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SARS-CoV-2 induces human endogenous retrovirus type W envelope protein expression in blood lymphocytes and in tissues of COVID-19 patients
SARS-CoV-2 induces human endogenous retrovirus type W envelope protein expression in blood lymphocytes and in tissues of COVID-19 patients
Patients with COVID-19 may develop abnormal inflammatory response and lymphopenia, followed in some cases by delayed-onset syndromes, often long-lasting after the initial SARS-CoV-2 infection. As viral infections may activate human endogenous retroviral elements (HERV), we studied the effect of SARS-CoV-2 on HERV-W and HERV-K envelope (ENV) expression, known to be involved in immunological and neurological pathogenesis of human diseases. Our results have showed that the exposure to SARS-CoV-2 virus activates early HERV-W and K transcription but only HERV-W ENV protein expression, in an infection- and ACE2-independent way within peripheral blood mononuclear cell cultures from one-third of healthy donors. Moreover, HERV-W ENV protein was significantly increased in serum and plasma of COVID-19 patients, correlating with its expression in CD3+ lymphocytes and with disease severity. Finally, HERV-W ENV was found expressed in post-mortem tissues of lungs, heart, brain olfactory bulb and nasal mucosa from acute COVID-19 patients in cell-types relevant for COVID-19-associated pathogenesis within affected organs, but different from those expressing of SARS-CoV-2 antigens. Altogether, the present study revealed that SARS-CoV-2 can induce HERV-W ENV expression in cells from individuals with symptomatic and severe COVID-19. Our data suggest that HERV-W ENV is likely to be involved in pathogenic features underlying symptoms of acute and post-acute COVID. It highlights the importance to further understand patients’ genetic susceptibility to HERV-W activation and the relevance of this pathogenic element as a prognostic marker and a therapeutic target in COVID-19 associated syndromes. ![Figure][1] ### Competing Interest Statement HP, BC, JB, JP, NQ received compensation for their work from Geneuro Innovation (France) ### Funding Statement This study was funded by the french National Agency for Researsch (ANR) - program RA-COVID-19 V15 (project name : COVERI) ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: - Ethics committee/IRB of SECRETARIA DE SALUD INSTITUTO NACIONAL DE ENFERMEDADES RESPIRATORIAS ISMAEL COSIO VILLEGAS (MEXICO)gave ethical approval for this work - Ethics committee/IRB of HOSPICES CIVILS DE LYON (HCL)/ BIOBANK OF CROIX ROUSSE HOSPITAL (FRANCE) gave ethical approval for this work - Ethics committee/IRB of SERVICIOS CIENTIFICO TECNICOS - SERVICIO DE BIOBANCO (BSSA)OF UNIVERSITY OF SARAGOZA (SPAIN) gave ethical approval for this work I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced in the present work are contained in the manuscript [1]: pending:yes
·medrxiv.org·
SARS-CoV-2 induces human endogenous retrovirus type W envelope protein expression in blood lymphocytes and in tissues of COVID-19 patients
Resources, Production Scales and Time Required for Producing RNA Vaccines for the Global Pandemic Demand
Resources, Production Scales and Time Required for Producing RNA Vaccines for the Global Pandemic Demand
To overcome pandemics, such as COVID-19, vaccines are urgently needed at very high volumes. Here we assess the techno-economic feasibility of producing RNA vaccines for the demand associated with a global vaccination campaign. Production process performance ...
·ncbi.nlm.nih.gov·
Resources, Production Scales and Time Required for Producing RNA Vaccines for the Global Pandemic Demand
Cutting Edge: Circulating Exosomes with COVID Spike Protein Are Induced by BNT162b2 (Pfizer–BioNTech) Vaccination prior to Development of Antibodies: A Novel Mechanism for Immune Activation by mRNA Vaccines
Cutting Edge: Circulating Exosomes with COVID Spike Protein Are Induced by BNT162b2 (Pfizer–BioNTech) Vaccination prior to Development of Antibodies: A Novel Mechanism for Immune Activation by mRNA Vaccines
Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) causes severe acute respiratory syndrome. mRNA vaccines directed at the SARS-CoV-2 spike protein resulted in development of Abs and protective immunity. To determine the mechanism, we analyzed the kinetics of induction of circulating
·jimmunol.org·
Cutting Edge: Circulating Exosomes with COVID Spike Protein Are Induced by BNT162b2 (Pfizer–BioNTech) Vaccination prior to Development of Antibodies: A Novel Mechanism for Immune Activation by mRNA Vaccines
Immune imprinting, breadth of variant recognition, and germinal center response in human SARS-CoV-2 infection and vaccination
Immune imprinting, breadth of variant recognition, and germinal center response in human SARS-CoV-2 infection and vaccination
During the SARS-CoV-2 pandemic, novel and traditional vaccine strategies have been deployed globally. We investigated whether antibodies stimulated by mRNA vaccination (BNT162b2), including third-dose boosting, differ from those generated by infection or adenoviral (ChAdOx1-S and Gam-COVID-Vac) or inactivated viral (BBIBP-CorV) vaccines. We analyzed human lymph nodes after infection or mRNA vaccination for correlates of serological differences. Antibody breadth against viral variants is lower after infection compared with all vaccines evaluated but improves over several months. Viral variant infection elicits variant-specific antibodies, but prior mRNA vaccination imprints serological responses toward Wuhan-Hu-1 rather than variant antigens. In contrast to disrupted germinal centers (GCs) in lymph nodes during infection, mRNA vaccination stimulates robust GCs containing vaccine mRNA and spike antigen up to 8 weeks postvaccination in some cases. SARS-CoV-2 antibody specificity, breadth, and maturation are affected by imprinting from exposure history and distinct histological and antigenic contexts in infection compared with vaccination.
·cell.com·
Immune imprinting, breadth of variant recognition, and germinal center response in human SARS-CoV-2 infection and vaccination
Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants
Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants
Virus-like particle (VLP) and live virus assays were used to investigate neutralizing immunity to Delta and Omicron SARS-CoV-2 variants in 239 samples from 125 fully vaccinated individuals. In uninfected, non-boosted individuals, VLP neutralization titers to Delta and Omicron were reduced 2.7-fold and 15.4-fold, respectively, compared to wild-type (WT), while boosted individuals (n=23) had 18-fold increased titers. Delta breakthrough infections (n=39) had 57-fold and 3.1-fold titers whereas Omicron breakthrough infections (n=14) had 5.8-fold and 0.32-fold titers compared to uninfected non-boosted and boosted individuals, respectively. The difference in titers (p=0.049) was related to a higher proportion of moderate to severe infections in the Delta cohort (p=0.014). Correlation of neutralizing and spike quantitative antibody titers was decreased with Delta or Omicron compared to WT. Neutralizing antibodies in Delta and Omicron breakthrough infections increase overall, but the relative magnitude of increase is greater in more clinically severe infection and against the specific infecting variant. ### Competing Interest Statement C.Y.C. is the director of the UCSF-Abbott Viral Diagnostics and Discovery and receives research support for SARS-CoV-2 studies from Abbott Laboratories. The other authors declare no competing interests. ### Funding Statement This work was funded by US CDC Epidemiology and Laboratory Capacity (ELC) for Infectious Diseases Grant 6NU50CK000539 to the California Department of Public Health (COVIDnet) (M-K.M., C.H., D.A.W., C.Y.C.), the Innovative Genomics Institute (IGI) at UC Berkeley and UC San Francisco (J.D., M.O., C.Y.C.), US Centers for Disease Control and Prevention contract 75D30121C10991 (C.Y.C.), the Roddenberry Foundation (M.O.), National Institutes of Health (NIH) grants R37AI083139 (M.O.), R21AI59666 (J.A.D.), and U54HL147127 (M.M.K.), the Howard Hughes Medical Institute (J.A.D.), the Gladstone Institutes (J.A.D. and M.O.), Abbott Laboratories (C.Y.C.), and the Sandler Program for Breakthrough Biomedical Research (C.Y.C.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The findings and conclusions in this article are those of the author(s) and do not necessarily represent the views or opinions of the California Department of Public Health or the California Health and Human Services Agency. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Institutional Review Board of UCSF gave ethical approval for this work Details in manuscript: Blood samples were collected through two methods. First, remnant whole blood and plasma samples from patients hospitalized with COVID-19 at UCSF were retrieved from UCSF Clinical Laboratories daily based on availability. Remnant samples were biobanked and retrospective medical chart reviews for relevant demographic and clinical metadata were performed under a waiver of consent and according to protocols approved by the UCSF Institutional Review Board (protocol numbers 10-01116 and 11-05519). Samples were obtained from pediatric and adult patients of all genders. No analyses based on sex or age were conducted. Second, plasma samples were also collected through the UMPIRE (UCSF EMPloyee and community member Immune REsponse) study, a longitudinal COVID-19 research study focused on collection of prospective whole blood and plasma samples from enrolled subjects to evaluate the immune response to vaccination, with and without boosting, and/or vaccine breakthrough infection. Informed consent for participation in the UMPIRE study and collection of data and samples were obtained according to a protocol approved by the UCSF Institutional Review Board (protocol number 20-33083). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.
·medrxiv.org·
Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants
Eric Feigl-Ding on Twitter
Eric Feigl-Ding on Twitter
📍“Cryptic” unknown #SARSCoV2 variants were found in New York City sewers, many never before found in humans. Some could infect cells with mouse🐁 and/or rat🐀 ACE2-receptor, & were resistant to different neutralizing monoclonal antibodies. So 🍕rat-COVID?https://t.co/AUZrdGAHxn pic.twitter.com/I9UPzNIWyy— Eric Feigl-Ding (@DrEricDing) February 7, 2022
·twitter.com·
Eric Feigl-Ding on Twitter
Viren sind nicht das Problem-bleiben Sie besonnen!
Viren sind nicht das Problem-bleiben Sie besonnen!
Vimeo hat meinen Kanal mit allen Beiträgen gelöscht. Nach LinkedIn und Youtube ist das eine weitere Steigerung der Zensur. Ich bin zu Odyssee gewechselt. Schande über VIMEO. Aber hier ist das gelöschte Video mit meinem Grußwort an die Spaziergänger.
·wodarg.com·
Viren sind nicht das Problem-bleiben Sie besonnen!
Eric Topol on Twitter
Eric Topol on Twitter
New: Remarkable 90% and durable protection (3 months) with booster vs Omicron vs hospital admission, the 1st US data, confirms + extends @UKHSA data👍https://t.co/5MgpcQp06Y pic.twitter.com/dkaJIma3H4— Eric Topol (@EricTopol) January 20, 2022
·twitter.com·
Eric Topol on Twitter
Does Influenza Transmission Occur from Asymptomatic Infection or Prior to Symptom Onset?
Does Influenza Transmission Occur from Asymptomatic Infection or Prior to Symptom Onset?
A better understanding of transmission dynamics is essential in influenza pandemic planning. If a substantial proportion of transmissions were to occur during the presymptomatic phase or from asymptomatic individuals, then infection control measures such ...
·ncbi.nlm.nih.gov·
Does Influenza Transmission Occur from Asymptomatic Infection or Prior to Symptom Onset?
Safety, tolerability and viral kinetics during SARS-CoV-2 human challenge
Safety, tolerability and viral kinetics during SARS-CoV-2 human challenge
To establish a novel SARS-CoV-2 human challenge model, 36 volunteers aged 18-29 years without evidence of previous infection or vaccination were inoculated with 10 TCID50 of a wild-type virus (SARS-CoV-2/human/GBR/484861/2020) intranasally. Two participants were excluded from per pr...
·researchsquare.com·
Safety, tolerability and viral kinetics during SARS-CoV-2 human challenge
Neutralization profile of Omicron variant convalescent individuals
Neutralization profile of Omicron variant convalescent individuals
Recently, the Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been described as immune escape variant. Here, we analyzed samples from BA.1 (Omicron) convalescent patients with different constellations of prior SARS-CoV-2 immunity regarding vaccination and previous infection with a non-Omicron variant and determined titers of neutralizing antibodies against different SARS-CoV-2 variants (D614G, Alpha, Beta, Delta, Gamma, Omicron). We found high neutralizing antibody titers against all variants for vaccinated individuals after BA.1 breakthrough infection or for individuals after infection with a pre-omicron variant followed by BA.1 infection. In contrast, samples from naive unvaccinated individuals after BA.1 infection mainly contained neutralizing antibodies against BA.1 but only occasionally against the other variants. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study did not receive any funding. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The ethics committee (EC) of the Medical University of Innsbruck has approved the study with EC numbers 1064/2021 and 1191/2021. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.
·medrxiv.org·
Neutralization profile of Omicron variant convalescent individuals
Limited cross-variant immunity after infection with the SARS-CoV-2 Omicron variant without vaccination
Limited cross-variant immunity after infection with the SARS-CoV-2 Omicron variant without vaccination
SARS-CoV-2 Delta and Omicron strains are the most globally relevant variants of concern (VOCs). While individuals infected with Delta are at risk to develop severe lung disease[1][1], Omicron infection causes less severe disease, mostly upper respiratory symptoms[2][2],[3][3]. The question arises whether rampant spread of Omicron could lead to mass immunization, accelerating the end of the pandemic. Here we show that infection with Delta, but not Omicron, induces broad immunity in mice. While sera from Omicron-infected mice only neutralize Omicron, sera from Delta-infected mice are broadly effective against Delta and other VOCs, including Omicron. This is not observed with the WA1 ancestral strain, although both WA1 and Delta elicited a highly pro-inflammatory cytokine response and replicated to similar titers in the respiratory tracts and lungs of infected mice as well as in human airway organoids. Pulmonary viral replication, pro-inflammatory cytokine expression, and overall disease progression are markedly reduced with Omicron infection. Analysis of human sera from Omicron and Delta breakthrough cases reveals effective cross-variant neutralization induced by both viruses in vaccinated individuals. Together, our results indicate that Omicron infection enhances preexisting immunity elicited by vaccines, but on its own may not induce broad, cross-neutralizing humoral immunity in unvaccinated individuals. ### Competing Interest Statement A.M.S. and J.A.D. are inventors on a patent application filed by the Gladstone Institutes and the University of California that covers the method and composition of SARS-CoV-2 VLP preparations for RNA transduction and expression in cells. J.A.D. is a cofounder of Caribou Biosciences, Editas Medicine, Scribe Therapeutics, Intellia Therapeutics, and Mammoth Biosciences. J.A.D. is a scientific advisory board member of Vertex, Caribou Biosciences, Intellia Therapeutics, eFFECTOR Therapeutics, Scribe Therapeutics, Mammoth Biosciences, Synthego, Algen Biotechnologies, Felix Biosciences, The Column Group, and Inari. J.A.D. is a director at Johnson & Johnson and Tempus and has research projects sponsored by Biogen, Pfizer, AppleTree Partners, and Roche. C.Y.C. is the director of the UCSF-Abbott Viral Diagnostics and Discovery Study and receives research support from Abbott Laboratories. C.Y.C. also receives support for SARS-CoV-2 research unrelated to this study from Mammoth Biosciences. ### Funding Statement This research is funded by grants from the National Institutes of Health: NIAID R37AI083139 to M.O., NIH/NIAID (F31 AI164671-01) to I.P.C., NHLBI U54HL147127 to M.M. A.M.S is supported by Natural Sciences and Engineering Research Council of Canada (NSERC PDF-533021-2019). M.O. and W.C.G also received support from the Roddenberry Foundation and M.O. received a gift from Pam and Ed Taft. J.A.D. acknowledges support from the National Institutes of Health (R21AI59666) and support from the Howard Hughes Medical Institute and the Gladstone Institutes. N.R. acknowledges support from the Van Auken Private Foundation, David Henke, and Pamela and Edward Taft; and Awards #2164 and #2208 from Fast Grants, a part of Emergent Ventures at the Mercatus Center, George Mason University. CYC acknowledges support by the Innovative Genomics Institute (IGI) at UC Berkeley and UC San Francisco, US Centers for Disease Control and Prevention contract 75D30121C10991, Abbott Laboratories, and the Sandler Program for Breakthrough Biomedical Research at UCSF. The group also acknowledges support from the James B. Pendleton Charitable Trust. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics committee/IRB of Advarra and UCSF gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced in the present work are contained in the manuscript [1]: #ref-1 [2]: #ref-2 [3]: #ref-3
·medrxiv.org·
Limited cross-variant immunity after infection with the SARS-CoV-2 Omicron variant without vaccination
Non-cell autonomous disruption of nuclear architecture as a potential cause of COVID-19 induced anosmia
Non-cell autonomous disruption of nuclear architecture as a potential cause of COVID-19 induced anosmia
SARS-CoV-2 infects less than 1% of cells in the human body, yet it can cause severe damage in a variety of organs. Thus, deciphering the non-cell autonomous effects of SARS-CoV-2 infection is imperative for understanding the cellular and molecular disruption it elicits. Neurological and cognitive defects are among the least understood symptoms of COVID-19 patients, with olfactory dysfunction being their most common sensory deficit. Here, we show that both in humans and hamsters SARS-CoV-2 infection causes widespread downregulation of olfactory receptors (OR) and of their signaling components. This non-cell autonomous effect is preceded by a dramatic reorganization of the neuronal nuclear architecture, which results in dissipation of genomic compartments harboring OR genes. Our data provide a potential mechanism by which SARS-CoV-2 infection alters the cellular morphology and the transcriptome of cells it cannot infect, offering insight to its systemic effects in olfaction and beyond.
·cell.com·
Non-cell autonomous disruption of nuclear architecture as a potential cause of COVID-19 induced anosmia