Verification and Validation of the Spalart-Allmaras Turbulence Model for Strand Grids

The strand-Cartesian grid approach is a unique method of generating and computing fluid dynamic simulations. The strand-Cartesian approach provides highly desirable qualities of fully-automatic grid generation and high-order accuracy. This thesis focuses on the implementation of the Spalart-Allmaras turbulence model to the strand-Cartesian grid framework. Verification and validation is required to ensure correct implementation of the turbulence model.Mathematical code verification is used to ensure correct implementation of new algorithms within the code framework. The Spalart-Allmaras model is verified with the Method of Manufactured Solutions (MMS). MMS shows second-order convergence, which implies that the new algorithms are correctly implemented.Validation of the strand-Cartesian solver is completed by simulating certain cases for comparison against the results of two independent compressible codes; CFL3D and FUN3D. The NASA-Langley turbulence resource provided the inputs and conditions required to run the cases, as well as the case results for these two codes. The strand solver showed excellent agreement with both NASA resource codes for a zero-pressure gradient flat plate and bump- in-channel. The treatment of the sharp corner on a NACA 0012 airfoil is investigated, resulting in an optimal external sharp corner configuration of strand vector smoothing with a base Cartesian grid and telescoping Cartesian refinement around the trailing edge. Results from the case agree well with those from CFL3D and FUN3D. Additionally, a NACA 4412 airfoil case is examined, and shows good agreement with CFL3D and FUN3D, resulting in validation for this case

Development of a Three-Dimensional High-Order Strand-Grids Approach

Development of a novel high-order flux correction method on strand grids is presented. The method uses a combination of flux correction in the unstructured plane and summation-by-parts operators in the strand direction to achieve high-fidelity solutions. Low-order truncation errors are cancelled with accurate flux and solution gradients in the flux correction method, thereby achieving a formal order of accuracy of 3, although higher orders are often obtained, especially for highly viscous flows. In this work, the scheme is extended to high-Reynolds number computations in both two and three dimensions. Turbulence closure is achieved with a robust version of the Spalart-Allmaras turbulence model that accommodates negative values of the turbulence working variable, and the Menter SST turbulence model, which blends the k-ε and k-ω turbulence models for better accuracy. A major advantage of this high-order formulation is the ability to implement traditional finite volume-like limiters to cleanly capture shocked and discontinuous flow. In this work, this approach is explored via a symmetric limited positive (SLIP) limiter. Extensive verification and validation is conducted in two and three dimensions to determine the accuracy and fidelity of the scheme for a number of different cases. Verification studies show that the scheme achieves better than third order accuracy for low and high-Reynolds number flow. Cost studies show that in three-dimensions, the third-order flux correction scheme requires only 30% more walltime than a traditional second-order scheme on strand grids to achieve the same level of convergence. In order to overcome meshing issues at sharp corners and other small-scale features, a unique approach to traditional geometry, coined asymptotic geometry, is explored. Asymptotic geometry is achieved by filtering out small-scale features in a level set domain through min/max flow. This approach is combined with a curvature based strand shortening strategy in order to qualitatively improve strand grid mesh quality

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

Rapid COVID-19 diagnosis in hospital is essential, though complicated by 30-50% of nose/throat swabs being negative by SARS-CoV-2 nucleic acid amplification testing (NAAT). Furthermore, the D614G spike mutant now dominates the pandemic and it is unclear how serological tests designed to detect anti-Spike antibodies perform against this variant. We assess the diagnostic accuracy of combined rapid antibody point of care (POC) and nucleic acid assays for suspected COVID-19 disease due to either wild type or the D614G spike mutant SARS-CoV-2. The overall detection rate for COVID-19 is 79.2% (95CI 57.8-92.9%) by rapid NAAT alone. Combined point of care antibody test and rapid NAAT is not impacted by D614G and results in very high sensitivity for COVID-19 diagnosis with very high specificity

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

Funder: Addenbrooke's Charitable Trust, Cambridge University Hospitals; FundRef: http://dx.doi.org/10.13039/501100002927Significant 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), 1032 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∙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

Age-related immune response heterogeneity to SARS-CoV-2 vaccine BNT162b2

Abstract: Although two-dose mRNA vaccination provides excellent protection against SARS-CoV-2, there is little information about vaccine efficacy against variants of concern (VOC) in individuals above eighty years of age1. Here we analysed immune responses following vaccination with the BNT162b2 mRNA vaccine2 in elderly participants and younger healthcare workers. Serum neutralization and levels of binding IgG or IgA after the first vaccine dose were lower in older individuals, with a marked drop in participants over eighty years old. Sera from participants above eighty showed lower neutralization potency against the B.1.1.7 (Alpha), B.1.351 (Beta) and P.1. (Gamma) VOC than against the wild-type virus and were more likely to lack any neutralization against VOC following the first dose. However, following the second dose, neutralization against VOC was detectable regardless of age. The frequency of SARS-CoV-2 spike-specific memory B cells was higher in elderly responders (whose serum showed neutralization activity) than in non-responders after the first dose. Elderly participants showed a clear reduction in somatic hypermutation of class-switched cells. The production of interferon-γ and interleukin-2 by SARS-CoV-2 spike-specific T cells was lower in older participants, and both cytokines were secreted primarily by CD4 T cells. We conclude that the elderly are a high-risk population and that specific measures to boost vaccine responses in this population are warranted, particularly where variants of concern are circulating

Complement lectin pathway activation is associated with COVID-19 disease severity, independent of MBL2 genotype subgroups

IntroductionWhile complement is a contributor to disease severity in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, all three complement pathways might be activated by the virus. Lectin pathway activation occurs through different pattern recognition molecules, including mannan binding lectin (MBL), a protein shown to interact with SARS-CoV-2 proteins. However, the exact role of lectin pathway activation and its key pattern recognition molecule MBL in COVID-19 is still not fully understood.MethodsWe therefore investigated activation of the lectin pathway in two independent cohorts of SARS-CoV-2 infected patients, while also analysing MBL protein levels and potential effects of the six major single nucleotide polymorphisms (SNPs) found in the MBL2 gene on COVID-19 severity and outcome.ResultsWe show that the lectin pathway is activated in acute COVID-19, indicated by the correlation between complement activation product levels of the MASP-1/C1-INH complex (p=0.0011) and C4d (p<0.0001) and COVID-19 severity. Despite this, genetic variations in MBL2 are not associated with susceptibility to SARS-CoV-2 infection or disease outcomes such as mortality and the development of Long COVID.ConclusionIn conclusion, activation of the MBL-LP only plays a minor role in COVID-19 pathogenesis, since no clinically meaningful, consistent associations with disease outcomes were noted

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

Funder: Lister Institute of Preventive Medicine; doi: https://doi.org/10.13039/501100001255Funder: University College London, Birkbeck MRC Doctoral Training ProgrammeFunder: The Jikei University School of MedicineFunder: Action Medical Research (GN2779)Funder: NIHR Clinical Lectureship (CL-2017-01-004)Funder: NIHR (ACF-2018-01-004) and the BMA FoundationFunder: Chan Zuckerberg Initiative (grant 2017-174169) and from Wellcome (WT211276/Z/18/Z and Sanger core grant WT206194)Funder: UKRI Innovation/Rutherford Fund Fellowship allocated by the MRC and the UK Regenerative Medicine Platform (MR/5005579/1 to M.Z.N.). M.Z.N. and K.B.M. have been funded by the Rosetrees Trust (M944)Funder: Barbour FoundationFunder: ERC Consolidator and EU MRG-Grammar awardsFunder: Versus Arthritis Cure Challenge Research Grant (21777), and an NIHR Research Professorship (RP-2017-08-ST2-002)Funder: European Molecular Biology Laboratory (EMBL)Abstract: Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy

SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion

Abstract: The B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha)1. In vitro, B.1.617.2 is sixfold less sensitive to serum neutralizing antibodies from recovered individuals, and eightfold less sensitive to vaccine-elicited antibodies, compared with wild-type Wuhan-1 bearing D614G. Serum neutralizing titres against B.1.617.2 were lower in ChAdOx1 vaccinees than in BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies to the receptor-binding domain and the amino-terminal domain. B.1.617.2 demonstrated higher replication efficiency than B.1.1.7 in both airway organoid and human airway epithelial systems, associated with B.1.617.2 spike being in a predominantly cleaved state compared with B.1.1.7 spike. The B.1.617.2 spike protein was able to mediate highly efficient syncytium formation that was less sensitive to inhibition by neutralizing antibody, compared with that of wild-type spike. We also observed that B.1.617.2 had higher replication and spike-mediated entry than B.1.617.1, potentially explaining the B.1.617.2 dominance. In an analysis of more than 130 SARS-CoV-2-infected health care workers across three centres in India during a period of mixed lineage circulation, we observed reduced ChAdOx1 vaccine effectiveness against B.1.617.2 relative to non-B.1.617.2, with the caveat of possible residual confounding. Compromised vaccine efficacy against the highly fit and immune-evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era

Turbulent Flow Validation in the Helios Strand Solver

This paper presents a validation of the turbulence models used in the strand solver that will appear in future versions of the Helios rotary-wing CFD/CSD software. We investigate turbulent flow validation of the strand-Cartesian approach for the Helios strand solver for high Reynolds number turbulent cases from the NASA-Langley turbulent online resource, comparing against two independent compressible codes: FUN3D and CFL3D. Second-order convergence of the solver is verified using the method of manufactured solutions implying correct spatial discretization of the turbulence model. A two-dimensional prototype strand solver is validated with zero-pressure gradient flat plate and bump-in-channel cases, and shows excellent agreement with FUN3D and CFL3D for various aspects of turbulent flow, including velocity profiles, turbulent viscosity profile, coefficient of surface pressure and drag. Further validation with a combined strand-Cartesian solver is conducted for NACA 0012 and NACA 4412 cases