Covid19-Sources

Two new papers @NatureMedicine and @JAMAInternalMed shed light on #LongCovid at 2-years. But there's no shortage of known unknowns.Reviewed in a new Ground Truths (link in my profile, because that would be it X-suppressed) pic.twitter.com/5CePVxePQa— Eric Topol (@EricTopol) August 21, 2023

The bigger surprise, the new BA.2.86 sample(USA, traveler from Japan) has no genomic connection to neither the Danish nor the Israeli branch. This makes the picture only more complicated as there must already be an ongoing worldwide spread! Trashed testing and surveillance… pic.twitter.com/B5pMLWymzZ— Harry Spoelstra (@HarrySpoelstra) August 22, 2023

These SARS-CoV vaccines all induced antibody and protection against infection with SARS-CoV. However, challenge of mice given any of the vaccines led to occurrence of Th2-type immunopathology suggesting hypersensitivity to SARS-CoV components was induced. Caution in proceeding to application of a SA …

Liebe User, durch die aktuell im Vergleich geringeren Hospitalisierungszahlen ist eine Adjustierung dieser Zahlen nicht verlässlich möglich. Deshalb wird die Adjustierung der Hospitalisierungen bis...

Communications Biology - Analysis of next-generation sequencing data linked with clinical metadata from individuals reinfected with SARS-CoV-2 in a Danish cohort reveals that Omicron reinfections...

We used a series of ‘brain training’ style tasks to assess how a COVID infection and persistent symptoms affected cognitive function.

Nature Communications - Wastewater-based epidemiology is increasingly used to predict disease occurrence. Here, the authors use SARS-CoV-2 RNA concentrations in wastewater in machine learning...

The coronavirus disease 2019 (COVID-19) pandemic underscores the need to better understand animal-to-human transmission of coronaviruses and adaptive evolution within new hosts. We scanned more than 182,000 severe acute respiratory syndrome coronavirus ...

Infection with SARS-CoV-2 can lead to Coronavirus disease-2019 (COVID-19) and result in severe acute respiratory distress syndrome (ARDS). Recent reports indicate an increased rate of fungal coinfections during COVID-19. With incomplete understanding of the pathogenesis and without any causative therapy available, secondary infections may be detrimental to the prognosis. We monitored 11 COVID-19 patients with ARDS for their immune phenotype, plasma cytokines, and clinical parameters on the day of ICU admission and on day 4 and day 7 of their ICU stay. Whole blood stimulation assays with lipopolysaccharide (LPS), heat-killed Listeria monocytogenes (HKLM), Aspergillus fumigatus, and Candida albicans were used to mimic secondary infections, and changes in immune phenotype and cytokine release were assessed. COVID-19 patients displayed an immune phenotype characterized by increased HLA-DR+CD38+ and PD-1+ CD4+ and CD8+ T cells, and elevated CD8+CD244+ lymphocytes, compared to healthy controls. Monocyte activation markers and cytokines IL-6, IL-8, TNF, IL-10, and sIL2Rα were elevated, corresponding to monocyte activation syndrome, while IL-1β levels were low. LPS, HKLM and Aspergillus fumigatus antigen stimulation provoked an immune response that did not differ between COVID-19 patients and healthy controls, while COVID-19 patients showed an attenuated monocyte CD80 upregulation and abrogated release of IL-6, TNF, IL-1α, and IL-1β toward Candida albicans. This study adds further...

Cellular & Molecular Immunology - Elevated exhaustion levels and reduced functional diversity of T cells in peripheral blood may predict severe progression in COVID-19 patients

A low count of CD4+ and CD8+ lymphocytes is a hallmark laboratory finding in the coronavirus disease 2019 (COVID-19). Using flow cytometry, we observed significantly higher CD95 (Fas) and PD-1 expression on both CD4+ T and CD8+ T cells in 42 COVID-19 patie …

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent of a major global outbreak of respiratory tract disease known as coronavirus disease-2019 (COVID-19). SARS-CoV-2 infects the lungs and may cause several immune-related complications such as lymphocytopenia and cytokine storm which are associated with the severity of the disease and predict mortality[1][1],[2][2]. The mechanism by which SARS-CoV-2 infection may result in immune system dysfunction is not fully understood. Here we show that SARS-CoV-2 infects human CD4+ T helper cells, but not CD8+ T cells, and is present in blood and bronchoalveolar lavage T helper cells of severe COVID-19 patients. We demonstrated that SARS-CoV-2 spike glycoprotein (S) directly binds to the CD4 molecule, which in turn mediates the entry of SARS-CoV-2 in T helper cells in a mechanism that also requires ACE2 and TMPRSS2. Once inside T helper cells, SARS-CoV-2 assembles viral factories, impairs cell function and may cause cell death. SARS-CoV-2 infected T helper cells express higher amounts of IL-10, which is associated with viral persistence and disease severity. Thus, CD4-mediated SARS-CoV-2 infection of T helper cells may explain the poor adaptive immune response of many COVID-19 patients. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by grants from FAEPEX-UNICAMP (#2295/20, #2458/20, #2266/20 and #2274/20), Sao Paulo Research Foundation (FAPESP) (#2019/16116-4, #2019/06372-3, #2020/04583-4, #2013/08293-7, #2020/04579-7, #2015/15626-8, #2018/14933-2, #2020/04746-0, #2019/00098-7, #2020/04919-2, #2017/01184-9), the National Institute of Science and Technology in Neuroimmunomodulation (INCT-NIM) (#465489/2014-1) and FINEP (#01.20.0003.00). A.S.F. and M.A.M. were supported by CNPq productivity awards (#306248/2017-4 and #310287/2018-9). A.J.R.F, G.G.D., A.C.C., N.S.B., L.B.M., F.C., V.C.C., A.B., T.L.K, G.S.P., R.G.L. were supported by FAPESP fellowships (#2019/17007-4, #2019/22398-2, #2019/05155-9, #2019/06459-1, #2019/04726-2, #2017/23920-9, #2016/24163-4, #2016/23328-0). V.O.B. and L.N.S. were supported by FAEPEX fellowship (#2295/20 and #2319/20). D.M. was supported by CAPES fellowship. ### 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 present study was approved by the University of Campinas Committee for Ethical Research (CAAE number 32078620.4.0000.5404). All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. 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 are storage in the university databank and will be provided under reasonable request. [1]: #ref-1 [2]: #ref-2

Background Lymphopenia is a typical symptom in the COVID-19 patients. While millions of patients are clinical recovered, little is known about the immune status of lymphocytes in these individuals. Methods A clinical recovered cohort (CR) of 55 COVID-19 individuals (discharged from hospital 4 to 11 weeks), and 55 age and sex matched healthy donors cohort (HD) were recruited. Detailed analysis on phenotype of the lymphocytes in peripheral blood mononuclear cells (PBMCs) was performed by flow cytometry. Findings Compared with cohort HD, the CD8+ T cells in cohort CR had higher Teff and Tem, but lower Tc1 (IFN-γ+), Tc2 (IL-4+) and Tc17 (IL-17A+) frequencies. The CD4+ T cells of CR had decreased frequency, especially on the Tcm subset. Moreover, CD4+ T cells of CR expressed lower PD-1 and had lower frequencies of Th1 (IFN-γ+), Th2 (IL-4+), Th17 (IL-17A+) as well as circulating Tfh (CXCR5+PD-1+). Accordingly, isotype-switched memory B cell (IgM-CD20hi) in CR had significantly lower proportion in B cells, though level of activation marker CD71 elevated. For CD3-HLA-DRlo lymphocytes of CR, besides levels of IFN-γ, Granzyme B and T-bet were lower, the correlation between T-bet and IFN-γ became irrelevant. In addition, taken into account of discharged days, all the lowered function associated phenotypes showed no recovery tendency within whole observation period. Interpretation The CR COVID-19 individuals still showed remarkable phenotypic alterations in lymphocytes after clinical recovery 4 to 11 weeks. This suggests SARS-CoV-2 infection imprints profoundly on lymphocytes and results in long-lasting potential dysfunctions. Funding Kunming Science and Technology Department (2020-1-N-037) ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement Funding Kunming Science and Technology Department (2020-1-N-037) ### 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: This study was reviewed and approved by the Medical Ethical Committee of Wuhan Jinyintan hospital (approval number KY-2020-47.01). All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. 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 I can provide the data of this study if required.

Given the known immuno- and neuro-pathogenicity of HERV-W ENV protein, it could promote certain pathogenic features of COVID-19 and therefore serve as a biomarker to predict clinical progression of disease and open to further studies for therapeutic intervention.

Coronavirus disease 2019 (COVID-19), caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread widely. The aim…

null

This cross-sectional study examines the differences in excess death rates between Republican and Democratic voters in Florida and Ohio after the COVID-19 vaccine became available for all adults.

Huaier Effects on Functional Compensation with Destructive Ribosomal RNA Structure after Anti-SARS-CoV-2 mRNA Vaccination. PubMed, SCI, Scopus, ESCI, PMC indexed

Among workers 35 to 44 years old, a stunning 34% more died than expected last quarter, with above-average rates in other age groups, too. But why?

Objective: To characterise Long COVID in a highly vaccinated population infected by Omicron. Design: Follow-up survey of persons testing positive for SARS-CoV-2 in Western Australia, 16 July-3 August 2022. Setting: Community Participants: 22,744 persons with COVID-19 who had agreed to participate in research at the time of diagnosis were texted a survey link 90 days later; non-responders were telephoned. Post stratification weights were applied to responses from 11,697 (51.4%) participants, 94.0% of whom had received = 3 vaccine doses. Main outcome measures: Prevalence of Long COVID - defined as reporting new or ongoing COVID-19 illness-related symptoms or health issues 90 days post diagnosis; associated health care utilisation, reductions in work/study and risk factors were assessed using log-binomial regression. Results: 18.2% (n=2,130) of respondents met case definition for Long COVID. Female sex, being 50-69 years of age, pre-existing health issues, residing in a rural or remote area, and receiving fewer vaccine doses were significant independent predictors of Long COVID (p 0.05). Persons with Long COVID reported a median of 6 symptoms, most commonly fatigue (70.6%) and difficulty concentrating (59.6%); 38.2% consulted a GP and 1.6% reported hospitalisation in the month prior to the survey due to ongoing symptoms. Of 1,778 respondents with Long COVID who were working/studying before their COVID-19 diagnosis, 17.9% reported reducing/discontinuing work/study. Conclusion: 90 days post Omicron infection, almost 1 in 5 respondents reported Long COVID symptoms; 1 in 15 of all persons with COVID-19 sought healthcare for associated health concerns =2 months after the acute illness. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study was funded by the Western Australia Department of Health ### 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: Human Research Ethics committee of Western Australia Department of Health 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, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present work are contained in the manuscript.

Viral respiratory tract infections are a leading cause of morbidity and mortality worldwide. Unfortunately, the transmission routes and shedding kinetics of respiratory viruses remain poorly understood. Air sampling techniques to quantify infectious viruses in the air are indispensable to improve in …

Background Type 2 diabetes (T2DM) incidence is increased after diagnosis of COVID-19. The impact of vaccination on this increase, for how long it persists, and the effect of COVID-19 on other types of diabetes remain unclear. Methods With NHS England approval, we studied diabetes incidence following COVID-19 diagnosis in pre-vaccination (N=15,211,471, January 2020-December 2021), vaccinated (N =11,822,640), and unvaccinated (N=2,851,183) cohorts (June-December 2021), using linked electronic health records. We estimated adjusted hazard ratios (aHRs) comparing diabetes incidence post-COVID-19 diagnosis with incidence before or without diagnosis up to 102 weeks post-diagnosis. Results were stratified by COVID-19 severity (hospitalised/non-hospitalised) and diabetes type. Findings In the pre-vaccination cohort, aHRS for T2DM incidence after COVID-19 (compared to before or without diagnosis) declined from 3.01 (95% CI: 2.76,3.28) in weeks 1-4 to 1.24 (1.12,1.38) in weeks 53-102. aHRS were higher in unvaccinated than vaccinated people (4.86 (3.69,6.41)) versus 1.42 (1.24,1.62) in weeks 1-4) and for hospitalised COVID-19 (pre-vaccination cohort 21.1 (18.8,23.7) in weeks 1-4 declining to 2.04 (1.65,2.51) in weeks 52-102), than non-hospitalised COVID-19 (1.45 (1.27,1.64) in weeks 1-4, 1.10 (0.98,1.23) in weeks 52-102). T2DM persisted for 4 months after COVID-19 for ∼73% of those diagnosed. Patterns were similar for Type 1 diabetes, though excess incidence did not persist beyond a year post-COVID-19. Interpretation Elevated T2DM incidence after COVID-19 is greater, and persists longer, in hospitalised than non-hospitalised people. It is markedly less apparent post-vaccination. Testing for T2DM after severe COVID-19 and promotion of vaccination are important tools in addressing this public health problem. Evidence before this study We searched PubMed for population-based observational studies published between December 1st 2019 and July 12th 2023 examining associations between SARS-CoV-2 infection or COVID-19 diagnosis (search string: SARS-CoV-2 or COVID* or coronavirus*) and subsequent incident diabetes (search term: diabetes). Of nineteen relevant studies; eight had a composite outcome of diabetes types, six stratified by diabetes type and five pertained to type-1-diabetes (T1DM) only. We did not identify any studies relating to gestational or other types of diabetes. Eleven studies were from the US, three from the UK, two from Germany, one from Canada, one from Denmark and one from South Korea. Most studies described cumulative relative risks (for infection versus no infection) one to two years post-SARS-CoV-2 infection of 1.2 to 2.6, though four studies found no associations with T1DM after the post-acute period. All studies lacked the power to compare diabetes relative risk by type, severity, and vaccination status in population subgroups. One study examined relative risks by vaccination status, but this used a composite outcome of diabetes and hyperlipidaemia and was conducted in a predominantly white male population. Two studies of T1DM found no evidence of elevated risk beyond 30 days after COVID-19 diagnosis, whilst two reported elevated risks at six months. Two studies of type 2 diabetes (T2DM) examined relative risks by time period post-infection: one study of US insurance claims reported a persistent association six months post-infection, whereas a large UK population-based study reported no associations after 12 weeks. However, the latter study used only primary care data, therefore COVID-19 cases were likely to have been under-ascertained. No large studies have investigated the persistence of diabetes diagnosed following COVID-19; key to elucidating the role of stress/steroid-induced hyperglycaemia. Added value of this study This study, which is the largest to address the question to date, analysed linked primary and secondary care health records with SARS-CoV-2 testing and COVID-19 vaccination data for 15 million people living in England. This enabled us to compare the elevation in diabetes incidence after COVID-19 diagnosis by diabetes type, COVID-19 severity and vaccination status, overall and in population subgroups. Importantly, excess diabetes incidence by time period since infection could also be quantified. Since healthcare in the UK is universal and free-at-the-point-of-delivery, almost the entire population is registered with primary care. Therefore the findings are likely to be generalisable. We found that, before availability of COVID-19 vaccination, a COVID-19 diagnosis (vs. no diagnosis) was associated with increased T2DM incidence which remained elevated by approximately 30% beyond one year after diagnosis. Though still present (with around 30% excess incidence at eight weeks), these associations were substantially attenuated in unvaccinated compared with vaccinated people. Excess incidence was greater in people hospitalised with COVID-19 than those who were not hospitalised after diagnosis. T1DM incidence was elevated up to, but not beyond, a year post COVID-19. Around 73% of people diagnosed with incident T2DM after COVID-19 still had evidence of diabetes four months after infection. Implications of all the available evidence There is a 30-50% elevated T2DM incidence post-COVID-19, but we report the novel finding that there is elevated incidence beyond one-year post-diagnosis. Elevated T1DM incidence did not appear to persist beyond a year, which may explain why previous studies disagree. For the first time in a general-population dataset, we demonstrate that COVID-19 vaccination reduces, but does not entirely ameliorate, excess diabetes incidence after COVID-19. This supports a policy of universal vaccination and suggests that other public health activities, such as enhanced diabetes screening after severe COVID-19, may be warranted, particularly in unvaccinated people. ### Competing Interest Statement NC is compensated by AstraZeneca for membership of Data Monitoring and Safety Committees for clinical trials. The other authors report no conflicts. ### Clinical Protocols ### Funding Statement This study was funded by the COVID-19 Longitudinal Health and Wellbeing National Core Study, funded by the UKRI Medical Research Council (MC\_PC\_20059); the COVID-19 Data and Connectivity National Core Study, funded by the UKRI Medical Research Council; and by the CONVALESCENCE long COVID study, funded by the UK National Institute for Health and Care Research (COVID-LT-009). This work was also supported by Health Data Research UK, which is funded by the UK Medical Research Council, Engineering and Physical Sciences Research Council, Economic and Social Research Council, Department of Health and Social Care (England), Chief Scientist Office of the Scottish Government Health and Social Care Directorates, Health and Social Care Research and Development Division (Welsh Government), Public Health Agency (Northern Ireland), British Heart Foundation and Wellcome. ### 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: Health Research Authority [REC reference 22/PR/0095] and the University of Bristol's Faculty of Health Sciences Ethics Committee [reference 117269] 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, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data were linked, stored, and analysed securely within the OpenSAFELY platform (https://opensafely.org/). Detailed pseudonymised patient data are potentially reidentifiable and therefore not shared. Details of access to OpenSAFELY secure data analytics platform is described on the OPENSAFELY (website https://opensafely.org/).

Die WHO hat bestätigt, dass eine Welle von Corona-Infektionen um den Erdball geht. Sie warnt vor einer existenziellen Bedrohung durch die Evolution der Viren, falls die öffentliche Gesundheitsinfrastruktur nicht in der Lage sein wird, diese neuesten Varianten unter Kontrolle zu halten.

The SARS-CoV-2 Omicron variant of concern (VOC) has multiple mutations in the spike (S) protein, which mediates viral infection and immunity. We analysed a sub lineage of Omicron, designated omicron XBB (XBB), that showed structural and functional changes in the S protein in response to the African selection pressures. We used molecular modelling to compare the S protein structures of the original Omicron and XBB found that XBB had a reduced receptor-binding domain (RBD) due to the loss of some β-sheets, which may increase its affinity to the human angiotensin-converting enzyme 2 (hACE2) receptor. We also used Fast Unconstrained Bayesian AppRoximation (FUBAR) and Recombination Detection Program 4 (RDP 4) to perform selection and recombination analysis respectively of the S protein sequences of Omicron and XBB and detected signals of positive selection and recombination in the N terminal domain (NTD) of the S1 subunit, which contains antibody-binding epitopes, and the RBD, which is involved in viral entry. Our results reveal the structural and functional adaptation of the Omicron XBB variant in Africa and its potential implications for viral pathogenesis and immunity. ### Competing Interest Statement The authors have declared no competing interest.

NIH-funded research links alterations to inflammatory protein, underscores vaccine importance.

In this Personal View, we discuss current knowledge on SARS-CoV-2 RNA or antigen persistence in children infected with SARS-CoV-2. Based on the evidence that the virus can persist in adults, we have done a literature review and analysed studies that looked for SARS-CoV-2 RNA or antigens in children undergoing autopsy, biopsy, or surgery for either death from COVID-19 or multisystem inflammatory syndrome, or assessments for long COVID-19 or other conditions. Our analysis suggests that in children, independent from disease severity, SARS-CoV-2 can spread systemically and persist for weeks to months.

In the published article, there was an error in the Funding statement. The funding statement was missing a second source. The published version is as follow: the authors received funding from the Agency for Science, Technology and Research (A*STAR) Career Development Award (C21112056). The correct Funding statement appears below.FUNDINGThe authors received funding from the Agency for Science, Technology and Research (A*STAR) Career Development Award (C21112056) and Singapore National Medical Research Council (OFYIRG19may- 0007). The authors apologize for this error and state that this does not change the scientific conclusions

The risk of developing venous thromboembolisms is elevated among cancer patients with COVID-19 taking anticancer drugs, new data show.

The laboratory accident hypothesis of COVID-19’s origins is a bust, but the popular consensus is unwilling to accept it.

null