Single-cell multi-omics analysis of the immune response in COVID-19

Publication: Nature

Emily Stephenson, Gary Reynolds, Rachel A. Botting, Fernando J. Calero-Nieto, Michael D. Morgan, Zewen Kelvin Tuong, Karsten Bach, Waradon Sungnak, Kaylee B. Worlock, Masahiro Yoshida, Natsuhiko Kumasaka, Katarzyna Kania, Justin Engelbert, Bayanne Olabi, Jarmila Stremenova Spegarova, Nicola K. Wilson, Nicole Mende, Laura Jardine, Louis C. S. Gardner, Issac Goh, Dave Horsfall, Jim McGrath, Simone Webb, Michael W. Mather, Rik G. H. Lindeboom, Emma Dann, Ni Huang, Krzysztof Polanski, Elena Prigmore, Florian Gothe, Jonathan Scott, Rebecca P. Payne, Kenneth F. Baker, Aidan T. Hanrath, Ina C. D. Schim van der Loeff, Andrew S. Barr, Amada Sanchez-Gonzalez, Laura Bergamaschi, Federica Mescia, Josephine L. Barnes, Eliz Kilich, Angus de Wilton, Anita Saigal, Aarash Saleh, Sam M. Janes, Claire M. Smith, Nusayhah Gopee, Caroline Wilson, Paul Coupland, Jonathan M. Coxhead, Vladimir Yu Kiselev, Stijn van Dongen, Jaume Bacardit, Hamish W. King, Anthony J. Rostron, A. John Simpson, Sophie Hambleton, Elisa Laurenti, Paul A. Lyons, Kerstin B. Meyer, Marko Z. Nikolić, Christopher J. A. Duncan, Kenneth G. C. Smith, Sarah A. Teichmann, Menna R. Clatworthy, John C. Marioni, Berthold Göttgens & Muzlifah Haniffa

20 April 2020


Summary

A UK-wide study has identified differences in people’s immune responses to COVID-19, depending on whether they have no symptoms or more serious reactions to the virus. Read the full story

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Development and validation of a dynamic 48-hour in-hospital prognostic risk stratification for COVID-19 in a UK teaching hospital: a retrospective cohort study

Publication: MedRxiV

Martin Wiegand, Sarah L. Cowan, Claire S. Waddington, David J. Halsall,  Victoria L. Keevil,  Brian D. M. Tom, Vince Taylor,  Effrossyni Gkrania-Klotsas, Jacobus Preller,  Robert J. B. Goudie

18 February 2021


Summary

Researchers propose a prognostic dynamic risk stratification for 48-hour in-hospital mortality in patients with COVID-19, using demographics and routinely-collected observations and laboratory tests: age, Clinical Frailty Scale score, heart rate, respiratory rate

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Single-dose BNT162b2 vaccine protects against asymptomatic SARS-CoV-2 infection

Publication: Authorea

Nick K Jones, Lucy Rivett, Chris Workman, Mark Ferris, Ashley Shaw, Paul J LehnerRob HowesGiles WrightNicholas J Matheson, Michael P Weekes

24 February 2020


Summary:

New data from Addenbrooke’s hospital in Cambridge suggests a significant drop in the spread of Covid-19 amongst staff following vaccination. It’s one of the first indications from UK scientists that the Pfizer vaccine reduces the transmission of SARS-CoV-2, the virus that causes Covid-19, as well as protecting people from getting ill. Read the full story.

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Genomic epidemiology of COVID-19 in care homes in the East of England

Publication: ELife

William L Hamilton, Dinesh Aggarwal, Charlotte Houldcroft, Ben Warne, Luke Meredith, Myra Hosmillo, Aminu Jahun,  Laura Caller, Sarah Caddy, Fahad Khokhar, Anna Yakovleva, Grant Hall, Theresa Feltwell, Malte Pinckert, Iliana Georgana, Yasmin Chaudhry, Nicholas Brown, Ewan Harrison,  Gordon Dougan, Sharon Peacock,   Ian Goodfellow,  M. Estee Torok

16 February 2021


Summary:

Approximately 70% of residents in the genomic analysis were admitted to hospital during the study period, providing extensive opportunities for transmission between care homes and hospitals. Limiting viral transmission between care home residents should be a key target for infection control to reduce COVID-19 mortality in this population

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Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections

Publication: OSF Preprints

Christopher J. R. Illingworth,  William L. Hamilton,  Ben Warne, Matthew Routledge, Ashley Popay, Chris Jackson, Tom Fieldman, Luke Meredith, Charlotte J. Houldcroft, Myra Hosmillo, Aminu Jahun, Laura Caller, Sarah Caddy, Anna Yakovleva, Grant Hall, Fahad A. Khokhar, Theresa Feltwell, Malte L. Pinckert, Iliana Georgana, Yasmin Chaudhry, Dominic Sparkes, Lucy Rivett, Nick K. Jones, Sushmita Sridhar, Sally Forrest, Tom Dymond, Kayleigh Grainger, Chris Workman, Effrossyni Gkrania-Klotsas, Nicholas M. Brown, Michael P. Weekes, Stephen Baker, Sharon J. Peacock, Ian Goodfellow, Theodore Gouliouris, Daniela De Angelis, M. Estée Török

15 February 2021


Summary

The SARS-CoV-2 virus has been noted both for its rapid spread, but also for the heterogeneity of transmission, with incidences noted of superspreading behaviour.

Researchers applied a novel network reconstruction algorithm to find patterns of viral transmission occurring between patients and health care workers.

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A2B-COVID: A method for evaluating potential SARS-CoV-2 transmission events

Publication: MedRxiV

Christopher J. R. Illingworth, ProfileWilliam L. Hamilton,  ProfileChris Jackson, Ashley Popay, Luke Meredith, Charlotte J. Houldcroft, Myra Hosmillo, Aminu Jahun, Matthew Routledge, Ben Warne, Laura Caller, Sarah Caddy, Anna Yakovleva, Grant Hall, Fahad A. Khokhar, Theresa Feltwell, Malte L. Pinckert, Iliana Georgana, Yasmin Chaudhry, Martin Curran, Surendra Parmar, Dominic Sparkes, Lucy Rivett, Nick K. Jones, Sushmita Sridhar, Sally Forrest, Tom Dymond, Kayleigh Grainger, Chris Workman, Effrossyni Gkrania-Klotsas, Nicholas M. Brown, Michael P. Weekes, Stephen Baker, Sharon J. Peacock, Theodore Gouliouris, Ian Goodfellow, Daniela de Angelis, M. Estée Török

27 October 2020


Summary:

A new software tool will help doctors identify where cases of COVID-19 were caused by transmission within a hospital, helping them to prevent further spread of the disease.

The new software package, A2B-Covid, combines knowledge about infection dynamics, data describing the movements of individuals, and genome sequence data to assess whether or not coronavirus has been transmitted between people in the hospital environment.

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Early immune pathology and persistent dysregulation characterise severe COVID-19

Publication: Medrxiv

Laura BergamaschiFederica MesciaLorinda TurnerAimee HansonPrasanti KotagiriBenjamin J. DunmoreHelene RuffieuxAloka De SaOisin HuhnMark R. WillsStephen BakerRainer DoffingerGordon DouganAnne ElmerIan G Goodfellow, Ravindra K. GuptaMyra HosmilloKelvin HunterNathalie KingstonPaul J. LehnerNicholas J. MathesonJeremy K. NicholsonAnna M. PetrunkinaSylvia RichardsonCaroline Saunders, James E.D. ThaventhiranErik J. M. ToonenMichael P. WeekesMark ToshnerChristoph HessJohn R. BradleyPaul A. LyonsKenneth G.C. Smith

15 January 2021


Summary

It may be possible to predict which patients will go on to develop severe or long-term COVID symptoms (sometimes known as ‘long COVID’).

Cambridge researchers looked at blood samples taken regularly over three months from more than 200 people, ranging from COVID-19 patients who were severely ill and needed ventilation to asymptomatic NHS staff who had tested positive for the virus but showed no symptoms.

The immune systems in patients who were the sickest showed early evidence of an abnormal inflammatory response, leading to a flood of immune cells which damaged healthy cells as well as the virus. Finding inflammation early in the blood samples and at the point of diagnosis could help doctors to identify and predict patients who will develop severe COVID-19.

The results have been released as a pre-print, read the full news story.

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Combined point of care nucleic acid and antibody testing for SARS-CoV-2 following emergence of D614G Spike Variant

Publication: Cell Reports Medicine

Petra Mlcochova, Dami Collier, Allyson Ritchie, Sonny M. Assennato, Myra Hosmillo, Neha Goel, Bo Meng, Krishna Chatterjee, Vivien Mendoza, Nigel Temperton, Leo Kiss, Leo C. James, Katarzyna A. Ciazynska, Xiaoli Xiong, John AG. Briggs, James A. Nathan, Federica Mescia, Laura Bergamaschi, Hongyi Zhang, Petros Barmpounakis, Nikos Demeris, Richard Skells, Paul A. Lyons, John Bradley, Steven Baker, Jean Pierre Allain, Kenneth GC. Smith, Rachel Bousfield, Michael Wilson, Dominic Sparkes, Glenn Amoroso, Effrosyni Gkrania-Klotsas, Susie Hardwick, Adrian Boyle, Ian Goodfellow, Ravindra K. Gupta 

1 September 2020


Summary

Testing patients for COVID-19 as soon as they arrive at hospital is essential to obtain a diagnosis and to make sure they receive the correct treatment as soon as possible.

In a recent Cambridge study, the use of the SAMBA II test reduced the amount of time patients spent on holding wards. Now Cambridge researchers wanted to go further to create a ‘gold-standard’ method of testing.

The most common form of testing is taking a swab of the nose and throat (known as PCR) to see if the virus is present. However, it can take as long as 14 days for an individual to show symptoms of COVID-19, by which time the virus may have moved from the nose and throat and into the lungs and other tissues and organs, making it harder to detect via a swab test. Another way to detect the virus is looking for antibodies (from blood samples) in individuals.

Cambridge researchers combined the two tests – PCR and the antibody test – to help identify who may have the virus. They found combining both tests was more effective to identify patients who had Covid than those who had just one of the tests. Read the full news story.

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Rapid point of care nucleic acid testing for SARS-CoV-2 in hospitalised patients: a clinical trial and implementation study

Publication: medRxiv

Dami A Collier, Sonny M Assennato, Nyarie Sithole, Katherine Sharrocks, Allyson Ritchie, Pooja Ravji, Matt Routledge, Dominic Sparkes, Jordan Skittrall, Ben Warne, Anna Smielewska, Isobel Ramsey, Neha Goel, Martin Curran, David Enoch, Rhys Tassell, Michelle Lineham, Devan Vaghela, Clare Leong, Hoi Ping Mok, John Bradley, Kenneth Gc Smith, Vivien Mendoza, Nikos Demiris, Martin Besser, Gordon Dougan, Paul J Lehner, Hongyi Zhang, Claire Waddington, Helen Lee,  Ravindra K Gupta

03 June 2020


Summary:

SAMBA II machines were deployed in the ED and holding wards at Addenbrooke’s hospital to help detect COVID-19 in patients as part of a research trial called COVIDx.

Researchers investigated whether using the new machines could accurately provide a faster diagnosis than standard testing practices and review how it would affect patient waiting times.

After collecting nose and throat swabs from over 140 patients, the samples were processed using the SAMBA II machine. Researchers found they were able to provide an accurate diagnostic result within 90 minutes, compared to the standard 24-48-hour lab waiting time. Read the full story.

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Whole-genome sequencing of a sporadic primary immunodeficiency cohort

Publication: Nature

James E. D. Thaventhiran, Hana Lango Allen, Kenneth G. C. Smith 

06 May 2020


Summary:

Cambridge researchers sequenced the entire genetic code of 974 people with PID. The team were able to identify variations in genes already known to cause PID. To help identify genetic causes for the remaining participants and other patients with PID, the team used a statistical program known as BeviMed. BeviMed can be used to predict genes that may cause PID, by comparing the genomes of cases and controls. Using this technique, the team were able to identify new genes that cause PID. Full press release here

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