1
|
Osterman A, Krenn F, Iglhaut M, Badell I, Lehner A, Späth PM, Stern M, Both H, Bender S, Muenchhoff M, Graf A, Krebs S, Blum H, Grimmer T, Durner J, Czibere L, Dächert C, Grzimek-Koschewa N, Protzer U, Kaderali L, Baldauf HM, Keppler OT. Automated antigen assays display a high heterogeneity for the detection of SARS-CoV-2 variants of concern, including several Omicron sublineages. Med Microbiol Immunol 2023; 212:307-322. [PMID: 37561226 PMCID: PMC10501957 DOI: 10.1007/s00430-023-00774-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Diagnostic tests for direct pathogen detection have been instrumental to contain the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) pandemic. Automated, quantitative, laboratory-based nucleocapsid antigen (Ag) tests for SARS-CoV-2 have been launched alongside nucleic acid-based test systems and point-of-care (POC) lateral-flow Ag tests. Here, we evaluated four commercial Ag tests on automated platforms for the detection of different sublineages of the SARS-CoV-2 Omicron variant of concern (VoC) (B.1.1.529) in comparison with "non-Omicron" VoCs. A total of 203 Omicron PCR-positive respiratory swabs (53 BA.1, 48 BA.2, 23 BQ.1, 39 XBB.1.5 and 40 other subvariants) from the period February to March 2022 and from March 2023 were examined. In addition, tissue culture-expanded clinical isolates of Delta (B.1.617.2), Omicron-BA.1, -BF.7, -BN.1 and -BQ.1 were studied. These results were compared to previously reported data from 107 clinical "non-Omicron" samples from the end of the second pandemic wave (February to March 2021) as well as cell culture-derived samples of wildtype (wt) EU-1 (B.1.177), Alpha VoC (B.1.1.7) and Beta VoC (B.1.351)). All four commercial Ag tests were able to detect at least 90.9% of Omicron-containing samples with high viral loads (Ct < 25). The rates of true-positive test results for BA.1/BA.2-positive samples with intermediate viral loads (Ct 25-30) ranged between 6.7% and 100.0%, while they dropped to 0 to 15.4% for samples with low Ct values (> 30). This heterogeneity was reflected also by the tests' 50%-limit of detection (LoD50) values ranging from 44,444 to 1,866,900 Geq/ml. Respiratory samples containing Omicron-BQ.1/XBB.1.5 or other Omicron subvariants that emerged in 2023 were detected with enormous heterogeneity (0 to 100%) for the intermediate and low viral load ranges with LoD50 values between 23,019 and 1,152,048 Geq/ml. In contrast, detection of "non-Omicron" samples was more sensitive, scoring positive in 35 to 100% for the intermediate and 1.3 to 32.9% of cases for the low viral loads, respectively, corresponding to LoD50 values ranging from 6181 to 749,792 Geq/ml. All four assays detected cell culture-expanded VoCs Alpha, Beta, Delta and Omicron subvariants carrying up to six amino acid mutations in the nucleocapsid protein with sensitivities comparable to the non-VoC EU-1. Overall, automated quantitative SARS-CoV-2 Ag assays are not more sensitive than standard rapid antigen tests used in POC settings and show a high heterogeneity in performance for VoC recognition. The best of these automated Ag tests may have the potential to complement nucleic acid-based assays for SARS-CoV-2 diagnostics in settings not primarily focused on the protection of vulnerable groups. In light of the constant emergence of new Omicron subvariants and recombinants, most recently the XBB lineage, these tests' performance must be regularly re-evaluated, especially when new VoCs carry mutations in the nucleocapsid protein or immunological and clinical parameters change.
Collapse
Affiliation(s)
- Andreas Osterman
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Franziska Krenn
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Iglhaut
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Irina Badell
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Andreas Lehner
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia M Späth
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Marcel Stern
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Hanna Both
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Sabine Bender
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID‑19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Timo Grimmer
- Department of Psychiatry and Psychotherapy, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Jürgen Durner
- Labor Becker MVZ GbR, Munich, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital, LMU München, Munich, Germany
| | | | - Christopher Dächert
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Natascha Grzimek-Koschewa
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Ulrike Protzer
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Hanna-Mari Baldauf
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany.
- COVID‑19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany.
| |
Collapse
|
2
|
Kegler A, Drewitz L, Arndt C, Daglar C, Rodrigues Loureiro L, Mitwasi N, Neuber C, González Soto KE, Bartsch T, Baraban L, Ziehr H, Heine M, Nieter A, Moreira-Soto A, Kühne A, Drexler JF, Seliger B, Laube M, Máthé D, Pályi B, Hajdrik P, Forgách L, Kis Z, Szigeti K, Bergmann R, Feldmann A, Bachmann M. A novel ACE2 decoy for both neutralization of SARS-CoV-2 variants and killing of infected cells. Front Immunol 2023; 14:1204543. [PMID: 37383226 PMCID: PMC10293748 DOI: 10.3389/fimmu.2023.1204543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/17/2023] [Indexed: 06/30/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to millions of infections and deaths worldwide. As this virus evolves rapidly, there is a high need for treatment options that can win the race against new emerging variants of concern. Here, we describe a novel immunotherapeutic drug based on the SARS-CoV-2 entry receptor ACE2 and provide experimental evidence that it cannot only be used for (i) neutralization of SARS-CoV-2 in vitro and in SARS-CoV-2-infected animal models but also for (ii) clearance of virus-infected cells. For the latter purpose, we equipped the ACE2 decoy with an epitope tag. Thereby, we converted it to an adapter molecule, which we successfully applied in the modular platforms UniMAB and UniCAR for retargeting of either unmodified or universal chimeric antigen receptor-modified immune effector cells. Our results pave the way for a clinical application of this novel ACE2 decoy, which will clearly improve COVID-19 treatment.
Collapse
Affiliation(s)
- Alexandra Kegler
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Laura Drewitz
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Claudia Arndt
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Mildred Scheel Early Career Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Cansu Daglar
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Liliana Rodrigues Loureiro
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Nicola Mitwasi
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Christin Neuber
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Karla Elizabeth González Soto
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Tabea Bartsch
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Larysa Baraban
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Holger Ziehr
- Department of Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Braunschweig, Germany
| | - Markus Heine
- Department of Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Braunschweig, Germany
| | - Annabel Nieter
- Department of Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Braunschweig, Germany
| | - Andres Moreira-Soto
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Arne Kühne
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jan Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Barbara Seliger
- Medical Faculty, Martin-Luther-University Halle-Wittenberg, Halle, Germany
- Institute of Translational Immunology, Medical High School, Brandenburg an der Havel, Germany
| | - Markus Laube
- Department of Radiopharmaceutical and Chemical Biology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Domokos Máthé
- Department of Biophysics and Radiation Biology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- Hungarian Centre of Excellence for Molecular Medicine, In Vivo Imaging Advanced Core Facility, Szeged, Hungary
- CROmed Translational Research Ltd., Budapest, Hungary
| | - Bernadett Pályi
- National Biosafety Laboratory, Division of Microbiological Reference Laboratories, National Public Health Center, Budapest, Hungary
| | - Polett Hajdrik
- Department of Biophysics and Radiation Biology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - László Forgách
- Semmelweis University School of Pharmacy, Semmelweis University, Budapest, Hungary
| | - Zoltán Kis
- National Biosafety Laboratory, Division of Microbiological Reference Laboratories, National Public Health Center, Budapest, Hungary
| | - Krisztián Szigeti
- Department of Biophysics and Radiation Biology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Ralf Bergmann
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Department of Biophysics and Radiation Biology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Anja Feldmann
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- National Center for Tumor Diseases Dresden (NCT), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Bachmann
- Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- National Center for Tumor Diseases Dresden (NCT), German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
3
|
Mahalingam G, Arjunan P, Periyasami Y, Dhyani AK, Devaraju N, Rajendiran V, Christopher AC, Kt RD, Dhanasingh I, Thangavel S, Murugesan M, Moorthy M, Srivastava A, Marepally S. Correlating the differences in the receptor binding domain of SARS-CoV-2 spike variants on their interactions with human ACE2 receptor. Sci Rep 2023; 13:8743. [PMID: 37253762 DOI: 10.1038/s41598-023-35070-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/12/2023] [Indexed: 06/01/2023] Open
Abstract
Spike glycoprotein of SARS-CoV-2 variants plays a critical role in infection and transmission through its interaction with human angiotensin converting enzyme 2 (hACE2) receptors. Prior findings using molecular docking and biomolecular studies reported varied findings on the difference in the interactions among the spike variants with the hACE2 receptors. Hence, it is a prerequisite to understand these interactions in a more precise manner. To this end, firstly, we performed ELISA with trimeric spike glycoproteins of SARS-CoV-2 variants including Wuhan Hu-1(Wild), Delta, C.1.2 and Omicron. Further, to study the interactions in a more specific manner by mimicking the natural infection, we developed hACE2 receptors expressing HEK-293T cell line, evaluated their binding efficiencies and competitive binding of spike variants with D614G spike pseudotyped virus. In line with the existing findings, we observed that Omicron had higher binding efficiency compared to Delta in both ELISA and Cellular models. Intriguingly, we found that cellular models could differentiate the subtle differences between the closely related C.1.2 and Delta in their binding to hACE2 receptors. Our study using the cellular model provides a precise method to evaluate the binding interactions between spike sub-lineages to hACE2 receptors.
Collapse
Affiliation(s)
- Gokulnath Mahalingam
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Porkizhi Arjunan
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Yogapriya Periyasami
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Ajay Kumar Dhyani
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Nivedita Devaraju
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Vignesh Rajendiran
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Abisha Crystal Christopher
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Ramya Devi Kt
- Department of Biotechnology, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Immanuel Dhanasingh
- Centre for Bio-Separation Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Saravanabhavan Thangavel
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Mohankumar Murugesan
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Mahesh Moorthy
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Alok Srivastava
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Srujan Marepally
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India.
| |
Collapse
|
4
|
Havranek B, Lindsey GW, Higuchi Y, Itoh Y, Suzuki T, Okamoto T, Hoshino A, Procko E, Islam SM. A computationally designed ACE2 decoy has broad efficacy against SARS-CoV-2 omicron variants and related viruses in vitro and in vivo. Commun Biol 2023; 6:513. [PMID: 37173421 PMCID: PMC10177734 DOI: 10.1038/s42003-023-04860-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
SARS-CoV-2, especially B.1.1.529/omicron and its sublineages, continues to mutate to evade monoclonal antibodies and antibodies elicited by vaccination. Affinity-enhanced soluble ACE2 (sACE2) is an alternative strategy that works by binding the SARS-CoV-2 S protein, acting as a 'decoy' to block the interaction between the S and human ACE2. Using a computational design strategy, we designed an affinity-enhanced ACE2 decoy, FLIF, that exhibited tight binding to SARS-CoV-2 delta and omicron variants. Our computationally calculated absolute binding free energies (ABFE) between sACE2:SARS-CoV-2 S proteins and their variants showed excellent agreement to binding experiments. FLIF displayed robust therapeutic utility against a broad range of SARS-CoV-2 variants and sarbecoviruses, and neutralized omicron BA.5 in vitro and in vivo. Furthermore, we directly compared the in vivo therapeutic efficacy of wild-type ACE2 (non-affinity enhanced ACE2) against FLIF. A few wild-type sACE2 decoys have shown to be effective against early circulating variants such as Wuhan in vivo. Our data suggest that moving forward, affinity-enhanced ACE2 decoys like FLIF may be required to combat evolving SARS-CoV-2 variants. The approach described herein emphasizes how computational methods have become sufficiently accurate for the design of therapeutics against viral protein targets. Affinity-enhanced ACE2 decoys remain highly effective at neutralizing omicron subvariants.
Collapse
Affiliation(s)
- Brandon Havranek
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, 19107, USA
- ComputePharma, LLC., Chicago, IL, USA
| | | | - Yusuke Higuchi
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Yumi Itoh
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tatsuya Suzuki
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Atsushi Hoshino
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Erik Procko
- Department of Biochemistry, University of Illinois, Urbana, IL, 61801, USA
- Cyrus Biotechnology, Inc., Seattle, WA, USA
| | - Shahidul M Islam
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- ComputePharma, LLC., Chicago, IL, USA.
- Department of Chemistry, Delaware State University, Dover, DE, 19901, USA.
| |
Collapse
|
5
|
Braeye T, Catteau L, Brondeel R, van Loenhout JAF, Proesmans K, Cornelissen L, Van Oyen H, Stouten V, Hubin P, Billuart M, Djiena A, Mahieu R, Hammami N, Van Cauteren D, Wyndham-Thomas C. Vaccine effectiveness against transmission of alpha, delta and omicron SARS-COV-2-infection, Belgian contact tracing, 2021-2022. Vaccine 2023; 41:3292-3300. [PMID: 37085456 PMCID: PMC10073587 DOI: 10.1016/j.vaccine.2023.03.069] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 04/08/2023]
Abstract
OBJECTIVES Vaccine effectiveness against transmission (VET) of SARS-CoV-2-infection can be estimated from secondary attack rates observed during contact tracing. We estimated VET, the vaccine-effect on infectiousness of the index case and susceptibility of the high-risk exposure contact (HREC). METHODS We fitted RT-PCR-test results from HREC to immunity status (vaccine schedule, prior infection, time since last immunity-conferring event), age, sex, calendar week of sampling, household, background positivity rate and dominant VOC using a multilevel Bayesian regression-model. We included Belgian data collected between January 2021 and January 2022. RESULTS For primary BNT162b2-vaccination we estimated initial VET at 96% (95%CI 95-97) against Alpha, 87% (95%CI 84-88) against Delta and 31% (95%CI 25-37) against Omicron. Initial VET of booster-vaccination (mRNA primary and booster-vaccination) was 87% (95%CI 86-89) against Delta and 68% (95%CI 65-70) against Omicron. The VET-estimate against Delta and Omicron decreased to 71% (95%CI 64-78) and 55% (95%CI 46-62) respectively, 150-200 days after booster-vaccination. Hybrid immunity, defined as vaccination and documented prior infection, was associated with durable and higher or comparable (by number of antigen exposures) protection against transmission. CONCLUSIONS While we observed VOC-specific immune-escape, especially by Omicron, and waning over time since immunization, vaccination remained associated with a reduced risk of SARS-CoV-2-transmission.
Collapse
Affiliation(s)
- Toon Braeye
- Department of Epidemiology and public health, Sciensano, Juliette Wytsmansstraat 14, 1000 Brussel, Belgium.
| | - Lucy Catteau
- Department of Epidemiology and public health, Sciensano, Juliette Wytsmansstraat 14, 1000 Brussel, Belgium
| | - Ruben Brondeel
- Department of Epidemiology and public health, Sciensano, Juliette Wytsmansstraat 14, 1000 Brussel, Belgium
| | - Joris A F van Loenhout
- Department of Epidemiology and public health, Sciensano, Juliette Wytsmansstraat 14, 1000 Brussel, Belgium
| | - Kristiaan Proesmans
- Department of Epidemiology and public health, Sciensano, Juliette Wytsmansstraat 14, 1000 Brussel, Belgium
| | - Laura Cornelissen
- Department of Epidemiology and public health, Sciensano, Juliette Wytsmansstraat 14, 1000 Brussel, Belgium
| | - Herman Van Oyen
- Department of Epidemiology and public health, Sciensano, Juliette Wytsmansstraat 14, 1000 Brussel, Belgium; Department of Public Health and Primary Care, Ghent University, Corneel Heymanslaan 10, 9000 Gent, Belgium
| | - Veerle Stouten
- Department of Epidemiology and public health, Sciensano, Juliette Wytsmansstraat 14, 1000 Brussel, Belgium
| | - Pierre Hubin
- Department of Epidemiology and public health, Sciensano, Juliette Wytsmansstraat 14, 1000 Brussel, Belgium
| | - Matthieu Billuart
- Department of Epidemiology and public health, Sciensano, Juliette Wytsmansstraat 14, 1000 Brussel, Belgium
| | - Achille Djiena
- Agence pour une Vie de Qualité, Rue de la Rivelaine 11, 6061 Charleroi, Belgium
| | - Romain Mahieu
- Common Community Commission Brussels, Rue Belliard 71/1, 1040 Brussels, Belgium
| | - Naima Hammami
- Agency for Care and Health, Infection Prevention and Control, Flemish Community, Koningin Maria Hendrikaplein 70 bus 55, 9000 Gent, Belgium
| | - Dieter Van Cauteren
- Department of Epidemiology and public health, Sciensano, Juliette Wytsmansstraat 14, 1000 Brussel, Belgium
| | - Chloé Wyndham-Thomas
- Department of Epidemiology and public health, Sciensano, Juliette Wytsmansstraat 14, 1000 Brussel, Belgium
| |
Collapse
|
6
|
Huang RC, Chiu CH, Shang HS, Perng CL, Chiang TT, Tsai CC, Wang CH. Clinical characteristics analysis of COVID-19 patients from the first significant community outbreak by SARS-CoV-2 variant B.1.1.7 in Taiwan as experienced from a single northern medical center. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:1036-1043. [PMID: 36057491 PMCID: PMC9381423 DOI: 10.1016/j.jmii.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 07/11/2022] [Accepted: 08/01/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND/PURPOSE Clinical characteristics of patients in the first community outbreak of coronavirus disease 2019 (COVID-19) by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant B.1.1.7 in Taiwan have not been characterized. METHODS SARS-CoV-2 positive specimens from inpatients between May 7 and June 15 in 2021were screen for SARS-CoV-2 B.1.1.7 lineage by VirSNiP assay. Clinical characteristics were reviewed and compared with those from Feb 1 to April 30, 2020 and from Jan 1 to March 31, 2022. RESULTS One hundred forty-one inpatients from May 7 to June 15, 2021 infected with SARS-CoV-2 B.1.1.7 lineage were included. The major presenting symptoms were fever (88.7%) and cough (59.6%). Incidence of relevant complications including pulmonary embolism, simultaneous infections with bacteria, virus, and fungi were 0.7%, 12.8%, 13.5%, and 2.1%, respectively. Old age, high Charlson comorbidity index, short of breath, and initial critical illness were independently associated with 28-day mortality (all p < 0.05). In comparison to COVID-19 inpatients from Feb 1 to April 30, 2020, patients from the outbreak by SARS-CoV-2 B.1.1.7 lineage were older, more severe in disease condition, higher mortality but less obvious initial presenting symptoms. After implementation of nationwide vaccination campaign in the next half year of 2021, COVID-19 inpatients from Jan 1 to March 31 in 2022 indicated less severe diseases than those infected with SARS-CoV-2 B.1.1.7 lineage. CONCLUSION COVID-19 inpatients by SARS-CoV-2 variant B.1.1.7 with old age, multiple comorbidities, and more severe disease conditions were associated with increased mortality. Vaccination for this vulnerable populations may be helpful.
Collapse
Affiliation(s)
- Ruei-Chang Huang
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chun-Hsiang Chiu
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Tsung-Ta Chiang
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chun-Chou Tsai
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Ching-Hsun Wang
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC,Corresponding author. Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, No. 325, Section 2, Cheng-Kung Road, Neihu 114, Taipei, Taiwan. Fax: +886-2-87927258
| |
Collapse
|
7
|
Sokhansanj BA, Rosen GL. Predicting COVID-19 disease severity from SARS-CoV-2 spike protein sequence by mixed effects machine learning. Comput Biol Med 2022; 149:105969. [PMID: 36041271 PMCID: PMC9384346 DOI: 10.1016/j.compbiomed.2022.105969] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/11/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022]
Abstract
Epidemiological studies show that COVID-19 variants-of-concern, like Delta and Omicron, pose different risks for severe disease, but they typically lack sequence-level information for the virus. Studies which do obtain viral genome sequences are generally limited in time, location, and population scope. Retrospective meta-analyses require time-consuming data extraction from heterogeneous formats and are limited to publicly available reports. Fortuitously, a subset of GISAID, the global SARS-CoV-2 sequence repository, includes "patient status" metadata that can indicate whether a sequence record is associated with mild or severe disease. While GISAID lacks data on comorbidities relevant to severity, such as obesity and chronic disease, it does include metadata for age and sex to use as additional attributes in modeling. With these caveats, previous efforts have demonstrated that genotype-patient status models can be fit to GISAID data, particularly when country-of-origin is used as an additional feature. But are these models robust and biologically meaningful? This paper shows that, in fact, temporal and geographic biases in sequences submitted to GISAID, as well as the evolving pandemic response, particularly reduction in severe disease due to vaccination, create complex issues for model development and interpretation. This paper poses a potential solution: efficient mixed effects machine learning using GPBoost, treating country as a random effect group. Training and validation using temporally split GISAID data and emerging Omicron variants demonstrates that GPBoost models are more predictive of the impact of spike protein mutations on patient outcomes than fixed effect XGBoost, LightGBM, random forests, and elastic net logistic regression models.
Collapse
Affiliation(s)
- Bahrad A Sokhansanj
- Ecological and Evolutionary Signal Processing & Informatics Laboratory, Drexel University, 3100 Chestnut St., Philadelphia, PA, 19104, United States of America.
| | - Gail L Rosen
- Ecological and Evolutionary Signal Processing & Informatics Laboratory, Drexel University, 3100 Chestnut St., Philadelphia, PA, 19104, United States of America.
| |
Collapse
|
8
|
Fernández‐Bastit L, Marfil S, Pradenas E, Valle R, Roca N, Rodon J, Pailler‐García L, Trinité B, Parera M, Noguera‐Julian M, Martorell J, Izquierdo‐Useros N, Carrillo J, Clotet B, Blanco J, Vergara‐Alert J, Segalés J. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and humoral responses against different variants of concern in domestic pet animals and stray cats from North-Eastern Spain. Transbound Emerg Dis 2022; 69:3518-3529. [PMID: 36167932 PMCID: PMC9538463 DOI: 10.1111/tbed.14714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/15/2022] [Accepted: 09/21/2022] [Indexed: 02/04/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic in humans, is able to infect several domestic, captive and wildlife animal species. Since reverse zoonotic transmission to pets has been demonstrated, it is crucial to determine their role in the epidemiology of the disease to prevent further spillover events and major spread of SARS-CoV-2. In the present study, we determined the presence of virus and the seroprevalence to SARS-CoV-2, as well as the levels of neutralizing antibodies (nAbs) against several variants of concern (VOCs) in pets (cats, dogs and ferrets) and stray cats from North-Eastern of Spain. We confirmed that cats and dogs can be infected by different VOCs of SARS-CoV-2 and, together with ferrets, are able to develop nAbs against the ancestral (B.1), Alpha (B.1.1.7), Beta (B.1.315), Delta (B.1.617.2) and Omicron (BA.1) variants, with lower titres against the latest in dogs and cats, but not in ferrets. Although the prevalence of active SARS-CoV-2 infection measured as direct viral RNA detection was low (0.3%), presence of nAbs in pets living in COVID-19-positive households was relatively high (close to 25% in cats, 10% in dogs and 40% in ferrets). It is essential to continue monitoring SARS-CoV-2 infections in these animals due to their frequent contact with human populations, and we cannot discard the probability of a higher animal susceptibility to new potential SARS-CoV-2 VOCs.
Collapse
Affiliation(s)
- Leira Fernández‐Bastit
- Unitat mixta d'Investigació IRTA‐UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA)Campus de la Universitat Autònoma de Barcelona (UAB)BellaterraCatalonia08193Spain,IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA)Campus de la Universitat Autònoma de Barcelona (UAB)BellaterraCatalonia08193Spain
| | | | | | - Rosa Valle
- Unitat mixta d'Investigació IRTA‐UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA)Campus de la Universitat Autònoma de Barcelona (UAB)BellaterraCatalonia08193Spain,IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA)Campus de la Universitat Autònoma de Barcelona (UAB)BellaterraCatalonia08193Spain
| | - Núria Roca
- Unitat mixta d'Investigació IRTA‐UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA)Campus de la Universitat Autònoma de Barcelona (UAB)BellaterraCatalonia08193Spain,IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA)Campus de la Universitat Autònoma de Barcelona (UAB)BellaterraCatalonia08193Spain
| | - Jordi Rodon
- Unitat mixta d'Investigació IRTA‐UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA)Campus de la Universitat Autònoma de Barcelona (UAB)BellaterraCatalonia08193Spain,IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA)Campus de la Universitat Autònoma de Barcelona (UAB)BellaterraCatalonia08193Spain
| | - Lola Pailler‐García
- Unitat mixta d'Investigació IRTA‐UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA)Campus de la Universitat Autònoma de Barcelona (UAB)BellaterraCatalonia08193Spain,IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA)Campus de la Universitat Autònoma de Barcelona (UAB)BellaterraCatalonia08193Spain
| | | | - Mariona Parera
- IrsiCaixa AIDS Research InstituteBadalona08916Spain,Infectious Diseases and Immunity, Faculty of MedicineUniversity of Vic‐Central University of Catalonia (UVic‐UCC)Barcelona08500Spain
| | - Marc Noguera‐Julian
- IrsiCaixa AIDS Research InstituteBadalona08916Spain,Infectious Diseases and Immunity, Faculty of MedicineUniversity of Vic‐Central University of Catalonia (UVic‐UCC)Barcelona08500Spain,Infectious Disease Networking Biomedical Research Center (CIBERINFEC)Carlos III Health InstituteMadridSpain
| | - Jaume Martorell
- Departament de Medicina i Cirugia AnimalsUniversitat Autònoma de Barcelona (UAB)Spain
| | - Nuria Izquierdo‐Useros
- IrsiCaixa AIDS Research InstituteBadalona08916Spain,Infectious Disease Networking Biomedical Research Center (CIBERINFEC)Carlos III Health InstituteMadridSpain,Germans Trias i Pujol Research Institute (IGTP)Can Ruti CampusBadalona08916Spain
| | - Jorge Carrillo
- IrsiCaixa AIDS Research InstituteBadalona08916Spain,Infectious Disease Networking Biomedical Research Center (CIBERINFEC)Carlos III Health InstituteMadridSpain,Germans Trias i Pujol Research Institute (IGTP)Can Ruti CampusBadalona08916Spain
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research InstituteBadalona08916Spain,Infectious Diseases and Immunity, Faculty of MedicineUniversity of Vic‐Central University of Catalonia (UVic‐UCC)Barcelona08500Spain,Lluita contra la SIDA FoundationHospital Universitari Germans Trias i PujolBadalona08916Spain
| | - Julià Blanco
- IrsiCaixa AIDS Research InstituteBadalona08916Spain,Infectious Diseases and Immunity, Faculty of MedicineUniversity of Vic‐Central University of Catalonia (UVic‐UCC)Barcelona08500Spain,Infectious Disease Networking Biomedical Research Center (CIBERINFEC)Carlos III Health InstituteMadridSpain,Germans Trias i Pujol Research Institute (IGTP)Can Ruti CampusBadalona08916Spain
| | - Júlia Vergara‐Alert
- Unitat mixta d'Investigació IRTA‐UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA)Campus de la Universitat Autònoma de Barcelona (UAB)BellaterraCatalonia08193Spain,IRTA. Programa de Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA)Campus de la Universitat Autònoma de Barcelona (UAB)BellaterraCatalonia08193Spain
| | - Joaquim Segalés
- Unitat mixta d'Investigació IRTA‐UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA)Campus de la Universitat Autònoma de Barcelona (UAB)BellaterraCatalonia08193Spain,Departament de Sanitat i Anatomia Animals, Facultat de VeterinàriaUniversitat Autònoma de BarcelonaCerdanyola del Vallès08193Spain
| |
Collapse
|
9
|
Durmaz V, Köchl K, Krassnigg A, Parigger L, Hetmann M, Singh A, Nutz D, Korsunsky A, Kahler U, König C, Chang L, Krebs M, Bassetto R, Pavkov-Keller T, Resch V, Gruber K, Steinkellner G, Gruber CC. Structural bioinformatics analysis of SARS-CoV-2 variants reveals higher hACE2 receptor binding affinity for Omicron B.1.1.529 spike RBD compared to wild type reference. Sci Rep 2022; 12:14534. [PMID: 36008461 PMCID: PMC9406262 DOI: 10.1038/s41598-022-18507-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 08/08/2022] [Indexed: 01/16/2023] Open
Abstract
To date, more than 263 million people have been infected with SARS-CoV-2 during the COVID-19 pandemic. In many countries, the global spread occurred in multiple pandemic waves characterized by the emergence of new SARS-CoV-2 variants. Here we report a sequence and structural-bioinformatics analysis to estimate the effects of amino acid substitutions on the affinity of the SARS-CoV-2 spike receptor binding domain (RBD) to the human receptor hACE2. This is done through qualitative electrostatics and hydrophobicity analysis as well as molecular dynamics simulations used to develop a high-precision empirical scoring function (ESF) closely related to the linear interaction energy method and calibrated on a large set of experimental binding energies. For the latest variant of concern (VOC), B.1.1.529 Omicron, our Halo difference point cloud studies reveal the largest impact on the RBD binding interface compared to all other VOC. Moreover, according to our ESF model, Omicron achieves a much higher ACE2 binding affinity than the wild type and, in particular, the highest among all VOCs except Alpha and thus requires special attention and monitoring.
Collapse
Affiliation(s)
| | | | | | | | - Michael Hetmann
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria.,Austrian Centre of Industrial Biotechnology, 8010, Graz, Austria
| | - Amit Singh
- Innophore GmbH, 8010, Graz, Austria.,Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria
| | | | | | | | | | - Lee Chang
- AWS Diagnostic Development Initiative-Global Social Impact, Seattle, WA, 98109, USA
| | - Marius Krebs
- Amazon Web Services EMEA SARL, 80807, Muenchen, Germany
| | | | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria
| | | | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria.,Field of Excellence BioHealth-University of Graz, 8010, Graz, Austria
| | - Georg Steinkellner
- Innophore GmbH, 8010, Graz, Austria. .,Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria.
| | - Christian C Gruber
- Innophore GmbH, 8010, Graz, Austria. .,Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria.
| |
Collapse
|