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1.
J Clin Immunol ; 2021 Dec 10.
Article in English | MEDLINE | ID: covidwho-1565436

ABSTRACT

Patients with primary antibody deficiency are at risk for severe and in many cases for prolonged COVID-19. Convalescent plasma treatment of immunocompromised individuals could be an option especially in countries with limited access to monoclonal antibody therapies. While studies in immunocompetent COVID19 patients have demonstrated only a limited benefit, evidence for the safety, timing, and effectiveness of this treatment in antibody-deficient patients is lacking. Here, we describe 16 cases with primary antibody deficiency treated with convalescent plasma in four medical centers. In our cohort, treatment was associated with a reduction in viral load and improvement of clinical symptoms, even when applied over a week after onset of infection. There were no relevant side effects besides a short-term fever reaction in one patient. Longitudinal full-genome sequencing revealed the emergence of mutations in the viral genome, potentially conferring an antibody escape in one patient with persistent viral RNA shedding upon plasma treatment. However, he resolved the infection after a second course of plasma treatment. Thus, our data suggest a therapeutic benefit of convalescent plasma treatment in patients with primary antibody deficiency even months after infection. While it appears to be safe, PCR follow-up for SARS-CoV-2 is advisable and early re-treatment might be considered in patients with persistent viral shedding.

3.
J Clin Microbiol ; : JCM0169821, 2021 Nov 10.
Article in English | MEDLINE | ID: covidwho-1511413

ABSTRACT

OBJECTIVE: This first pilot on external quality assessment (EQA) of SARS-CoV-2 whole genome sequencing, initiated by the ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD) and Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing. METHODS: Ten samples with varying viral loads were sent out to 15 clinical laboratories who had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centres were compared on were identification of 1) SNPs and indels, 2) Pango lineages, and 3) clusters between samples. RESULTS: The participating laboratories used a wide array of methods and analysis pipelines. Most were able to generate whole genomes for all samples. Genomes were sequenced to varying depth (up to 100-fold difference across centres). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignment. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data. CONCLUSIONS: The pilot EQA was an overall success. It was able to show the high quality of participating labs and provide valuable feedback in cases where problems occurred, thereby improving the sequencing setup of laboratories. A larger follow-up EQA should, however, improve on defining the variables and format of the report. Additionally, contamination and/or minority variants should be a further aspect of assessment.

4.
Preprint in English | EuropePMC | ID: ppcovidwho-292291

ABSTRACT

In spring 2021, an increasing number of infections was observed caused by the hitherto rarely described SARS-CoV-2 variant A.27 in south-west Germany. From December 2020 to June 2021 this lineage has been detected in 31 countries. Phylogeographic analyses of A.27 sequences obtained from national and international databases reveal a global spread of this lineage through multiple introductions from its inferred origin in Western Africa. Variant A.27 is characterized by a mutational pattern in the spike gene that includes the L18F, L452R and N501Y spike amino acid substitutions found in various variants of concern but lacks the globally dominant D614G. Neutralization assays demonstrated an escape of A.27 from convalescent and vaccine-elicited antibody-mediated immunity. Moreover, the therapeutic monoclonal antibody Bamlanivimab and partially the REGN-COV2 cocktail failed to block infection by A.27. Our data emphasize the need for continued global monitoring of novel lineages because of the independent evolution of new escape mutations.

5.
Nat Commun ; 12(1): 6405, 2021 11 04.
Article in English | MEDLINE | ID: covidwho-1505001

ABSTRACT

The origin of SARS-CoV-2 variants of concern remains unclear. Here, we test whether intra-host virus evolution during persistent infections could be a contributing factor by characterizing the long-term SARS-CoV-2 infection dynamics in an immunosuppressed kidney transplant recipient. Applying RT-qPCR and next-generation sequencing (NGS) of sequential respiratory specimens, we identify several mutations in the viral genome late in infection. We demonstrate that a late viral isolate exhibiting genome mutations similar to those found in variants of concern first identified in UK, South Africa, and Brazil, can escape neutralization by COVID-19 antisera. Moreover, infection of susceptible mice with this patient's escape variant elicits protective immunity against re-infection with either the parental virus and the escape variant, as well as high neutralization titers against the alpha and beta SARS-CoV-2 variants, B.1.1.7 and B.1.351, demonstrating a considerable immune control against such variants of concern. Upon lowering immunosuppressive treatment, the patient generated spike-specific neutralizing antibodies and resolved the infection. Our results suggest that immunocompromised patients could be a source for the emergence of potentially harmful SARS-CoV-2 variants.


Subject(s)
COVID-19/immunology , COVID-19/virology , SARS-CoV-2/immunology , Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , Genome, Viral , Humans , Immune Evasion , Immunocompromised Host , Male , Middle Aged , Mutation , Neutralization Tests , Phylogeny , SARS-CoV-2/chemistry , SARS-CoV-2/classification , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics
6.
Infection ; 49(6): 1299-1306, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1482322

ABSTRACT

PURPOSE: Thorough knowledge of the nature and frequency of co-infections is essential to optimize treatment strategies and risk assessment in cases of coronavirus disease 2019 (COVID-19). This study aimed to evaluate the multiplex polymerase chain reaction (PCR) screening approach for community-acquired bacterial pathogens (CABPs) at hospital admission, which could facilitate identification of bacterial co-infections in hospitalized COVID-19 patients. METHODS: Clinical data and biomaterials from 200 hospitalized COVID-19 patients from the observational cohort of the Competence Network for community-acquired pneumonia (CAPNETZ) prospectively recruited between March 17, 2020, and March 12, 2021 in 12 centers in Germany and Switzerland, were included in this study. Nasopharyngeal swab samples were analyzed on hospital admission using multiplex real-time reverse transcription (RT)-PCR for a broad range of CABPs. RESULTS: In total of 200 patients Staphylococcus aureus (27.0%), Haemophilus influenzae (13.5%), Streptococcus pneumoniae (5.5%), Moraxella catarrhalis (2.5%), and Legionella pneumophila (1.5%) were the most frequently detected bacterial pathogens. PCR detection of bacterial pathogens correlated with purulent sputum, and showed no correlation with ICU admission, mortality, and inflammation markers. Although patients who received antimicrobial treatment were more often admitted to the ICU and had a higher mortality rate, PCR pathogen detection was not significantly related to antimicrobial treatment. CONCLUSION: General CABP screening using multiplex PCR with nasopharyngeal swabs may not facilitate prediction or identification of bacterial co-infections in the early phase of COVID-19-related hospitalization. Most patients with positive PCR results appear to be colonized rather than infected at that time, questioning the value of routine antibiotic treatment on admission in COVID-19 patients.


Subject(s)
COVID-19 , Coinfection , Community-Acquired Infections , Legionella pneumophila , Pneumonia , Cohort Studies , Coinfection/diagnosis , Coinfection/epidemiology , Community-Acquired Infections/diagnosis , Humans , Multiplex Polymerase Chain Reaction , Prospective Studies , SARS-CoV-2
7.
Emerg Microbes Infect ; 10(1): 1515-1518, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1313723

ABSTRACT

We show a shift in the prevalence of respiratory viral pathogens in community-acquired pneumonia patients during the COVID-19 pandemic. Our data support the efficiency of non-pharmaceutical interventions on virus circulation except for rhinoviruses. The consequences of an altered circulation on subsequent winter seasons remain unclear and support the importance of systematic virological surveillance.


Subject(s)
COVID-19/epidemiology , Community-Acquired Infections/epidemiology , Pneumonia/epidemiology , Respiratory Tract Infections/epidemiology , Adult , Aged , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , COVID-19/virology , Community-Acquired Infections/microbiology , Community-Acquired Infections/virology , Female , Germany/epidemiology , Humans , Male , Middle Aged , Pandemics , Pneumonia/microbiology , Pneumonia/virology , Prevalence , Prospective Studies , Respiratory Tract Infections/microbiology , Respiratory Tract Infections/virology , SARS-CoV-2/genetics , SARS-CoV-2/physiology , Viruses/classification , Viruses/genetics , Viruses/isolation & purification , Young Adult
9.
Nat Med ; 27(1): 78-85, 2021 01.
Article in English | MEDLINE | ID: covidwho-1065910

ABSTRACT

Emerging data indicate that SARS-CoV-2-specific CD8+ T cells targeting different viral proteins are detectable in up to 70% of convalescent individuals1-5. However, very little information is currently available about the abundance, phenotype, functional capacity and fate of pre-existing and induced SARS-CoV-2-specific CD8+ T cell responses during the natural course of SARS-CoV-2 infection. Here, we define a set of optimal and dominant SARS-CoV-2-specific CD8+ T cell epitopes. We also perform a high-resolution ex vivo analysis of pre-existing and induced SARS-CoV-2-specific CD8+ T cells, applying peptide-loaded major histocompatibility complex class I (pMHCI) tetramer technology. We observe rapid induction, prolonged contraction and emergence of heterogeneous and functionally competent cross-reactive and induced memory CD8+ T cell responses in cross-sectionally analyzed individuals with mild disease following SARS-CoV-2 infection and three individuals longitudinally assessed for their T cells pre- and post-SARS-CoV-2 infection. SARS-CoV-2-specific memory CD8+ T cells exhibited functional characteristics comparable to influenza-specific CD8+ T cells and were detectable in SARS-CoV-2 convalescent individuals who were seronegative for anti-SARS-CoV-2 antibodies targeting spike (S) and nucleoprotein (N). These results define cross-reactive and induced SARS-CoV-2-specific CD8+ T cell responses as potentially important determinants of immune protection in mild SARS-CoV-2 infection.


Subject(s)
CD8-Positive T-Lymphocytes/immunology , COVID-19/immunology , COVID-19/blood , Case-Control Studies , Convalescence , Coronavirus Nucleocapsid Proteins/chemistry , Cross Reactions , Cross-Sectional Studies , Epitopes, T-Lymphocyte , Flow Cytometry , HLA-B Antigens/immunology , Humans , Immunologic Memory , Longitudinal Studies , Phosphoproteins/chemistry , SARS-CoV-2/physiology , Spike Glycoprotein, Coronavirus/chemistry
10.
JAMA Pediatr ; 175(6): 586-593, 2021 06 01.
Article in English | MEDLINE | ID: covidwho-1044436

ABSTRACT

Importance: School and daycare closures were enforced as measures to confine the novel coronavirus disease 2019 (COVID-19) pandemic, based on the assumption that young children may play a key role in severe acute respiratory coronavirus 2 (SARS-CoV-2) spread. Given the grave consequences of contact restrictions for children, a better understanding of their contribution to the COVID-19 pandemic is of great importance. Objective: To describe the rate of SARS-CoV-2 infections and the seroprevalence of SARS-CoV-2 antibodies in children aged 1 to 10 years, compared with a corresponding parent of each child, in a population-based sample. Design, Setting, and Participants: This large-scale, multicenter, cross-sectional investigation (the COVID-19 BaWü study) enrolled children aged 1 to 10 years and a corresponding parent between April 22 and May 15, 2020, in southwest Germany. Exposures: Potential exposure to SARS-CoV-2. Main Outcomes and Measures: The main outcomes were infection and seroprevalence of SARS-CoV-2. Participants were tested for SARS-CoV-2 RNA from nasopharyngeal swabs by reverse transcription-polymerase chain reaction and SARS-CoV-2 specific IgG antibodies in serum by enzyme-linked immunosorbent assays and immunofluorescence tests. Discordant results were clarified by electrochemiluminescence immunoassays, a second enzyme-linked immunosorbent assay, or an in-house Luminex-based assay. Results: This study included 4964 participants: 2482 children (median age, 6 [range, 1-10] years; 1265 boys [51.0%]) and 2482 parents (median age, 40 [range, 23-66] years; 615 men [24.8%]). Two participants (0.04%) tested positive for SARS-CoV-2 RNA. The estimated SARS-CoV-2 seroprevalence was low in parents (1.8% [95% CI, 1.2-2.4%]) and 3-fold lower in children (0.6% [95% CI, 0.3-1.0%]). Among 56 families with at least 1 child or parent with seropositivity, the combination of a parent with seropositivity and a corresponding child with seronegativity was 4.3 (95% CI, 1.19-15.52) times higher than the combination of a parent who was seronegative and a corresponding child with seropositivity. We observed virus-neutralizing activity for 66 of 70 IgG-positive serum samples (94.3%). Conclusions and Relevance: In this cross-sectional study, the spread of SARS-CoV-2 infection during a period of lockdown in southwest Germany was particularly low in children aged 1 to 10 years. Accordingly, it is unlikely that children have boosted the pandemic. This SARS-CoV-2 prevalence study, which appears to be the largest focusing on children, is instructive for how ad hoc mass testing provides the basis for rational political decision-making in a pandemic.


Subject(s)
Antibodies, Viral/blood , COVID-19/diagnosis , COVID-19/epidemiology , SARS-CoV-2/isolation & purification , Adult , Age Distribution , Age Factors , Aged , COVID-19/blood , COVID-19 Serological Testing , Child , Child, Preschool , Cross-Sectional Studies , Germany/epidemiology , Humans , Immunoglobulin A/blood , Immunoglobulin G/blood , Immunoglobulin M/blood , Male , Middle Aged , Parents , Prevalence , Seroepidemiologic Studies
11.
Preprint | SSRN | ID: ppcovidwho-5070

ABSTRACT

Background: School and day-care closures were enforced as measures to confine the COVID-19 pandemic based on the assumption that young children may play a key role in SARS-CoV-2 spreading. However, infection prevalence in children under 10 years of age is not very well analysed. Methods: The COVID-19 BaWü study is a large-scale multicentre cross-sectional investigation of children aged 1–10 years and one of their parents, both not diagnosed with COVID-19 before, in southwest Germany. We tested for SARS-CoV-2 RNA from nasopharyngeal swabs by RT-PCR and for SARS-CoV-2 specific IgG antibodies in serum by ELISA and immunofluorescence. Discordant results were clarified by ECLIA, a second ELISA or an in-house Luminex-based assay. We used mixed effects logistic regression to estimate the seroprevalence and to analyse the association between SARS-CoV-2 seropositivity and covariates. Findings: Between April 22nd and May 15th, 2020, we enrolled 4964 subjects, 2482 children and 2482 corresponding parents. 0•04% tested positive for SARS-CoV-2 RNA. The estimated SARS-CoV-2 seroprevalence was low in parents (1•8%;95% CI, 1•2–2•4%) and 3-fold lower in children (0•6%;95% CI, 0•3–1•0%). We observed virus-neutralizing activity for 66 of 70 IgG-positive sera (94•3%). Interpretation: The spread of SARS-CoV-2 infection during a period of lock-down in southwest Germany was particularly low in children aged 1–10 years. Accordingly, it is unlikely that children have boosted the pandemic. This largest reported SARS-CoV-2 prevalence study focussing on children is instructive for how ad hoc mass testing provides the basis for rational political decision making in a pandemic setting. Funding: Grant from the Federal State of Baden-Württemberg, Germany Declaration of Interests: All authors state no conflict of interest. Ethics Approval Statement: The study protocol was approved by the independent Ethics committees of each centre. The study was conducted according to the Declaration of Helsinki. Written informed consent was obtained from all parents/guardians, with assent from children when appropriate for their age.

12.
Front Immunol ; 11: 2086, 2020.
Article in English | MEDLINE | ID: covidwho-771524

ABSTRACT

Immunosuppressive therapies increase the susceptibility of patients to infections. The current pandemic with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compels clinicians to develop recommendations for successful clinical management and surveillance of immunocompromised patients at high risk for severe disease progression. With only few case studies published on SARS-CoV-2 infection in patients with rheumatic diseases, we report a 25-year-old male who developed moderate coronavirus disease 2019 (COVID-19) with fever, mild dyspnea, and no major complications despite having received high-dose prednisolone, cyclophosphamide, and rituximab for the treatment of highly active, life-threatening eosinophilic granulomatosis with polyangiitis (EGPA).


Subject(s)
Betacoronavirus/genetics , Churg-Strauss Syndrome/complications , Churg-Strauss Syndrome/drug therapy , Coronavirus Infections/complications , Cyclophosphamide/therapeutic use , Granulomatosis with Polyangiitis/complications , Granulomatosis with Polyangiitis/drug therapy , Immunosuppressive Agents/therapeutic use , Pneumonia, Viral/complications , Adult , Antiviral Agents/therapeutic use , COVID-19 , Coronavirus Infections/drug therapy , Coronavirus Infections/virology , Drug Therapy, Combination , Glucocorticoids/therapeutic use , Humans , Immunocompromised Host , Male , Pandemics , Pneumonia, Viral/drug therapy , Pneumonia, Viral/virology , Prednisolone/therapeutic use , RNA, Viral/genetics , Reverse Transcriptase Polymerase Chain Reaction , Rituximab/therapeutic use , SARS-CoV-2 , Treatment Outcome
13.
Infection ; 48(6): 971-974, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-631448

ABSTRACT

PURPOSE: The first SARS-CoV-2 cases in Europe were reported in January 2020. Recently, concern arose on unrecognized infections before this date. For a better understanding of the pandemic, we retrospectively analyzed patient samples for SARS-CoV-2 from the prospective CAPNETZ study cohort. METHODS: We used nasopharyngeal swab samples from a cohort of well characterized patients with community acquired pneumonia of the CAPNETZ study group, recruited from different geographic regions across Germany, Austria, the Netherlands, and Switzerland between 02nd December 2019 and 28th April 2020. Multiplex real-time RT-PCR for a broad range of respiratory pathogens and SARS-CoV-2 real-time RT-PCR were performed on all samples. RESULTS: In our cohort, respiratory pathogens other than SARS-CoV-2 were detected in 21.5% (42/195) of patients with rhinovirus as the most frequently detected pathogen. The detection rate increased to 29.7% (58/195) when SARS-CoV-2 was included. No SARS-CoV-2 positive sample was detected before end of March 2020. CONCLUSIONS: Respiratory viral pathogens accounted for a considerable number of positive results but no SARS-CoV-2 case was identified before the end of March 2020.


Subject(s)
COVID-19/epidemiology , Community-Acquired Infections/epidemiology , Pneumonia/epidemiology , Adult , Aged , Aged, 80 and over , COVID-19/diagnosis , COVID-19/virology , Cohort Studies , Community-Acquired Infections/diagnosis , Community-Acquired Infections/etiology , Community-Acquired Infections/history , Female , Germany , History, 21st Century , Humans , Male , Middle Aged , Multiplex Polymerase Chain Reaction , Pneumonia/diagnosis , Pneumonia/etiology , Pneumonia/history , SARS-CoV-2 , Young Adult
14.
Am J Transplant ; 20(11): 3239-3245, 2020 11.
Article in English | MEDLINE | ID: covidwho-592123

ABSTRACT

In the coronavirus disease 2019 (COVID-19) pandemic, organ transplant recipients are considered to be at high risk for an unfavorable outcome. However, in particular the role of immunosuppression in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains undetermined. Here, we present a 62-year-old male COVID-19 patient with recent heart transplantation who developed only mild symptoms, but had prolonged virus shedding, and summarize the available data on COVID-19 in cardiac allograft recipients. Initially the patient presented with a transient episode of fever and sore throat but no other symptoms, in particular no cough or dyspnea at rest. After diagnosis, immunosuppression was continued unchanged. On day 7, his temperature increased again with concurrent mild rise of C-reactive protein, IL-6, and pro-B-type natriuretic peptide levels. Hydroxychloroquine was started and continued for 7 days. While the patient no longer had clinical symptoms 20 days after initial presentation, virus culture of throat swabs on days 18 and 21 confirmed active virus replication and SARS-CoV-2 PCR remained positive on day 35 with copy numbers similar to the onset of infection. In conclusion, the immunosuppression regimen in transplant recipients with mild COVID-19-associated symptoms may be continued unchanged. However, it may contribute to delayed virus polymerase chain reaction conversion and thus possible prolonged infectivity.


Subject(s)
COVID-19/epidemiology , Heart Failure/surgery , Heart Transplantation/methods , RNA, Viral/analysis , SARS-CoV-2/genetics , Virus Shedding , Aged , Antiviral Agents/therapeutic use , COVID-19/drug therapy , COVID-19/virology , Comorbidity , Heart Failure/epidemiology , Humans , Male , Middle Aged , Pandemics , Transplant Recipients
15.
Dtsch Med Wochenschr ; 145(11): 740-746, 2020 Jun.
Article in German | MEDLINE | ID: covidwho-535976

ABSTRACT

- Case numbers in China are clearly declining, case numbers in many European regions are no longer increasing exponentially.- Data on mortality from SARS-CoV-2 infection are contradictory; mortality is certainly lower than for SARS and MERS, but probably higher than for most seasonal flu outbreaks in recent years- The main complication of SARS-CoV-2 infection is pneumonia with development of acute respiratory distress syndrome (ARDS)- Asymptomatic and oligosymptomatic courses with virus shedding are not uncommon; they may be more frequent in children than in adults. Virus excretion in asymptomatic people and in the pre-symptomatic phase of an infection is relevant for transmission- An effective antiviral therapy has not yet been established. Steroids for anti-inflammatory therapy are not recommended- It is very important to prepare all actors in the health care system for a longer-term burden of inpatients and complications and to create the necessary capacities. Low-threshold diagnostic testing and rapid detection of infection chains remain essential for better control of the pandemic. An effective vaccine is urgent.


Subject(s)
Coronavirus Infections/epidemiology , Pandemics/classification , Pneumonia, Viral/classification , COVID-19 , Coronavirus Infections/classification , Coronavirus Infections/diagnosis , Coronavirus Infections/therapy , Coronavirus Infections/virology , Global Health/statistics & numerical data , Humans
16.
J Clin Virol ; 127: 104381, 2020 06.
Article in English | MEDLINE | ID: covidwho-102384

ABSTRACT

BACKGROUND: A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in China in late 2019 and subsequently caused a pandemic. Surveillance is important to better appreciate this evolving pandemic and to longitudinally monitor the effectiveness of public health measures. OBJECTIVES: We aimed to provide a rapid, easy to establish and costeffective laboratory-based surveillance tool for SARS-CoV-2. STUDY DESIGN: We used minipools of RNA prepared from nucleic acid extractions of routine respiratory samples. We technically validated the assay and distributed the protocol within an informal network of five German university laboratories. RESULTS: We tested a total of 70 minipools resembling 700 samples shortly before the upsurge of cases in Germany from 17.02.2020 to 10.03.2020. One minipool reacted positive and after resolution one individual sample tested SARS-CoV-2 positive. This sample was from a hospitalized patient not suspected of having contracted SARS-CoV-2. CONCLUSIONS: Our approach of a laboratory-based surveillance for SARSCoV-2 using minipools proved its concept is easily adaptable and resource-saving. It might assist not only public health laboratories in SARS-CoV-2 surveillance.


Subject(s)
Coronavirus Infections/diagnosis , Epidemiological Monitoring , Molecular Diagnostic Techniques/methods , Pneumonia, Viral/diagnosis , RNA, Viral/isolation & purification , Reverse Transcriptase Polymerase Chain Reaction , Betacoronavirus/isolation & purification , Bronchoalveolar Lavage Fluid/virology , COVID-19 , Germany/epidemiology , Humans , Pandemics , Pharynx/virology , Prospective Studies , SARS-CoV-2 , Sputum/virology
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