Scalable and robust SARS-CoV-2 testing in an academic center

Aitken, J D; Ambrose, Karen; Barrell, Sam; Beale, Rupert; Bineva-Todd, Ganka; Biswas, Dhruva; Byrne, Richard; Caidan, Simon; Cherepanov, Peter; Churchward, Laura; Clark, Graham; Crawford, Margaret; Cubitt, Laura; Dearing, Vicky; Earl, Christopher; Edwards, A.; Ekin, Chris; Fidanis, Efthymios; Gaiba, Alessandra; Gamblin, S.J.; Gandhi, Sonia; Goldman, Jacki; Goldstone, Robert; Grant, Paul; Greco, Maria; Heaney, Judith; Hindmarsh, Steve; Houlihan, Catherine; Howell, Michael; Hubank, Michael; Hughes, Deborah; Instrell, Rachael; Jackson, Deborah J.; Jamal‐Hanjani, Mariam; Jiang, Ming; Johnson, Mark; Jones, Leigh; Kanu, Nnennaya; Kassiotis, George; Kirk, Stuart A.; Kjær, Svend; Levett, Andrew; Levett, Lisa J.; Levi, Marcel; Lu, Wei-Ting; MacRae, James I.; Matthews, J. B.; McCoy, Laura E; Moore, Catherine; Moore, David

doi:10.1038/s41587-020-0588-y

Cited by 36 publications

(31 citation statements)

References 8 publications

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“…SARS-CoV-2 nucleic acids were detected in nasopharyngeal swabs from hospitalised patients by a diagnostic RT-qPCR assay using custom primers and probes 16 , Assays were run by Health Services Laboratories (HSL), London, UK. Diagnostic RT-qPCR assays for SARS-CoV-2 infection in health care workers was run at the Francis Crick Institute, as previously described 17 . SARS-CoV-2 RNA-positive samples (RNA amplified by Aptima Hologic) were subjected to real-time whole-genome sequencing at the UCLH Advanced Pathogen Diagnostics Unit.…”

Section: Methodsmentioning

confidence: 99%

Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains

Faulkner

et al. 2021

Preprint

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We examined the immunogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant B.1.1.7 that arose in the United Kingdom and spread globally. Antibodies elicited by B.1.1.7 infection exhibited significantly reduced recognition and neutralisation of parental strains or of the South Africa B.1.351 variant, than of the infecting variant. The drop in cross-reactivity was more pronounced following B.1.1.7 than parental strain infection, indicating asymmetric heterotypic immunity induced by SARS-CoV-2 variants.

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Section: Methodsmentioning

confidence: 99%

Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains

Faulkner

et al. 2021

Preprint

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“…SARS-CoV-2 RT-PCR was performed from oronasopharyngeal swabs within the Crick Covid19 testing pipeline (Aitken et al, 2020). The complete standard operating procedure is available on the Covid19 consortium website: https://www.crick.ac.uk/research/covid-19/covid19-consortium.…”

Section: Methods Detailsmentioning

confidence: 99%

“…We classified severity of COVID-19 according to the WHO (World Health Organisation) clinical progression scale (Aitken et al, 2020). Uninfected: uninfected, no viral RNA detected - 0; Mild (ambulatory): asymptomatic, viral RNA detected - 1 / symptomatic, independent - 2 / symptomatic, assistance needed - 3; Moderate (hospitalised): no oxygen therapy (If hospitalised for isolation only, record status as for ambulatory patient) - 4 / oxygen by mask or nasal prongs - 5; Severe (hospitalised): oxygen by non-invasive ventilation or high flow – 6 / intubation and mechanical ventilation, pO 2 /FiO 2 ≥ 150 or SpO 2 /FiO 2 ≥ 200 - 7 / mechanical ventilation, pO 2 /FiO 2 < 150 (SpO 2 /FiO 2 < 200) or vasopressors - 8 / mechanical ventilation, pO 2 /FiO 2 < 150 and vasopressors, dialysis, or extracorporeal membrane oxygenation - 9; Dead - 10.…”

Section: Methods Detailsmentioning

confidence: 99%

Adaptive immunity to SARS-CoV-2 in cancer patients: The CAPTURE study

Fendler¹,

Au²,

Boos³

et al. 2020

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SUMMARYThere is a pressing need to characterise the nature, extent and duration of immune response to SARS-CoV-2 in cancer patients and inform risk-reduction strategies and preserve cancer outcomes. CAPTURE is a prospective, longitudinal cohort study of cancer patients and healthcare workers (HCWs) integrating longitudinal immune profiling and clinical annotation. We evaluated 529 blood samples and 1051 oronasopharyngeal swabs from 144 cancer patients and 73 HCWs and correlated with >200 clinical variables. In patients with solid cancers and HCWs, S1-reactive and neutralising antibodies to SARS-CoV-2 were detectable five months post-infection. SARS-CoV-2-specific T-cell responses were detected, and CD4+ T-cell responses correlated with S1 antibody levels. Patients with haematological malignancies had impaired but partially compensated immune responses. Overall, cancer stage, disease status, and therapies did not correlate with immune responses. These findings have implications for understanding individual risks and potential effectiveness of SARS-CoV-2 vaccination in the cancer population.

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“…In early May 2020 the Crick prepared to support testing during the pandemic by establishing the Crick COVID‐19 Consortium that successfully developed a diagnostic polymerase chain reaction (PCR) pipeline (1,2). The Flow STP was engaged to support COVID‐19 research at the Crick, helping to develop novel flow cytometry assays utilizing SARS‐CoV‐2 virus‐specific proteins.…”

Section: Challenge Approachmentioning

confidence: 99%

Adapting to the Coronavirus Pandemic: Building and Incorporating a Diagnostic Pipeline in a Shared Resource Laboratory

et al. 2020

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AT the beginning of February 2020, the COVID-19 outbreak in the UK gathered pace and it seemed highly probable that the United Kingdom would follow similar lockdown restriction policies seen in other European countries. The Crick's Flow Cytometry Science Technology Platform (Flow STP) helped prepare scientists to finish current experiments and store experimental material during lockdown to enable an efficient restart upon the eventual lifting of the restrictions. During this time safety measures were introduced into the Flow STP, including social distancing, that directly reduced the number of instruments available for use. When lockdown was announced in the United Kingdom on the 23rd March 2020 the total number of staff allowed into the Crick was reduced to a core group of key workers. The Flow STP was given key worker status and operated to provide flow cytometry to Crick scientists whose sole focus was now COVID-19. In the lead-up to lockdown communications were sent to scientists to highlight the possible implications of the pandemic on Flow STP operation. There were significant changes in the way the Flow STP operated due to the challenges faced outlined in Table 1. In early May 2020 the Crick prepared to support testing during the pandemic by establishing the Crick COVID-19 Consortium that successfully developed a diagnostic polymerase chain reaction (PCR) pipeline (1,2). The Flow STP was engaged to support COVID-19 research at the Crick, helping to develop novel flow cytometry assays utilizing SARS-CoV-2 virus-specific proteins. The STP was tasked with building a new clinical diagnostic lab and running a novel enzymelinked immunosorbent assay (ELISA) that had been developed for detecting antibodies against the S1 spike of the SARS-CoV-2 virus. The key processes required are outlined in Figure 1.

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Scalable and robust SARS-CoV-2 testing in an academic center

Cited by 36 publications

References 8 publications

Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains

Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains

Adaptive immunity to SARS-CoV-2 in cancer patients: The CAPTURE study

Adapting to the Coronavirus Pandemic: Building and Incorporating a Diagnostic Pipeline in a Shared Resource Laboratory

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