Page 14 - Periodic ISSUE 8

Se quencing

SARS-CoV-2 RNA

Divya Popat (Jesus, 2017), DPhil student in the MinION device in several outbreak situations in the
Vallance group, reports on how Oxford Nanopore past including Lassa Fever, Swine Flu, Yellow Fever,
Technologies Ltd, a spin-out company from Zika and Ebola . This experience supported the
[4]
[3]
the Department of Chemistry, has enabled the rapid deployment of MinION devices for the current
surveillance of the RNA sequence of SARS-CoV-2 outbreak. Oxford Nanopore Technologies is supplying
Tarick El-Baba and Corinne Lutomski, members of the Robinson group, performing key COVID-19 research
on their favourite machines. A husband and wife team – no masks necessary! to understand its transmission and evolution. the devices to countries all around the world to enable
rapid, large scale sequencing analysis of samples from
Oxford Nanopore Technologies was founded in 2005 patients testing positive for COVID-19.
by Hagan Bayley, Professor of Chemical Biology in the
techniques to consider the role that the SARS-CoV-2 allow mutations in the virus to be characterised. This is Department of Chemistry. The company specialises in
“spike glycoprotein” may play in coronavirus infections. an important element in the study of the epidemiology the nanopore sequencing of DNA/RNA and focuses on The surveillance of the rapidly mutating sequence of
Similar protein features are known to play a role in HIV, of this new virus. increasing the ease of use of the nanopore sequencing SARS-CoV-2 RNA can help to provide information
Ebola, and SARS-CoV-1 (responsible for the 2002– Reference: Wu, Q. et al. (2020, doi.org/ technique and automation. The company’s first product about the degree to which it is related to other viruses,
2004 SARS outbreak), but it is currently unknown how 10.1101/2020.06.01.127019). was the ‘MinION’, the only portable, real-time device the mode and speed of evolution, geographical spread
they work in the SARS-CoV-2 protein that causes Oxford Nanopore – a spinout company from the for direct nanopore sequencing of DNA and RNA. In and adaptation to human hosts. This information can
COVID-19. be used to assist in epidemiological investigations.
Department of Chemistry (see page 15), that also this device, ionic currents are passed through up to Fast generation and sharing of data can lead to a
works with Professor Brown’s research group – has 512 protein nanopores; characteristic modulations of better public health response as well as supporting
References: Young, G., and Hundt, N. et al., Science 360 (2018)
6387 423–427 (doi.org/10.1126/science.aar5839), Soltermann, developed the LamPORE test for COVID-19. This the currents are measured as the nucleic acids pass vaccine development and diagnostic capabilities. For
F. et al., Angew. Chem. Int. Ed. 59 (2020) 27 10774–10779 (doi. diagnostic tool can detect the presence of the SARS- through the nanopores, enabling their sequences to these reasons, the rapid nanopore sequencing MinION
org/10.1002/anie.202001578)”.
CoV-2 virus in a patient’s sample within 90 minutes. be read. The MinION has the capacity to read 7-12 devices have been of paramount importance in the
The UK Department of Health and Social Care has million RNA sequences within hours and stream the data monitoring of COVID-19.
Working to change the landscape of ordered hundreds of thousands of these tests for rapid directly to a computer in real-time, enabling the rapid
COVID-19 testing
testing in settings like screening healthcare workers. identification of viral pathogens. Nanopore technology is also applicable to the detection
Tom Brown, postdoctoral researcher Lapatrada and identification of small molecules
Taemaitree, and spin-out company ATDBio are working As well as detecting the COVID-19 virus, a further test The company sent hundreds of their handheld ‘MinION’ (e.g. pharmaceuticals) and reactive molecules
with several research groups, companies and NHS using the same technology is being developed that devices to China’s Centre of Disease Control and (e.g. chemical warfare
Trusts to make chemically modified synthetic DNA for will be able to detect not only coronavirus but more Prevention, which allowed the first RNA sequences of agents), as well as
use in improved COVID-19 point-of-care diagnostic common winter respiratory illnesses such as influenza. SARS-CoV-2 to be recorded. additional biological
testing and high-throughput screening. Widespread Being able to distinguish between these diseases will Their technology was key to identifying the strain macromolecules
testing will be increasingly important in determining the be vital as we approach the winter flu season with the of the coronavirus when it first appeared and including proteins and
true scale of the spread of the COVID-19 pandemic by coronavirus pandemic still ongoing. understanding its transmission and evolution. The their post-translationally
[1]
identifying both infected individuals and asymptomatic Thank you MinION device was also used in work published in modified forms, all of which
carriers. The Department has been beginning to re-open over late January 2020 which indicated person-to-person are important in medicine.
the past weeks and months, and special thanks should transmission of the virus through air travel.
[2]
These tests are used in several different contexts go to all the buildings and facilities staff who ensured The scientific community had previously used the
including the screening of healthcare workers in that the labs remained safely operational for crucial
hospitals and care homes, surveillance of travellers at work during the lockdown period, and who have
airports, and to determine the main mechanisms of worked tirelessly over the past months to help make a References:
[1] N. Zhu et al., N Eng J Med, 2020, 382;8, 727-733
COVID-19 infection. The tests are also designed to safe working environment as people return to work. [2] J. F. Chan, The Lancet, 2020, 395, 514-523
[3] N. Faria et al., Nature, 2017, 546, 406-410
[4] J. Quick et al., Nature, 2016, 530, 228- 232.
MinION device from Oxford Nanopore.

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