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(searched for: doi:10.1038/s41591-021-01355-0)
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Clinical and Experimental Nephrology pp 1-8; https://doi.org/10.1007/s10157-021-02130-8

Abstract:
Because patients on maintenance hemodialysis (HD) have an impaired immune response to pathogens, they are at higher risk of severe coronavirus disease 2019 (COVID-19). However, data on antibody production among HD patients with COVID-19 is scarce. Thus, we performed a retrospective cohort study evaluating severe acute respiratory syndrome coronavirus two antibody (SARS-CoV-2) production within 1 month after COVID-19 onset in hospitalized patients on HD.
, Valéria O. Silva, , Elaine M. Matsuda, Elaine L. de Oliveira, Edilene P. R. da Silveira, Ana K. De Souza Lima, , , Marisa A. Hong, et al.
Published: 24 August 2021
Journal of Medical Virology; https://doi.org/10.1002/jmv.27290

Abstract:
Many aspects of the humoral immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), such as its role in protection after natural infection, are still unclear. We evaluated IgA and IgG response to spike subunits 1 and 2 (S1 and S2) and Nucleocapsid proteins of SARS-COV-2 in serum samples of 109 volunteers with viral RNA detected or seroconversion with different clinical evolution (asymptomatic, mild, moderate, and severe coronavirus disease 2019), using the ViraChip® Test Kit. We observed that the quantification of antibodies to all antigens had a positive correlation to disease severity, which was strongly associated with the presence of comorbidities. Seroreversion was not uncommon even during the short (median of 77 days) observation, occurring in 15% of mild-asymptomatic cases at a median of 55 days for IgG and 46 days for IgA. The time to reach the maximal antibody response did not differ significantly among recovered and deceased volunteers. Our study illustrated the dynamic of anti-S1, anti-N, and anti-S2 IgA and IgG antibodies, and suggests that high production of IgG and IgA does not guarantee protection to disease severity and that functional responses that have been studied by other groups, such as antibody avidity, need further attention.
Published: 17 August 2021
Current Opinion in Virology, Volume 50, pp 119-127; https://doi.org/10.1016/j.coviro.2021.08.004

Abstract:
Type I and type III interferons are among the most potent anti-viral cytokines produced by the immune system. The recent outbreak of SARS-CoV-2, which causes COVID-19, underscores the vital role of these cytokines in controlling the virus and dictating disease severity. Here we delineate the pathways that lead to interferon production in response to SARS-CoV-2 encounter, and elucidate how this virus hinders the production and action of these cytokines; we also highlight that these interferon families serve protective as well as detrimental roles in patients with COVID-19, and conclude that a better understanding of the time, dose, localization, and activity of specific members of the interferon families is imperative for designing more efficient therapeutic interventions against this disease.
Rosetta Pedotti, Erwan Muros-Le Rouzic, Catarina Raposo, Sven Schippling, Nikki Jessop
Multiple Sclerosis and Related Disorders, Volume 55, pp 103203-103203; https://doi.org/10.1016/j.msard.2021.103203

Abstract:
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to major challenges in the therapeutic management of patients living with multiple sclerosis (PLwMS), particularly regarding the use of disease-modifying therapies. Despite an extraordinary scientific effort to study SARS-CoV-2 in PLwMS, the heterogeneity of COVID-19 manifestations, immunological mechanisms induced by the natural infection or the vaccines, and the extent of protection through the vaccines, major knowledge gaps remain. Here, we describe the scientific evidence generation plan developed by Roche/Genentech to better understand the impact of the COVID-19 pandemic in PLwMS treated with the B-cell depleting monoclonal antibody ocrelizumab.
, Jian Liu, Carolina Lucas, Jon Klein, , Linda Cantley, Louis Fazen, Julian Campillo Luna, Martin Slade, Carrie A Redlich
Published: 8 August 2021
Abstract:
Background Tests for SARS-CoV-2 immunity are needed to help assess responses to vaccination, which can be heterogeneous and may wane over time. The plaque reduction neutralization test (PRNT) is considered the gold standard for measuring serum neutralizing antibodies but requires high level biosafety, live viral cultures and days to complete. We hypothesized that competitive enzyme linked immunoassays (ELISAs) based on SARS-CoV-2 spike protein’s receptor binding domain (RBD) attachment to its host receptor, the angiotensin converting enzyme 2 receptor (ACE2r), would correlate with PRNT, given the central role of RBD-ACE2r interactions in infection and published studies to date, and enable evaluation of vaccine responses. Methods and Findings Configuration and development of a competitive ELISA with plate-bound RBD and soluble biotinylated ACE2r was accomplished using pairs of pre/post vaccine serum. When the competitive ELISA was used to evaluate N=32 samples from COVID-19 patients previously tested by PRNT, excellent correlation in IC50 results were observed (rs= .83, p < 0.0001). When the competitive ELISA was used to evaluate N=41 vaccinated individuals and an additional N=14 unvaccinated recovered COVID-19 patients, significant differences in RBD-ACE2r inhibitory activity were associated with prior history of COVID-19 and type of vaccine received. In longitudinal analyses pre and up to 200 days post vaccine, surrogate neutralizing activity increased markedly after primary and booster vaccine doses, but fell substantially, up to <12% maximal levels within 6 months. Conclusions A competitive ELISA based on inhibition of RBD-ACE2r attachment correlates well with PRNT, quantifies significantly higher activity among vaccine recipients with prior COVID (vs. those without), and highlights marked declines in surrogate neutralizing activity over a 6 month period post vaccination. The findings raise concern about the duration of vaccine responses and potential need for booster shots.
, Stefano Milleri, , Sarah Nosari, Ida Paciello, , Alessandra Gentili, Adhuna Phogat, , Margherita Leonardi, et al.
Published: 4 August 2021
Abstract:
Summary Background The emerging threat represented by SARS-CoV-2 variants, demands the development of therapies for better clinical management of COVID-19. MAD0004J08 is an extremely potent Fc-engineered monoclonal antibody (mAb) able to neutralise in vitro all current SARS-CoV-2 variants of concern (VoCs). This ongoing study, evaluates safety, pharmacokinetics and SARS-CoV-2 sera neutralization effect of MAD0004J08 when administered as single dose intramuscularly in healthy adults. Method We conducted a dose escalation study with sequential enrolment of three cohorts, each with an increasing dose level of MAD0004J08 (48mg, 100mg and 400mg). Within each cohort, 10 young healthy adults were randomized with 4:1 ratio to a single intramuscular (i.m.) injection of MAD0004J08 or placebo. The primary endpoint is the proportion of subjects with severe and/or serious treatment emergent adverse events (TEAEs) within 7 days post-treatment. Secondary endpoints reported in this paper are the proportion of subjects with solicited TEAEs up 7 days post dosing, MAD0004J08 serum concentrations and neutralising activity versus the original SARS-COV-2 Wuhan virus at different timepoints post-dosing. As post-hoc analyses, we compared the sera neutralising titres of subjects who received MAD0004J08 with those of people that had received the COVID-19 BNT162b2 mRNA vaccine in the previous sixty days (n=10) and COVID-19 convalescent patients (n=20), and assessed serum neutralisation activity against the B.1.1.7 (alpha), B.1.351 (beta) and B.1.1.248 (gamma) SARS-CoV-2 variants of concern. Findings A total of 30 subjects, 10 per cohort, were enrolled and randomized. Data up to 30 days were available and analysed in this report. No severe TEAEs were reported in any of the cohorts in the 7 days post-treatment. MAD0004J08 was detected in the sera of treated subjects within few hours post-administration and reached almost maximal levels on day 8. The geometric mean neutralising titres (GMT) assessed against the original Wuhan virus peaked on day 8 and ranged 226 – 905, 905 – 2,560, and 1,280 – 5,120 for cohort 1, 2 and 3 respectively. The sera neutralising GMT in MAD0004J08 treated subjects in all the three cohorts were found to be 1·5-54·5-fold higher compared to sera from convalescent patients and 1·83– 76·4-fold higher compared to sera from COVID-19 vaccinees. Finally, GMT in MAD0004J08 treated subjects showed high neutralising titres versus the B.1.1.7 (alpha), B.1.351 (beta) and B.1.1.248 (gamma) SARS-CoV-2 VoCs. Interpretation A single dose administration of MAD0004J08 via i.m. route is safe and well tolerated and results in a rapid systemic distribution of the MAD0004J08 and sera neutralising titres higher than COVID-19 convalescent and vaccinated subjects. A single dose administration of MAD0004J08 is also sufficient to effectively neutralise major SARS-CoV-2 variants of concern. Based on these results, a Phase 2-3 trial is ongoing to further assess the safety, dosage, and efficacy of MAD0004J08 in asymptomatic or mild-moderate symptomatic COVID-19 patients. Funding EU Malaria Fund, Ministero dello Sviluppo Economico, Ministero della Salute, Regione Toscana, Toscana Life Sciences Sviluppo and European Research Council. Research in context Evidence before this study We searched PUBMED, MEDLINE and MedRxiv for clinical trials, meta-analyses and randomized controlled trials evaluating the antibody neutralization titres vs. different SARS-CoV-2 variants of concern obtained from subjects who received monoclonal antibodies for the treatment of COVID-19 using the following search terms: (“COVID-19” OR “SARS-CoV-2”) AND (“monoclonal antibody” OR “neutralising antibody”) AND (“variants” OR “variants of concern”). No relevant studies were identified. Added value of this study This is the first human study assessing safety, PK and neutralising potential of MAD0004J08, a monoclonal antibody against SARS-CoV-2 wild type Wuhan virus and variants of concern, administered intramuscularly at low dosages (48, 100 and 400 mg). MAD0004J08 showed to be safe and well tolerated in the tested dose range. Anti-spike antibodies were detected in the sera of tested SARS-CoV-2 negative healthy adults few hours post-injection. In addition, the sera obtained from MAD0004J08treated subjects, showed to have high neutralisation titres against the Wuhan virus, the B.1.1.7 (alpha), B.1.351 (beta) and B.1.1.248 (gamma) variants of concern. Implications of all the available evidence A potent monoclonal antibody such as MAD0004J08, capable of neutralising multiple variants of concern of SARS-CoV-2 rapidly and long lastingly when given as a single intramuscular injection. The antibody, presently tested in a phase 2-3 efficacy trial, can be a major advancement in the prophylaxis and clinical management of COVID-19, because of its broad spectrum, ease of use in non-hospital settings and economic sustainability.
Kaiming Tao, , Janin Nouhin, Hector Bonilla, , Robert W. Shafer
Clinical Microbiology Reviews; https://doi.org/10.1128/cmr.00109-21

Abstract:
The development of effective antiviral therapy for COVID-19 is critical for those awaiting vaccination, as well as for those who do not respond robustly to vaccination. This review summarizes 1 year of progress in the race to develop antiviral therapies for COVID-19, including research spanning preclinical and clinical drug development efforts, with an emphasis on antiviral compounds that are in clinical development or that are high priorities for clinical development.
, Chantal B. F. Vogels, Inci Yildirim, Jessica E. Rothman, Peiwen Lu, Valter Monteiro, Jeff R. Gelhausen, Melissa Campbell, , Alexandra Tabachikova, et al.
Published: 18 July 2021
Abstract:
The emergence of SARS-CoV-2 variants with mutations in major neutralizing antibody-binding sites can affect humoral immunity induced by infection or vaccination1–6. We analysed the development of anti-SARS-CoV-2 antibody and T cell responses in previously infected (recovered) or uninfected (naive) individuals that received mRNA vaccines to SARS-CoV-2. While previously infected individuals sustained higher antibody titers than uninfected individuals post-vaccination, the latter reached comparable levels of neutralization responses to the ancestral strain than previously infected individuals 7 days after the second vaccine dose. T cell activation markers measured upon spike or nucleocapsid peptide in vitro stimulation showed a progressive increase after vaccination in the time-points analysed. Comprehensive analysis of plasma neutralization using 16 authentic isolates of distinct locally circulating SARS-CoV-2 variants revealed a range of reduction in the neutralization capacity associated with specific mutations in the spike gene: lineages with E484K and N501Y/T (e.g., B.1.351 and P.1) had the greatest reduction, followed by lineages with L452R (e.g., B.1.617.2) or with E484K (without N501Y/T). While both groups retained neutralization capacity against all variants, plasma from previously infected vaccinated individuals displayed overall better neutralization capacity when compared to plasma from uninfected individuals that also received two vaccine doses, pointing to vaccine boosters as a relevant future strategy to alleviate the impact of emerging variants on antibody neutralizing activity.
Published: 12 July 2021
by MDPI
Viruses, Volume 13; https://doi.org/10.3390/v13071346

Abstract:
The SARS-CoV-2 virus causing COVID-19 disease has emerged expeditiously in the world and has been declared pandemic since March 2020, by World Health Organization (WHO). The destructive effects of SARS-CoV-2 infection are increased among the patients with pre-existing chronic conditions and, in particular, this review focuses on patients with underlying cardiovascular complications. The expression pattern and potential functions of SARS-CoV-2 binding receptors and the attributes of SARS-CoV-2 virus tropism in a physio-pathological state of heart and blood vessel are precisely described. Of note, the atheroprotective role of ACE2 receptors is reviewed. A detailed description of the possible detrimental role of SARS-CoV-2 infection in terms of vascular leakage, including endothelial glycocalyx dysfunction and bradykinin 1 receptor stimulation is concisely stated. Furthermore, the potential molecular mechanisms underlying SARS-CoV-2 induced clot formation in association with host defense components, including activation of FXIIa, complements and platelets, endothelial dysfunction, immune cell responses with cytokine-mediated action are well elaborated. Moreover, a brief clinical update on patient with COVID-19 disease with underlying cardiovascular complications and those who had new onset of cardiovascular complications post-COVID-19 disease was also discussed. Taken together, this review provides an overview of the mechanistic aspects of SARS-CoV-2 induced devastating effects, in vital organs such as the heart and vessels.
William M Souza, Mariene R Amorim, Renata Sesti-Costa, Lais D Coimbra, Natalia S Brunetti, Daniel A Toledo-Teixeira, Gabriela F de Souza, Stefanie P Muraro, Pierina L Parise, Priscilla P Barbosa, et al.
Published: 8 July 2021
Abstract:
Summary Background Mutations accrued by SARS-CoV-2 lineage P.1—first detected in Brazil in early January, 2021—include amino acid changes in the receptor-binding domain of the viral spike protein that also are reported in other variants of concern, including B.1.1.7 and B.1.351. We aimed to investigate whether isolates of wild-type P.1 lineage SARS-CoV-2 can escape from neutralising antibodies generated by a polyclonal immune response. Methods We did an immunological study to assess the neutralising effects of antibodies on lineage P.1 and lineage B isolates of SARS-CoV-2, using plasma samples from patients previously infected with or vaccinated against SARS-CoV-2. Two specimens (P.1/28 and P.1/30) containing SARS-CoV-2 lineage P.1 (as confirmed by viral genome sequencing) were obtained from nasopharyngeal and bronchoalveolar lavage samples collected from patients in Manaus, Brazil, and compared against an isolate of SARS-CoV-2 lineage B (SARS.CoV2/SP02.2020) recovered from a patient in Brazil in February, 2020. Isolates were incubated with plasma samples from 21 blood donors who had previously had COVID-19 and from a total of 53 recipients of the chemically inactivated SARS-CoV-2 vaccine CoronaVac: 18 individuals after receipt of a single dose and an additional 20 individuals (38 in total) after receipt of two doses (collected 17–38 days after the most recent dose); and 15 individuals who received two doses during the phase 3 trial of the vaccine (collected 134–230 days after the second dose). Antibody neutralisation of P.1/28, P.1/30, and B isolates by plasma samples were compared in terms of median virus neutralisation titre (VNT50, defined as the reciprocal value of the sample dilution that showed 50% protection against cytopathic effects). Findings In terms of VNT50, plasma from individuals previously infected with SARS-CoV-2 had an 8·6 times lower neutralising capacity against the P.1 isolates (median VNT50 30 [IQR <20–45] for P.1/28 and 30 [<20–40] for P.1/30) than against the lineage B isolate (260 [160–400]), with a binominal model showing significant reductions in lineage P.1 isolates compared with the lineage B isolate (p≤0·0001). Efficient neutralisation of P.1 isolates was not seen with plasma samples collected from individuals vaccinated with a first dose of CoronaVac 20–23 days earlier (VNT50s below the limit of detection [<20] for most plasma samples), a second dose 17–38 days earlier (median VNT50 24 [IQR <20–25] for P.1/28 and 28 [<20–25] for P.1/30), or a second dose 134–260 days earlier (all VNT50s below limit of detection). Median VNT50s against the lineage B isolate were 20 (IQR 20–30) after a first dose of CoronaVac 20–23 days earlier, 75 (<20–263) after a second dose 17–38 days earlier, and 20 (<20–30) after a second dose 134–260 days earlier. In plasma collected 17–38 days after a second dose of CoronaVac, neutralising capacity against both P.1 isolates was significantly decreased (p=0·0051 for P.1/28 and p=0·0336 for P.1/30) compared with that against the lineage B isolate. All data were corroborated by results obtained through plaque reduction neutralisation tests. Interpretation SARS-CoV-2 lineage P.1 might escape neutralisation by antibodies generated in response to polyclonal stimulation against previously circulating variants of SARS-CoV-2. Continuous genomic surveillance of SARS-CoV-2 combined with antibody neutralisation assays could help to guide national immunisation programmes. Funding São Paulo Research Foundation, Brazilian Ministry of Science, Technology and Innovation and Funding Authority for Studies, Medical Research Council, National Council for Scientific and Technological Development, National Institutes of Health. Translation For the Portuguese translation of the abstract see Supplementary Materials section.
, Hyung J. Chun
Published: 23 June 2021
Frontiers in Immunology, Volume 12; https://doi.org/10.3389/fimmu.2021.693085

Abstract:
COVID-19 is a viral disease caused by a novel coronavirus, SARS-CoV-2, and is responsible for a pandemic since being identified in January 2020, resulting in a severe acute respiratory syndrome (SARS). Although most patients with COVID-19 may experience an asymptomatic, mild, or self-limited illness, many patients rapidly develop dyspnea and pneumonia, requiring hospitalization for pulmonary support. Patients with severe COVID-19 symptoms manifest cytokine release syndrome (CRS), which is associated with systemic inflammation, hemodynamic instability, and multi-organ failure (1). Progression from milder respiratory symptoms to acute respiratory distress syndrome (ARDS) is currently believed to be driven largely due to CRS and be one of main reasons for COVID-19 mortality. The CRS phase of SARS-CoV-2 is thought to occur due to an influx of neutrophils and macrophages as well as elevations of inflammatory cytokines, with higher levels of IL-6, IL-1, IL-8, and IL-18 (1, 2). In CRS, a variety of pro-inflammatory cytokines, including IL-1, IL-6, IL-8, CXCL-10, interferon (INF)-induced chemokines, and tumor necrosis factor (TNF)-α are secreted by alveolar macrophages that drive the inflammatory response and promote further influx of neutrophils, monocytes, and other inflammatory cells (1, 3). During the later stages of COVID-19, there are increases in pro-inflammatory cytokines and low levels of antiviral antibodies and adaptive immune responses noted, similar to previously reported results about SARS-CoV, suggesting innate immunity rather than the adaptive immunity as the driving force for excessive inflammation in COVID-19 associated ARDS (3, 4). In Meizlish et al., proteomic profiling of hospitalized patients with COVID-19 revealed prominent signatures of neutrophil activation in those patients with critical illness (5). Markers of neutrophilic activation, such as granulocyte colony-stimulating factor [G-CSF] and interleukin-8 [IL-8] and neutrophil-derived effectors (resistin [RETN], lipocalin-2 [LCN2]) had the greatest discriminatory power in this study for identifying patients with severe COVID-19 (5). This study represented important findings given that neutrophils are often the first responders in the innate immune response but can have notable collateral damage. Complement activation has also been suggested to play an important role and be a distinct entity in severe COVID-19 infection. In Ma et al., circulating markers of complement activation were found to be higher in patients with respiratory failure in COVID-19 compared to those with non-respiratory failure with COVID-19 and influenza (6). The complement pathway can typically be activated by 3 arms: classical pathway, alternative pathway, and lectin pathway. In this study, increased activation of the alterative pathway was noted and was found to be associated with worse outcomes in COVID-19 infection (6). Studies are currently ongoing to shed more light on the adaptive immunity and antibody response associated with COVID-19. There is data that demonstrates the ability of the SARS-CoV-2 virus to elicit neutralizing antibody response in sera and for those antibodies to be isolated (7, 8). There is evidence that the antibody response is largely mounted against the spike and nucleocapsid proteins of the SARS-CoV-2 virus and the severity of infection is associated with an increase in magnitude and breadth of the humoral response (9). The kinetics of the humoral response equally important, in addition to the magnitude of it, as delayed production of neutralizing antibodies has also been showed to be linked to fatality and impaired viral clearance (10). Activation of human innate immune cells, such as macrophages, through binding of viral antigens from SARS-CoV-2 to cell-surface toll-like receptors (TLRs) has been demonstrated to be a vital mediator of COVID-19 immunopathogenesis (11–13). TLRs are a family of 10 transmembrane receptor proteins (TLR1-TLR10) that recognize pathogen-associated molecular patterns (PAMPs) on viruses, bacteria, and other foreign molecules. TLRs play a major role in the initiation of the innate immune response, with the production of inflammatory cytokines, type I IFN, and other mediators (11–13). The SARS-CoV-2 viral spike protein binds to the extracellular domains of various TLRs, with strongest binding to TLR4. It has been shown that pathogenic human coronaviruses induce oxidized phospholipids that promote acute lung injury by increase lung macrophage cytokine/chemokine production via TLR4 (12). Similarly, SARS-CoV specific GU rich ssRNA fragments induce a high level of TNF- α, IL-6, and IL-12 via TLR7 and TLR8 (14). Collectively, recent in vitro and in vivo experiments suggest that TLRs and innate immunity pro-inflammatory signaling may be important in CRS and major immunopathologic consequences. Immunomodulatory agents, which are commonly used in rheumatologic conditions, have garnered interest for COVID-19 and the hyperinflammatory state. Certain agents are being used to target individual mediators of the inflammatory pathway to mitigate CRS; for example, tocilizumab, which is a monoclonal antibody against the receptor for IL-6, has shown some potential benefit for improving lung function and decreasing length of hospitalization in a large single-center trial (15, 16). Other studies have shown conflicting results with little to no benefit for tocilizumab in mortality of patients with COVID-19 (15, 17–19). In addition, studies have investigated the benefit of steroid use in COVID-19 patients, given their ability for broad-based immunosuppression. In a trial from University of Oxford including 6000 patients with COVID-19 taking 6mg dexamethasone daily, there was lower mortality in ventilated patients and those on oxygen therapy, with on overall decrease in 28-day all cause mortality (15). However, the use of steroids has only been indicated in a subset of COVID-19 patients...
, Joseph C. Gonzalez, Benjamin L. Sievers, Vamsee Mallajosyula, Megha Dubey, Yik-Ling Bowie Cheng, Kim Quyen Thi Tran, Srijoni Chakraborty, Arianna Cassidy, Steven T. Chen, et al.
Published: 25 May 2021
Abstract:
Serologic markers that predict severe COVID-19 disease trajectories could enable early medical interventions and reduce morbidity and mortality. We found that distinct features of IgG Fab and Fc domain structures were present within three days of a positive test that predicted two separate disease trajectories in a prospective cohort of patients with COVID-19. One trajectory was defined by early production of neutralizing antibodies and led to mild disease. A distinct trajectory, characterized by an initial period of mild symptoms followed by rapid progression to more severe outcomes, was predicted by the absence of early neutralizing antibody responses with concomitant production of afucosylated IgGs. Elevated frequencies of monocytes expressing the receptor for afucosylated IgGs, FcγRIIIa (CD16a), were an additional antecedent in patients with the more severe outcomes. In mechanistic studies, afucosylated immune complexes in the lung triggered an inflammatory infiltrate and cytokine production that was dependent on CD16a. Finally, in healthy subjects, mRNA SARS-CoV-2 vaccination elicited neutralizing antibodies that were enriched for Fc fucosylation and sialylation and distinct from both infection-induced trajectories. These data show the importance of combined Fab and Fc domain functions in the antiviral response, define an early antibody signature in people who progressed to more severe COVID-19 outcomes and have implications for novel therapeutic strategies targeting FcγRIIIa pathways.
Published: 15 May 2021
Abstract:
Background The worldwide pandemic caused by SARS-CoV-2 has claimed millions of lives and has had a profound effect on global life. Understanding the pathogenicity of the virus and the body’s response to infection is crucial in improving patient management, prognosis, and therapeutic strategies. To address this, we performed functional transcriptomic profiling to better understand the generic and specific effects of SARS-CoV-2 infection. Methods Whole blood RNA sequencing was used to profile a well characterised cohort of patients hospitalised with COVID-19, during the first wave of the pandemic prior to the availability of approved COVID-19 treatments and who went on to survive or die of COVID-19, and patients hospitalised with influenza virus infection between 2017 and 2019. Clinical parameters between patient groups were compared, and several bioinformatic tools were used to assess differences in transcript abundances and cellular composition. Results The analyses revealed contrasting innate and adaptive immune programmes, with transcripts and cell subsets associated with the innate immune response elevated in patients with influenza, and those involved in the adaptive immune response elevated in patients with COVID-19. Topological analysis identified additional gene signatures that differentiated patients with COVID-19 from patients with influenza, including insulin resistance, mitochondrial oxidative stress and interferon signalling. An efficient adaptive immune response was furthermore associated with patient survival, while an inflammatory response predicted death in patients with COVID-19. A potential prognostic signature was found based on a selection of transcript abundances, associated with circulating immunoglobulins, nucleosome assembly, cytokine production and T cell activation, in the blood transcriptome of COVID-19 patients, upon admission to hospital, which can be used to stratify patients likely to survive or die. Conclusions The results identified distinct immunological signatures between SARS-CoV-2 and influenza, prognostic of disease progression and indicative of different targeted therapies. The altered transcript abundances associated with COVID-19 survivors can be used to predict more severe outcomes in patients with COVID-19.
Published: 19 February 2021
Abstract:
Background SARS-CoV-2 shedding dynamics influence the risk of transmission and clinical manifestations of COVID-19. Yet, the relationships between SARS-CoV-2 shedding dynamics in the upper (URT) and lower respiratory tract (LRT) and age, sex and COVID-19 severity remain unclear. Methods Using systematic review, we developed a dataset of case characteristics (age, sex and COVID-19 severity) and quantitative respiratory viral loads (rVLs). We then conducted stratified analyses to assess SARS-CoV-2 shedding across disease course, COVID-19 severity, the respiratory tract, sex and age groups (aged 0 to 17 years, 18 to 59 years, and 60 years or older). Results The systematic dataset included 1,266 adults and 136 children with COVID-19. In the URT, adults with severe COVID-19 had higher rVLs at 1 day from symptom onset (DFSO) than adults (P = 0.005) or children (P = 0.017) with nonsevere illness. Between 1-10 DFSO, severe adults had comparable rates of SARS-CoV-2 clearance from the URT as nonsevere adults (P = 0.479) and nonsevere children (P = 0.863). In the LRT, severe adults showed higher rVLs post-symptom onset than nonsevere adults (P = 0.006). In the analyzed period (4-10 DFSO), severely affected adults had no significant trend in SARS-CoV-2 clearance from LRT (P = 0.105), whereas nonsevere adults showed a clear trend (P < 0.001). After stratifying for disease severity, sex and age (including child vs. adult) were not predictive of the duration of respiratory shedding. The estimated accuracy for using URT shedding as a prognostic indicator for COVID-19 severity was up to 65%, whereas it was up to 81% for LRT shedding. Conclusions High, persistent LRT shedding of SARS-CoV-2 characterized severe COVID-19 in adults. After symptom onset, severe cases tended to have slightly higher URT shedding than their nonsevere counterparts. Disease severity, rather than age or sex, predicted SARS-CoV-2 kinetics. LRT specimens more accurately prognosticate COVID-19 severity than do URT specimens. Funding Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant, NSERC Senior Industrial Research Chair and the Toronto COVID-19 Action Fund.
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