an Infectious Diseases and Microbiology Specialist Trainee working at COG-UK and the UK Health Security Agency (UKHSA), and a Wellcome PhD Clinical Fellow at the University of Cambridge, who has dedicated his research to better understanding COVID-19 transmission, to help devise more effective infection control measures.

“Each COVID-19 infection that someone carries has a genomic signature. When one person passes their infection onto another person, they pass on this signature,” Dr Dinesh Aggarwal tells us. “We can use this to look at the signature between individuals to understand how SARS-CoV-2 transmission occurs.”

In the early days of the pandemic, concerns about how virus transmission would unfold amongst unvaccinated university students, and whether infections amongst students would impact the surrounding (and potentially more vulnerable) community rippled throughout campuses. Dinesh, with his colleagues at the University of Cambridge, COG-UK, and the UKHSA, made it his mission to learn more. “It was imperative to understand the transmission dynamics as this was critical to the implementation of effective infection control measures, as well as minimising disruption to teaching, research, and the mental health of students and staff.”

The University of Cambridge was a prime setting to conduct this study, where students already been identified as having COVID-19 through student screening programmes and its close links to the COVID-19 Genomics UK Consortium (COG-UK).

“The university setting was perfect for a genomic epidemiological study because the screening programme consistently had high levels of student engagement, and it was a relatively closed environment with mixing of unvaccinated students.” The collaboration of multi-disciplinary world-class organisations meant findings could be efficiently communicated to the university, public health organisations, and research community.

By using genomic sequencing, Dinesh was able to reveal an unusually large cluster of infections amongst students, with reassuringly few community cases involved. Drivers for transmission were often linked back to the university where shared accommodation, courses, and academic years were important considerations for development of transmission clusters. Consequently, these have become an important touchstone for targeted infection control measures, such as enhanced asymptomatic screening within accommodation blocks to mitigate further spread.

Dinesh believes that forging strong links between the local health protection team, UKHSA (formerly Public Health England), local hospitals and the universities, to enable gathering of detailed epidemiological and contact tracing information with genomics is crucial in helping to paint a clearer picture of COVID-19 transmission dynamics, and therefore how to effectively manage it.

According to Dinesh, one of the most important takeaways from his study is the relevance of combining detailed epidemiological data with genomic sequences. “Genomics has been vital in response to COVID-19,” says Dinesh. “By doing genomics without epidemiology, or doing epidemiology without genomics, you lose a lot of information”. This requires close collaboration between the people who provide the epidemiological data, often public health bodies, and the people who facilitate sequencing, such as COG-UK. “As in many situations, when you work together and share knowledge, you end up in a much stronger position”.

Read the full publication and results HERE.


COVID-19 Genomics UK (COG-UK)

The COVID-19 Genomics UK (COG-UK) consortium works in partnership to harness the power of SARS-CoV-2 genomics in the fight against COVID-19.

Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative collaboration of NHS organisations, the four public health agencies of the UK, the Wellcome Sanger Institute and sixteen academic partners. A full list of collaborators can be found here.

The COVID-19 pandemic, caused by SARS-CoV-2, represents a major threat to health. The COG-UK consortium was formed in March 2020 to deliver SARS-CoV-2 genome sequencing and analysis to inform public health policy and to support the establishment of a national pathogen sequencing service, with sequence data now predominantly generated by the Wellcome Sanger Institute and the Public Health Agencies.

SARS-CoV-2 genome sequencing and analysis plays a key role in the COVID-19 public health response by enabling the identification, tracking and analysis of variants of concern, and by informing the design of vaccines and therapeutics. COG-UK works collaboratively to deliver world-class research on pathogen sequencing and analysis, maximise the value of genomic data by ensuring fair access and data linkage, and provide a training programme to enable equity in global sequencing.