RESUMEN
Certain serum proteins, including CRP and D-dimer, have prognostic value in patients with SARS-CoV-2 infection. Nonetheless, these factors are non-specific, and provide limited mechanistic insight into the peripheral blood mononuclear cell (PBMC) populations which drive the pathogenesis of severe COVID-19. To identify novel cellular phenotypes associated with disease progression, we here describe a comprehensive, unbiased analysis of the total and plasma membrane proteomes of PBMCs from a cohort of 40 unvaccinated individuals with SARS-CoV-2 infection, spanning the whole spectrum of disease severity. Combined with RNA-seq and flow cytometry data from the same donors, we define a comprehensive multi-omic profile for each severity level, revealing cumulative immune cell dysregulation in progressive disease. In particular, the cell surface proteins CEACAMs1, 6 and 8, CD177, CD63 and CD89 are strongly associated with severe COVID-19, corresponding to the emergence of atypical CD3+CD4+CD177+ and CD16+CEACAM1/6/8+ mononuclear cells. Utilisation of these markers may facilitate real-time patient assessment by flow cytometry, and identify immune cell populations that could be targeted to ameliorate immunopathology.
RESUMEN
Human coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has multiple neurological consequences, but its long-term effect on brain health is still uncertain. The cerebrovascular consequences of COVID-19 may also affect brain health. Here we assess cerebrovascular health in 45 hospitalised patients using the resting state fluctuation amplitudes (RSFA) from functional magnetic resonance imaging, in relation to disease severity and in contrast with 42 controls. Widespread changes in frontoparietal RSFA were related to the severity of the acute COVID-19 episode, as indexed by COVID-19 WHO Progression Scale, inflammatory and coagulatory biomarkers. This relationship was not explained by chronic cardiorespiratory dysfunction, age, or sex. Exploratory analysis suggests that the level of cerebrovascular dysfunction is associated with cognitive, mental, and physical health at follow-up. The principal findings were consistent across univariate and multivariate approaches. The results indicate chronic cerebrovascular impairment following severe acute COVID-19, with the potential for long-term consequences on cognitive function and mental wellbeing.
RESUMEN
COVID-19 has been associated with many neurological complications including stroke, delirium and encephalitis. Furthermore, many individuals experience a protracted post-viral syndrome which is dominated by neuropsychiatric symptoms, and is seemingly unrelated to COVID-19 severity. The true frequency and underlying mechanisms of neurological injury are unknown, but exaggerated host inflammatory responses appear to be a key driver of severe COVID-19 more broadly. We sought to investigate the dynamics of, and relationship between, serum markers of brain injury (neurofilament light [NfL], Glial Fibrillary Acidic Protein [GFAP] and total Tau) and markers of dysregulated host response including measures of autoinflammation (proinflammatory cytokines) and autoimmunity. Brain injury biomarkers were measured using the Quanterix Simoa HDx platform, cytokine profiling by Luminex (R&D) and autoantibodies by a custom protein microarray. During hospitalisation, patients with COVID-19 demonstrated elevations of NfL and GFAP in a severity-dependant manner, and there was evidence of ongoing active brain injury at follow-up 4 months later. Raised NfL and GFAP were associated with both elevations of pro-inflammatory cytokines and the presence of autoantibodies; autoantibodies were commonly seen against lung surfactant proteins as well as brain proteins such as myelin associated glycoprotein, but reactivity was seen to a large number of different antigens. Furthermore, a distinct process characterised by elevation of serum total Tau was seen in patients at follow-up, which appeared to be independent of initial disease severity and was not associated with dysregulated immune responses in the same manner as NfL and GFAP.
RESUMEN
Severe Covid-19 is associated with elevated plasma Factor V (FV) and increased risk of thromboembolism. We report that neutrophils, T regulatory cells (Tregs), and monocytes from patients with severe Covid-19 express FV, and expression correlates with T cell lymphopenia. In vitro full length FV, but not FV activated by thrombin cleavage, suppresses T cell proliferation. Increased and prolonged FV expression by cells of the innate and adaptive immune systems may contribute to lymphopenia in severe Covid-19. Activation by thrombin destroys the immunosuppressive properties of FV. Anticoagulation in Covid-19 patients may have the unintended consequence of suppressing the adaptive immune system.
RESUMEN
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.
RESUMEN
SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2, and amino acid variation in Spike is increasingly appreciated. Given both vaccines and therapeutics are designed around Wuhan-1 Spike, this raises the theoretical possibility of virus escape, particularly in immunocompromised individuals where prolonged viral replication occurs. Here we report chronic SARS-CoV-2 with reduced sensitivity to neutralising antibodies in an immune suppressed individual treated with convalescent plasma, generating whole genome ultradeep sequences by both short and long read technologies over 23 time points spanning 101 days. Although little change was observed in the overall viral population structure following two courses of remdesivir over the first 57 days, N501Y in Spike was transiently detected at day 55 and V157L in RdRp emerged. However, following convalescent plasma we observed large, dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and{Delta} H69/{Delta}V70 in the S1 N-terminal domain NTD of the Spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype diminished in frequency, before returning during a final, unsuccessful course of convalescent plasma. In vitro, the Spike escape double mutant bearing{Delta} H69/{Delta}V70 and D796H conferred decreased sensitivity to convalescent plasma, whilst maintaining infectivity similar to wild type. D796H appeared to be the main contributor to decreased susceptibility, but incurred an infectivity defect. The{Delta} H69/{Delta}V70 single mutant had two-fold higher infectivity compared to wild type and appeared to compensate for the reduced infectivity of D796H. Consistent with the observed mutations being outside the RBD, monoclonal antibodies targeting the RBD were not impacted by either or both mutations, but a non RBD binding monoclonal antibody was less potent against{Delta} H69/{Delta}V70 and the double mutant. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy associated with emergence of viral variants with reduced susceptibility to neutralising antibodies.
RESUMEN
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