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23 April, 2020 - 09:57 By Kate Sweeney

Sanger Institute adds muscle to coronavirus campaign

Global genome sequencing giant Wellcome Sanger Institute in Cambridge has thrown its considerable muscle in terms of staff, resources and know-how into the campaign to halt coronavirus.

Significant projects and collaborations have been initiated, from investigating the cellular receptors the virus uses to invade our bodies, to understanding how the immune system may play a role in disease severity. 

Sanger is also working with public health laboratories, Institutes and Universities across the UK to sequence SARS-CoV-2 virus genomes to trace its spread.

Some laboratory staff are joining national testing centres and others are volunteering in their local communities.

Sanger says its COVID-19 sequencing effort is now ramping up, with thousands of SARS-CoV-2 virus samples being sequenced and data returned for analysis. 

The work will help track the spread of the coronavirus – within regions and across the country. It will allow researchers to monitor for any new strains, and help with public health planning and clinical decision making.

Researchers in the Sanger Institute Cellular Genetics programme, led by Dr Sarah Teichmann, have meanwhile analysed multiple Human Cell Atlas (HCA) datasets to investigate where COVID-19 may enter the body.

These vast datasets are cellular maps of the body, built using single cell RNA sequencing to show which of our cells are using which of our 20,000 genes. The data can reveal which proteins are active in any given cell, and are available online at www.covid19cellatlas.org

The researchers are probing for individual cells that have both of two key virus entry proteins present; ACE2 and TMPRSS2. They are looking in cells of the airways (lungs, throat and nose) as well as eyes, intestines and a range of other tissues. 

Cells where these proteins are present are likely to be the initial infection route for the virus. Identifying the type and location of these cells will help researchers understand exactly how the virus is transmitted between people and spreads.

A consortium of researchers from the Cellular Genetics Programme are using cell atlas technologies to analyse COVID-19 patient samples, including paediatric and adult patients, young and old adults, mild and severely affected patients as well as people with pre-existing primary immunodeficiencies. 

This coherent effort to analyse the blood and tissue response to infection in depth includes analysis of the placentas of infected mothers by Dr Roser Vento, to gain insight into possible pathways of transmission from mothers to babies.


Dr Kerstin Meyer. Image courtesy – Wellcome Sanger Institute

Dr Kerstin Meyer, a Principal Staff Scientist at the Sanger Institute, is working with Dr Marko Nikolic at University College London to investigate why children are relatively unaffected by the SARS-CoV-2 virus. 

They are looking at the presence of the viral entry genes ACE2 and TMPRSS2 in cells from the nose. They are also studying the immune response to the virus; they will identify and characterise the cell types that are responding to infection, and follow these over time.

The team will use single cell transcriptomics, combined with protein profiling (CITE-seq), as well as serum analysis and genotyping, to study children infected with SARS-CoV-2 with both mild and severe symptoms. 

Their study design is aligned with a similar study in adults, led by Professor Menna Clatworthy and Professor Muzlifah Haniffa, allowing them to study and contrast samples from patients of different ages.

Understanding the molecular changes that drive disease severity could help understand how best to treat patients, as well as assist in the development and evaluation of safe vaccines. Other research projects are either underway or starting up across the Institute.

Sanger has shared available personal protective equipment (PPE) with local NHS services and is exploring more ways that it can help. Viral extraction reagents that it had ordered have been diverted to national testing centres.

In response to the Government call for experienced laboratory staff to support national testing centres, Sanger is supporting any staff who wish to do this on secondment. Staff will continue to be paid by the Institute rather than the testing centres.

For those wishing to help in other ways volunteering leave has been extended for 2020 for COVID-19 related activity.

The majority of staff are working from home and  campus access is being closely managed to keep numbers on site to an absolute minimum. But for key workers on site – those working on COVID-19 research projects, looking after animals and staff from the catering, security, cleaning and facilities teams – Sanger has introduced additional measures to keep them safe.

As well as following government guidelines on hand washing and staying two metres apart, the institute is spreading out across campus to make use of the space it has available. The cafe, for example, has been reconfigured to allow social distancing. It is allocating larger rooms for working areas and making use of remote-working technology even within rooms and buildings.

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