Atypical B cells and impaired SARS-CoV-2 neutralisation following booster vaccination in the elderly.

Age is a major risk factor for hospitalization and death after SARS-CoV-2 infection, even in vaccinees. Suboptimal responses to a primary vaccination course have been reported in the elderly, but there is little information regarding the impact of age on responses to booster third doses. Here we show that individuals 70 or older who received a primary two dose schedule with AZD1222 and booster third dose with mRNA vaccine achieved significantly lower neutralizing antibody responses against SARS-CoV-2 spike pseudotyped virus compared to those younger than 70. One month after the booster neither the concentration of serum binding anti spike IgG antibody, nor the frequency of spike-specific B cells showed differences by age grouping. However, the impaired neutralization potency and breadth post-third dose in the elderly was associated with enrichment of circulating "atypical" spike-specific B cells expressing CD11c and FCRL5. Single cell RNA sequencing confirmed an expansion of TBX21-, ITGAX-expressing B cells in the elderly that enriched for B cell activation/receptor signalling pathway genes. Importantly we also observed impaired T cell responses to SARS-CoV-2 spike peptides in the elderly post-booster, both in terms of IFNgamma and IL2 secretion, as well as a decrease in T cell receptor signalling pathway genes. This expansion of atypical B cells and impaired T cell responses may contribute to the generation of less affinity-matured antibodies, with lower neutralizing capacity post-third dose in the elderly. Altogether, our data reveal the extent and potential mechanistic underpinning of the impaired vaccine responses present in the elderly after a booster dose, contributing to their increased susceptibility to COVID-19 infection.

Defining factors that influence vaccine-induced, cross-variant neutralizing antibodies for SARS-CoV-2 in Asians

The scale and duration of neutralizing antibody responses targeting SARS-CoV-2 viral variants represents a critically important serological parameter that predicts protective immunity for COVID-19. In this study, we present longitudinal data illustrating the impact of age, sex and comorbidities on the kinetics and strength of vaccine-induced neutralizing antibody responses for key variants in an Asian volunteer cohort. We demonstrate a reduction in neutralizing antibody titres across all groups six months post-vaccination and show a marked reduction in the serological binding and neutralizing response targeting Omicron compared to other viral variants. We also highlight the increase in cross-protective neutralizing antibody responses against Omicron induced by a third dose (booster) of vaccine. These data illustrate how key virological factors such as immune escape mutation combined with host factors such as age and sex of the vaccinated individuals influence the strength and duration of cross-protective serological immunity for COVID-19.

Obesity associated with attenuated tissue immune cell responses in COVID-19

Obesity is common and associated with more severe COVID-19, proposed to be in part related to an adipokine-driven pro-inflammatory state. Here we analysed single cell transcriptomes from bronchiolar lavage in three adult cohorts, comparing obese (Ob, body mass index (BMI) >30m2) and non-obese (N-Ob, BMI <30m2). Surprisingly, we found that Ob subjects had attenuated lung immune/inflammatory responses in SARS-CoV-2 infection, with decreased expression of interferon (IFN), IFN{gamma} and tumour necrosis factor (TNF) alpha response gene signatures in almost all lung epithelial and immune cell subsets, and lower expression of IFNG and TNF in specific lung immune cells. Analysis of peripheral blood immune cells in an independent adult cohort showed a similar, but less marked, reduction in type I IFN and IFN{gamma} response genes, as well as decreased serum IFN, in Ob patients with SARS-CoV-2. Nasal immune cells from Ob children with COVID-19 also showed reduced enrichment of IFN and IFN{gamma} response genes. Altogether, these findings show blunted tissue immune responses in Ob COVID-19 patients, with clinical implications.

The impact of hypoxia on B cells in COVID-19

Prominent early features of COVID-19 include severe, often clinically silent, hypoxia and a pronounced reduction in B cells, the latter important in defence against SARS-CoV-2. This brought to mind the phenotype of mice with VHL-deficient B cells, in which Hypoxia-Inducible Factors are constitutively active, suggesting hypoxia might drive B cell abnormalities in COVID-19. We demonstrated the breadth of early and persistent defects in B cell subsets in moderate/severe COVID-19, including reduced marginal zone-like, memory and transitional B cells, changes we also observed in B cell VHL-deficient mice. This was corroborated by hypoxia-related transcriptional changes in COVID-19 patients, and by similar B cell abnormalities in mice kept in hypoxic conditions, including reduced marginal zone and germinal center B cells. Thus hypoxia might contribute to B cell pathology in COVID-19, and in other hypoxic states. Through this mechanism it may impact on COVID-19 outcome, and be remediable through early oxygen therapy.

Early immune pathology and persistent dysregulation characterise severe COVID-19

In a study of 207 SARS-CoV2-infected individuals with a range of severities followed over 12 weeks from symptom onset, we demonstrate that an early robust bystander CD8 T cell immune response, without systemic inflammation, is characteristic of asymptomatic or mild disease. Those presenting to hospital had delayed bystander responses and systemic inflammation already evident at around symptom onset. Such early evidence of inflammation suggests immunopathology may be inevitable in some individuals, or that preventative intervention might be needed before symptom onset. Viral load does not correlate with the development of this pathological response, but does with its subsequent severity. Immune recovery is complex, with profound persistent cellular abnormalities correlating with a change in the nature of the inflammatory response, where signatures characteristic of increased oxidative phosphorylation and reactive-oxygen species-associated inflammation replace those driven by TNF and IL-6. These late immunometabolic inflammatory changes and unresolved immune defects may have clinical implications.

Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission

Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Over a 3-week period (April 2020), 1,032 asymptomatic HCWs were screened for SARS-CoV-2 in a large UK teaching hospital. Symptomatic staff and symptomatic household contacts were additionally tested. Real-time RT-PCR was used to detect viral RNA from a throat+nose self-swab. 3% of HCWs in the asymptomatic screening group tested positive for SARS-CoV-2. 17/30 (57%) were truly asymptomatic/pauci-symptomatic. 12/30 (40%) had experienced symptoms compatible with coronavirus disease 2019 (COVID-19) >7 days prior to testing, most self-isolating, returning well. Clusters of HCW infection were discovered on two independent wards. Viral genome sequencing showed that the majority of HCWs had the dominant lineage B{middle dot}1. Our data demonstrates the utility of comprehensive screening of HCWs with minimal or no symptoms. This approach will be critical for protecting patients and hospital staff. Appendix: The CITIID-NIHR COVID-19 BioResource CollaborationO_ST_ABSPrincipal InvestigatorsC_ST_ABSStephen Baker, John Bradley, Gordon Dougan, Ian Goodfellow, Ravi Gupta, Paul J. Lehner, Paul A. Lyons, Nicholas J. Matheson, Kenneth G.C. Smith, M. Estee Torok, Mark Toshner, Michael P. Weekes Infectious Diseases DepartmentNicholas K. Jones, Lucy Rivett, Matthew Routledge, Dominic Sparkes, Ben Warne SARS-CoV-2 testing teamJosefin Bartholdson Scott, Claire Cormie, Sally Forrest, Harmeet Gill, Iain Kean, Mailis Maes, Joana Pereira-Dias, Nicola Reynolds, Sushmita Sridhar, Michelle Wantoch, Jamie Young COG-UK Cambridge Sequencing TeamSarah Caddy, Laura Caller, Theresa Feltwell, Grant Hall, William Hamilton, Myra Hosmillo, Charlotte Houldcroft, Aminu Jahun, Fahad Khokhar, Luke Meredith, Anna Yakovleva NIHR BioResourceHelen Butcher, Daniela Caputo, Debra Clapham-Riley, Helen Dolling, Anita Furlong, Barbara Graves, Emma Le Gresley, Nathalie Kingston, Sofia Papadia, Hannah Stark, Kathleen E. Stirrups, Jennifer Webster Research nursesJoanna Calder, Julie Harris, Sarah Hewitt, Jane Kennet, Anne Meadows, Rebecca Rastall, Criona O,Brien, Jo Price, Cherry Publico, Jane Rowlands, Valentina Ruffolo, Hugo Tordesillas NIHR Cambridge Clinical Research FacilityKaren Brookes, Laura Canna, Isabel Cruz, Katie Dempsey, Anne Elmer, Naidine Escoffery, Stewart Fuller, Heather Jones, Carla Ribeiro, Caroline Saunders, Angela Wright Cambridge Cancer Trial CentreRutendo Nyagumbo, Anne Roberts Clinical Research Network EasternAshlea Bucke, Simone Hargreaves, Danielle Johnson, Aileen Narcorda, Debbie Read, Christian Sparke, Lucy Warboys Administrative staff, CUHKirsty Lagadu, Lenette Mactavous CUH NHS Foundation TrustTim Gould, Tim Raine, Ashley Shaw Cambridge Cancer Trials CentreClaire Mather, Nicola Ramenatte, Anne-Laure Vallier Legal/EthicsMary Kasanicki CUH Improvement and Transformation TeamPenelope-Jane Eames, Chris McNicholas, Lisa Thake Clinical Microbiology & Public Health Laboratory (PHE): Neil Bartholomew, Nick Brown, Martin Curran, Surendra Parmar, Hongyi Zhang Occupational HealthAilsa Bowring, Mark Ferris, Geraldine Martell, Natalie Quinnell, Giles Wright, Jo Wright Health and SafetyHelen Murphy Department of Medicine Sample LogisticsBenjamin J. Dunmore, Ekaterina Legchenko, Stefan Graf, Christopher Huang, Josh Hodgson, Kelvin Hunter, Jennifer Martin, Federica Mescia, Ciara ODonnell, Linda Pointon, Joy Shih, Rachel Sutcliffe, Tobias Tilly, Zhen Tong, Carmen Treacy, Jennifer Wood Department of Medicine Sample Processing and Acquisition: Laura Bergamaschi, Ariana Betancourt, Georgie Bowyer, Aloka De Sa, Maddie Epping, Andrew Hinch, Oisin Huhn, Isobel Jarvis, Daniel Lewis, Joe Marsden, Simon McCallum, Francescsa Nice, Ommar Omarjee, Marianne Perera, Nika Romashova, Mateusz Strezlecki, Natalia Savoinykh Yarkoni, Lori Turner Epic team/other computing supportBarrie Bailey, Afzal Chaudhry, Rachel Doughton, Chris Workman Statistics/modellingRichard J. Samworth, Caroline Trotter