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Article ; Online: The complexities of SARS-CoV-2 serology.

Houlihan, Catherine F / Beale, Rupert

2020 Volume 20, Issue 12, Page(s) 1350–1351

MeSH term(s)	Adaptive Immunity ; Antibodies, Neutralizing/blood ; Antibodies, Viral/blood ; Asymptomatic Infections ; COVID-19/blood ; COVID-19/diagnosis ; COVID-19/immunology ; COVID-19 Serological Testing/methods ; COVID-19 Serological Testing/standards ; Coronavirus Nucleocapsid Proteins/immunology ; Humans ; Phosphoproteins/immunology ; Prognosis ; SARS-CoV-2/immunology ; SARS-CoV-2/isolation & purification ; Sensitivity and Specificity ; Spike Glycoprotein, Coronavirus/immunology
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Coronavirus Nucleocapsid Proteins ; Phosphoproteins ; Spike Glycoprotein, Coronavirus ; nucleocapsid phosphoprotein, SARS-CoV-2 ; spike protein, SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-09-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2061641-7
ISSN	1474-4457 ; 1473-3099
ISSN (online)	1474-4457
ISSN	1473-3099
DOI	10.1016/S1473-3099(20)30699-X
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Article ; Online: Immunity to SARS-CoV-2 variants of concern.

Altmann, Daniel M / Boyton, Rosemary J / Beale, Rupert

Science (New York, N.Y.)

2021 Volume 371, Issue 6534, Page(s) 1103–1104

MeSH term(s)	BNT162 Vaccine ; COVID-19 ; COVID-19 Vaccines ; Humans ; SARS-CoV-2 ; Vaccines
Chemical Substances	COVID-19 Vaccines ; Vaccines ; BNT162 Vaccine (N38TVC63NU)
Language	English
Publishing date	2021-02-08
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abg7404
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Zs.MG 77: Show issues

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Article: The complexities of SARS-CoV-2 serology

Houlihan, Catherine F / Beale, Rupert

Lancet infect. dis

Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #786430
Database	COVID19

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Article ; Online: The complexities of SARS-CoV-2 serology

Houlihan, Catherine F / Beale, Rupert

The Lancet Infectious Diseases ; ISSN 1473-3099

2020

Keywords	Infectious Diseases ; covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
DOI	10.1016/s1473-3099(20)30699-x
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Coombs-positive Paroxysmal Nocturnal Haemoglobinuria.

Kalam, Sabrina / Beale, Rupert / Hughes, Derralynn / Kulasekararaj, Austin / Srirangalingam, Umasuthan

Oxford medical case reports

2020 Volume 2020, Issue 3, Page(s) omz125

Abstract: Autoimmune haemolytic anaemia (AIHA) and paroxysmal nocturnal haemoglobinuria (PNH) are two distinct causes of haemolytic anaemia. They have different mechanisms that underpin their pathogenesis and, therefore, require different treatment strategies. The ...

Abstract	Autoimmune haemolytic anaemia (AIHA) and paroxysmal nocturnal haemoglobinuria (PNH) are two distinct causes of haemolytic anaemia. They have different mechanisms that underpin their pathogenesis and, therefore, require different treatment strategies. The direct antiglobulin test (DAT) or Coombs test is positive in cases of immune-mediated haemolytic anaemia and, thus, is positive in AIHA but negative in PNH. We report a case of a woman presenting with a haemolytic anaemia who was found to have concomitant evidence of AIHA and PNH. The case highlights the importance of carrying out a comprehensive haemolysis work-up in patients who present with haemolytic anaemia.
Language	English
Publishing date	2020-03-30
Publishing country	England
Document type	Case Reports
ZDB-ID	2766251-2
ISSN	2053-8855
ISSN	2053-8855
DOI	10.1093/omcr/omz125
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Article ; Online: Infecting human hematopoietic stem and progenitor cells with SARS-CoV-2.

Huerga Encabo, Hector / Ulferts, Rachel / Sharma, Aneesh / Beale, Rupert / Bonnet, Dominique

STAR protocols

2021 Volume 2, Issue 4, Page(s) 100903

Abstract: Determining how hematopoietic stem and progenitor cells (HSPCs) can be infected by viruses is necessary to understand and predict how the immune system will drive the host response. We present here a protocol to analyze the capacity of SARS-CoV-2 to ... ...

Abstract	Determining how hematopoietic stem and progenitor cells (HSPCs) can be infected by viruses is necessary to understand and predict how the immune system will drive the host response. We present here a protocol to analyze the capacity of SARS-CoV-2 to infect different subsets of human HSPCs, inlcuding procedures for SARS-CoV-2 production and titration, isolation of human HSPCs from different sources (bone marrow, umbilical cord, or peripheral blood), and quantification of SARS-Cov-2 infection capacity by RT-qPCR and colony forming unit assay. For complete details on the use and execution of this protocol, please refer to Huerga Encabo et al. (2021).
MeSH term(s)	Bone Marrow/virology ; COVID-19/pathology ; COVID-19/virology ; COVID-19 Nucleic Acid Testing/methods ; Colony-Forming Units Assay/methods ; Fetal Blood/virology ; Hematopoietic Stem Cells/pathology ; Hematopoietic Stem Cells/virology ; Humans ; SARS-CoV-2/isolation & purification
Language	English
Publishing date	2021-10-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2021.100903
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The V-ATPase complex regulates non-canonical Atg8-family protein lipidation through ATG16L1 recruitment.

Timimi, Lewis / Figueras-Novoa, Carmen / Marcassa, Elena / Florey, Oliver / Baillie, J Kenneth / Beale, Rupert / Ulferts, Rachel

Autophagy

2022 Volume 18, Issue 3, Page(s) 707–708

Abstract: Conjugation of the Atg8 (autophagy related 8) family of ubiquitin-like proteins to phospholipids of the phagophore is a hallmark of macroautophagy/autophagy. Consequently, Atg8 family members, especially LC3B, are commonly used as a marker of ... ...

Abstract	Conjugation of the Atg8 (autophagy related 8) family of ubiquitin-like proteins to phospholipids of the phagophore is a hallmark of macroautophagy/autophagy. Consequently, Atg8 family members, especially LC3B, are commonly used as a marker of autophagosomes. However, the Atg8 family of proteins are not found solely attached to double-membrane autophagosomes. In non-canonical Atg8-family protein lipidation they become conjugated to single membranes. We have shown that this process is triggered by recruitment of ATG16L1 by the vacuolar-type H
MeSH term(s)	Autophagy ; Autophagy-Related Protein 8 Family/metabolism ; Autophagy-Related Proteins/metabolism ; Humans ; Microtubule-Associated Proteins/metabolism ; Proton-Translocating ATPases/metabolism
Chemical Substances	ATG16L1 protein, human ; Autophagy-Related Protein 8 Family ; Autophagy-Related Proteins ; GABARAPL2 protein, human ; Microtubule-Associated Proteins ; Proton-Translocating ATPases (EC 3.6.3.14)
Language	English
Publishing date	2022-03-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2454135-7
ISSN	1554-8635 ; 1554-8627
ISSN (online)	1554-8635
ISSN	1554-8627
DOI	10.1080/15548627.2022.2029233
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Article ; Online: Antibody correlates of protection against Delta infection after vaccination: A nested case-control within the UK-based SIREN study.

Atti, Ana / Insalata, Ferdinando / Carr, Edward J / Otter, Ashley D / Foulkes, Sarah / Wu, Mary Y / Cole, Michelle J / Linley, Ezra / Semper, Amanda / Brooks, Tim / Hopkins, Susan / Charlett, Andre / Beale, Rupert / Hall, Victoria

The Journal of infection

2023 Volume 87, Issue 5, Page(s) 420–427

Abstract: Objectives: To investigate serological correlates of protection against SARS-CoV-2 B.1.617.2 (Delta) infection after two vaccinations.: Methods: We performed a case-control study, where cases were Delta infections after the second vaccine dose and ... ...

Abstract	Objectives: To investigate serological correlates of protection against SARS-CoV-2 B.1.617.2 (Delta) infection after two vaccinations. Methods: We performed a case-control study, where cases were Delta infections after the second vaccine dose and controls were vaccinated, never infected participants, matched by age, gender and region. Sera were tested for anti-SARS-CoV-2 Spike antibody levels (anti-S) and neutralising antibody titres (nAbT), using live virus microneutralisation against Ancestral, Delta and Omicron (BA.1, B.1.1.529). We modelled the decay of anti-S and nAbT for both groups, inferring levels at matched calendar times since the second vaccination. We assessed differences in inferred antibody titres between groups and used conditional logistic regression to explore the relationship between titres and odds of infection. Results: In total, 130 sequence-confirmed Delta cases and 318 controls were included. Anti-S and Ancestral nAbT decayed similarly between groups, but faster in cases for Delta nAbT (p = 0.02) and Omicron nAbT (p = 0.002). At seven days before infection, controls had higher anti-S levels (p < 0.0001) and nAbT (p < 0.0001; all variants) at matched calendar time. A two-fold increase in anti-S levels was associated with a 29% ([95% CI 14-42%]; p = 0.001) reduction in odds of Delta infection. Delta nAbT>40 were associated with reduced odds of Delta infection (89%, [69-96%]; p < 0.0001), with additional benefits for titres >100 (p = 0.009) and >400 (p = 0.007). Conclusions: We have identified correlates of protection against SARS-CoV-2 Delta, with potential implications for vaccine deployment, development, and public health response.
MeSH term(s)	Humans ; Case-Control Studies ; Antibodies, Neutralizing ; Vaccination ; Antibodies, Viral ; Vaccines ; Hepatitis D ; United Kingdom/epidemiology
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Vaccines
Language	English
Publishing date	2023-09-07
Publishing country	England
Document type	Journal Article
ZDB-ID	424417-5
ISSN	1532-2742 ; 0163-4453
ISSN (online)	1532-2742
ISSN	0163-4453
DOI	10.1016/j.jinf.2023.07.007
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Article ; Online: Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections.

Hellewell, Joel / Russell, Timothy W / Beale, Rupert / Kelly, Gavin / Houlihan, Catherine / Nastouli, Eleni / Kucharski, Adam J

BMC medicine

2021 Volume 19, Issue 1, Page(s) 106

Abstract: Background: Routine asymptomatic testing using RT-PCR of people who interact with vulnerable populations, such as medical staff in hospitals or care workers in care homes, has been employed to help prevent outbreaks among vulnerable populations. ... ...

Abstract	Background: Routine asymptomatic testing using RT-PCR of people who interact with vulnerable populations, such as medical staff in hospitals or care workers in care homes, has been employed to help prevent outbreaks among vulnerable populations. Although the peak sensitivity of RT-PCR can be high, the probability of detecting an infection will vary throughout the course of an infection. The effectiveness of routine asymptomatic testing will therefore depend on testing frequency and how PCR detection varies over time. Methods: We fitted a Bayesian statistical model to a dataset of twice weekly PCR tests of UK healthcare workers performed by self-administered nasopharyngeal swab, regardless of symptoms. We jointly estimated times of infection and the probability of a positive PCR test over time following infection; we then compared asymptomatic testing strategies by calculating the probability that a symptomatic infection is detected before symptom onset and the probability that an asymptomatic infection is detected within 7 days of infection. Results: We estimated that the probability that the PCR test detected infection peaked at 77% (54-88%) 4 days after infection, decreasing to 50% (38-65%) by 10 days after infection. Our results suggest a substantially higher probability of detecting infections 1-3 days after infection than previously published estimates. We estimated that testing every other day would detect 57% (33-76%) of symptomatic cases prior to onset and 94% (75-99%) of asymptomatic cases within 7 days if test results were returned within a day. Conclusions: Our results suggest that routine asymptomatic testing can enable detection of a high proportion of infected individuals early in their infection, provided that the testing is frequent and the time from testing to notification of results is sufficiently fast.
MeSH term(s)	Bayes Theorem ; COVID-19/diagnosis ; COVID-19/pathology ; COVID-19 Nucleic Acid Testing/methods ; Female ; Humans ; Male ; Polymerase Chain Reaction/methods
Language	English
Publishing date	2021-04-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2131669-7
ISSN	1741-7015 ; 1741-7015
ISSN (online)	1741-7015
ISSN	1741-7015
DOI	10.1186/s12916-021-01982-x
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Article ; Online: Swab pooling enables rapid expansion of high-throughput capacity for SARS-CoV-2 community testing.

Fagg, Jamie / Beale, Rupert / Futschik, Matthias E / Turek, Elena / Chapman, David / Halstead, Susan / Jones, Marc / Cole-Hamilton, Joanna / Gunson, Rory / Sudhanva, Malur / Klapper, Paul E / Vansteenhouse, Harper / Tunkel, Sarah / Dominiczak, Anna / Peto, Timothy Ea / Fowler, Tom

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

2023 Volume 167, Page(s) 105574

Abstract: Background: The challenges of rapid upscaling of testing capacity were a major lesson from the COVID-19 pandemic response. The need for process adjustments in high-throughput testing laboratories made sample pooling a challenging option to implement.: ...

Abstract	Background: The challenges of rapid upscaling of testing capacity were a major lesson from the COVID-19 pandemic response. The need for process adjustments in high-throughput testing laboratories made sample pooling a challenging option to implement. Objective: This study aimed to evaluate whether pooling samples at source (swab pooling) was as effective as qRT-PCR testing of individuals in identifying cases of SARS-CoV-2 in real-world community testing conditions using the same high-throughput pipeline. Methods: Two cohorts of 10 (Pool10: 1,030 participants and 103 pools) and 6 (Pool6: 1,284 participants and 214 pools) samples per pool were tested for concordance, sensitivity, specificity, and Ct value differences with individual testing as reference. Results: Swab pooling allowed unmodified application of an existing high-throughput SARS-Cov-2 testing pipeline with only marginal loss of accuracy. For Pool10, concordance was 98.1% (95% Confidence interval: 93.3-99.8%), sensitivity was 95.7% (85.5-99.5%), and specificity was 100.0% (93.6-100.0%). For Pool6, concordance was 97.2% (94.0-99.0%), sensitivity was 97.5% (93.7-99.3%), and specificity was 96.4% (87.7-99.6%). Differences of outcomes measure between pool size were not significant. Most positive individual samples, which were not detected in pools, had very low viral concentration. If only individual samples with a viral concentration > 400 copies/ml (i.e. Ct value < 30) were considered positive, the overall sensitivity of pooling increased to 99.5%. Conclusion: The study demonstrated high sensitivity and specificity by swab pooling and the immediate capability of high-throughput laboratories to implement this method making it an option in planning of rapid upscaling of laboratory capacity for future pandemics.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19/diagnosis ; COVID-19 Testing ; Pandemics ; Laboratories
Language	English
Publishing date	2023-08-19
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2023.105574
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