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Ivanusic D, Maier J, Icli S, Falcone V, Bernauer H, Bannert N. tANCHOR-cell-based assay for monitoring of SARS-CoV-2 neutralizing antibodies rapidly adaptive to various receptor-binding domains. iScience 2024; 27:109123. [PMID: 38380248 PMCID: PMC10877956 DOI: 10.1016/j.isci.2024.109123] [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: 05/17/2023] [Revised: 10/24/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
Conventional neutralizing enzyme-linked immunosorbent assay (ELISA) systems for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mimic the protein-protein interaction between angiotensin-converting enzyme 2 (ACE2) and the receptor-binding domain (RBD). However, an easy and rapidly adaptative ELISA-based system for testing neutralizing antibodies against upcoming SARS-CoV-2 variants is urgently needed. In this study, we closed this gap by developing a tANCHOR-cell-based RBD neutralization assay that avoids time-consuming protein expression and purification followed by coating on ELISA plates. This cell-based assay can be rapidly adopted to monitor neutralizing antibodies (NAbs) against upcoming SARS-CoV-2 variants. We show that the results obtained with the tANCHOR-cell-based assay system strongly correlate with commercially available surrogate assays for testing NAbs. Moreover, this technique can directly measure binding between cell-surface-exposed RBDs and soluble ACE2. With this technique, the degree of antibody escape elicited by emerging SARS-CoV-2 variants in current vaccination regimens can be determined rapidly and reliably.
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Affiliation(s)
- Daniel Ivanusic
- Sexually transmitted bacterial pathogens and HIV (FG18), Robert Koch-Institute, 13353 Berlin, Germany
| | - Josef Maier
- ATG:biosynthetics GmbH, 79249 Merzhausen, Germany
| | - Suheda Icli
- Sexually transmitted bacterial pathogens and HIV (FG18), Robert Koch-Institute, 13353 Berlin, Germany
| | - Valeria Falcone
- Freiburg University Medical Center, Faculty of Medicine, Institute of Virology, University of Freiburg, 79104 Freiburg, Germany
| | | | - Norbert Bannert
- Sexually transmitted bacterial pathogens and HIV (FG18), Robert Koch-Institute, 13353 Berlin, Germany
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Kim JW, Lee JH, Kim HJ, Heo K, Lee Y, Jang HJ, Lee HY, Park JW, Cho YB, Shin HG, Yang HR, Lee HE, Song JY, Lee S. Empowering SARS-CoV-2 variant neutralization with a bifunctional antibody engineered with tandem heptad repeat 2 peptides. J Med Virol 2024; 96:e29506. [PMID: 38445718 DOI: 10.1002/jmv.29506] [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: 11/17/2023] [Revised: 01/28/2024] [Accepted: 02/23/2024] [Indexed: 03/07/2024]
Abstract
With the global pandemic and the continuous mutations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the need for effective and broadly neutralizing treatments has become increasingly urgent. This study introduces a novel strategy that targets two aspects simultaneously, using bifunctional antibodies to inhibit both the attachment of SARS-CoV-2 to host cell membranes and viral fusion. We developed pioneering IgG4-(HR2)4 bifunctional antibodies by creating immunoglobulin G4-based and phage display-derived human monoclonal antibodies (mAbs) that specifically bind to the SARS-CoV-2 receptor-binding domain, engineered with four heptad repeat 2 (HR2) peptides. Our in vitro experiments demonstrate the superior neutralization efficacy of these engineered antibodies against various SARS-CoV-2 variants, ranging from original SARS-CoV-2 strain to the recently emerged Omicron variants, as well as SARS-CoV, outperforming the parental mAb. Notably, intravenous monotherapy with the bifunctional antibody neutralizes a SARS-CoV-2 variant in a murine model without causing significant toxicity. In summary, this study unveils the significant potential of HR2 peptide-driven bifunctional antibodies as a potent and versatile strategy for mitigating SARS-CoV-2 infections. This approach offers a promising avenue for rapid development and management in the face of the continuously evolving SARS-CoV-2 variants, holding substantial promise for pandemic control.
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Affiliation(s)
- Ji Woong Kim
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ji Hyun Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Hyun Jung Kim
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Kyun Heo
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
- Department of Chemistry, Kookmin University, Seoul, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul, Republic of Korea
| | - Yoonwoo Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Hui Jeong Jang
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Ho-Young Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Jun Won Park
- Division of Biomedical Convergence, Kangwon National University, Chuncheon, Republic of Korea
| | - Yea Bin Cho
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ha Gyeong Shin
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ha Rim Yang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Hee Eon Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Jin Young Song
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Sukmook Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
- Department of Chemistry, Kookmin University, Seoul, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul, Republic of Korea
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Teixeira DG, Rodrigues-Neto JF, da Cunha DCS, Jeronimo SMB. Understanding SARS-CoV-2 spike glycoprotein clusters and their impact on immunity of the population from Rio Grande do Norte, Brazil. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 118:105556. [PMID: 38242186 DOI: 10.1016/j.meegid.2024.105556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
SARS-CoV-2 genome underwent mutations since it started circulating within the human population. The aim of this study was to understand the fluctuation of the spike clusters concomitant to the population immunity either due to natural infection and/or vaccination in a state of Brazil that had both high rate of natural infection and vaccination coverage. A total of 1725 SARS-CoV-2 sequences from the state of Rio Grande do Norte, Brazil, were retrieved from GISAID and subjected to cluster analysis. Immunoinformatics were used to predict T- and B-cell epitopes, followed by simulation to estimate either pro- or anti-inflammatory responses and to correlate with circulating variants. From March 2020 to June 2022, the state of Rio Grande do Norte reported 579,931 COVID-19 cases with a 1.4% fatality rate across the three major waves: May-Sept 2020, Feb-Aug 2021, and Jan-Mar 2022. Cluster 0 variants (wild type strain, Zeta) were prevalent in the first wave and Delta (AY.*), which circulated in Brazil in the latter half of 2021, featuring fewer unique epitopes. Cluster 1 (Gamma (P.1 + P.1.*)) dominated the first half of 2021. Late 2021 had two new clusters, Cluster 2 (Omicron, (B.1.1.529 + BA.*)), and Cluster 3 (BA.*) with the most unique epitopes, in addition to Cluster 4 (Delta sub lineages) which emerged in the second half of 2021 with fewer unique epitopes. Cluster 1 epitopes showed a high pro-inflammatory propensity, while others exhibited a balanced cytokine induction. The clustering method effectively identified Spike groups that may contribute to immune evasion and clinical presentation, and explain in part the clinical outcome.
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Affiliation(s)
- Diego Gomes Teixeira
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - João Firmino Rodrigues-Neto
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil; Escola Multicampi de Ciências Médicas do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Caicó, Rio Grande do Norte, Brazil
| | - Dayse Caroline Severiano da Cunha
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Selma Maria Bezerra Jeronimo
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil; Departmento de Bioquímica, Centro de Biociências, Universidade Federal do Rio Grande Norte, Natal, Rio Grande do Norte, Brazil; Instituto Nacional de Ciência e Tecnologia de Doenças Tropicais, Natal, Rio Grande do Norte, Brazil.
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Triebelhorn J, Schneider J, Spinner CD, Iakoubov R, Voit F, Wagner L, Erber J, Rothe K, Berthele A, Pernpeintner V, Strauß EM, Renders L, Willmann A, Minic M, Vogel E, Christa C, Hoffmann D, Protzer U, Jeske SD. Clinical and immunological outcomes of SARS-CoV-2-infected vaccine responders, vaccine non-responders, and unvaccinated patients evaluated for neutralizing monoclonal antibody treatment at a single German tertiary care center: a retrospective cohort study with prospective follow-up. Infection 2024:10.1007/s15010-023-02171-z. [PMID: 38305828 DOI: 10.1007/s15010-023-02171-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024]
Abstract
PURPOSE This study assessed the clinical and immunological outcomes of SARS-CoV-2-infected patients with risk factors for severe disease depending on their immunological status. METHODS In this retrospective study with single follow-up visit, clinical outcome and humoral immunity was monitored in SARS-CoV-2 infected patients at risk. The results were compared based on the patients' initial immunological status: unvaccinated (UV), patients who did not develop neutralizing antibodies after vaccination (vaccine non-responders, VNR), and patients who expressed neutralizing antibodies after vaccination (vaccine responders, VR). Patients who lacked neutralizing antibodies (VNR and UV) were treated with nMABs. RESULTS In total, 113 patients at risk of severe COVID-19 consented to participate in the study. VR and UV were not admitted to the hospital. During the observation period, UVs had the highest rate of SARS-CoV-2 re-infections. Three of 41 VNRs (7.3%) were hospitalized due to severe COVID-19, with two of them having undergone iatrogenic B-cell depletion. The humoral immune response after infection was significantly lower in the VNR group than in the VR group in terms of anti-N, anti-receptor-binding domain (RBD), anti-S antibody titers, and anti-S antibody avidity. In a sub-analysis of VNR, B cell-deficient non-responders had significantly lower levels of anti-N antibodies and anti-S avidity after infection than other VNRs. CONCLUSION VNR, particularly B-cell-depleted VNR, remained at risk of hospitalization due to COVID-19. In the VR group, however, no clinical complications or severe disease were observed, despite not receiving nMAbs. Tailoring the administration of nMABs according to patient vaccination and immunological status may be advisable.
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Affiliation(s)
- J Triebelhorn
- Department of Internal Medicine II, University Hospital rechts der Isar, Technical University of Munich, Ismaninger Straße 22, 81675, Munich, Germany.
| | - J Schneider
- Department of Internal Medicine II, University Hospital rechts der Isar, Technical University of Munich, Ismaninger Straße 22, 81675, Munich, Germany
| | - C D Spinner
- Department of Internal Medicine II, University Hospital rechts der Isar, Technical University of Munich, Ismaninger Straße 22, 81675, Munich, Germany
| | - R Iakoubov
- Department of Internal Medicine II, University Hospital rechts der Isar, Technical University of Munich, Ismaninger Straße 22, 81675, Munich, Germany
| | - F Voit
- Department of Internal Medicine II, University Hospital rechts der Isar, Technical University of Munich, Ismaninger Straße 22, 81675, Munich, Germany
| | - L Wagner
- Department of Internal Medicine II, University Hospital rechts der Isar, Technical University of Munich, Ismaninger Straße 22, 81675, Munich, Germany
| | - J Erber
- Department of Internal Medicine II, University Hospital rechts der Isar, Technical University of Munich, Ismaninger Straße 22, 81675, Munich, Germany
| | - K Rothe
- Institute of Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, Munich, Germany
| | - A Berthele
- Department of Neurology, University Hospital rechts der Isar, Technical University of Munich, Munich, Germany
| | - V Pernpeintner
- Department of Neurology, University Hospital rechts der Isar, Technical University of Munich, Munich, Germany
| | - E-M Strauß
- Department of Neurology, University Hospital rechts der Isar, Technical University of Munich, Munich, Germany
| | - L Renders
- Department of Nephrology, University Hospital rechts der Isar, Technical University of Munich, Munich, Germany
| | - A Willmann
- Institute of Virology, School of Medicine, Technical University of Munich/Helmholtz Centre Munich, Munich, Germany
| | - M Minic
- Institute of Virology, School of Medicine, Technical University of Munich/Helmholtz Centre Munich, Munich, Germany
| | - E Vogel
- Institute of Virology, School of Medicine, Technical University of Munich/Helmholtz Centre Munich, Munich, Germany
| | - C Christa
- Institute of Virology, School of Medicine, Technical University of Munich/Helmholtz Centre Munich, Munich, Germany
| | - D Hoffmann
- Institute of Virology, School of Medicine, Technical University of Munich/Helmholtz Centre Munich, Munich, Germany
| | - U Protzer
- Institute of Virology, School of Medicine, Technical University of Munich/Helmholtz Centre Munich, Munich, Germany
| | - S D Jeske
- Institute of Virology, School of Medicine, Technical University of Munich/Helmholtz Centre Munich, Munich, Germany
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Burgos G, Ambuludí A, Morales-Jadán D, Garcia-Bereguiain MA, Muslin C, Armijos-Jaramillo V. A tool for the cheap and rapid screening of SARS-CoV-2 variants of concern (VoCs) by Sanger sequencing. Microbiol Spectr 2023; 11:e0506422. [PMID: 37676038 PMCID: PMC10586709 DOI: 10.1128/spectrum.05064-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 07/05/2023] [Indexed: 09/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus that, since March 2020, has been responsible for a global and ongoing pandemic. Its rapid spread over the past nearly 3 years has caused novel variants to arise. To monitor the circulation and emergence of SARS-CoV-2 variants, surveillance systems based on nucleotide mutations are required. In this regard, we searched in the spike, ORF8, and nucleocapsid genes to detect variable sites among SARS-CoV-2 variants. We describe polymorphic genetic regions that enable us to differentiate between the Alpha, Beta, Gamma, Delta, and Omicron variants of concern (VoCs). We found 21 relevant mutations, 13 of which are unique for Omicron lineages BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5. This genetic profile enables the discrimination between VoCs using only four reverse transcription PCR fragments and Sanger sequencing, offering a cheaper and faster alternative to whole-genome sequencing for SARS-CoV-2 surveillance. IMPORTANCE Our work describes a new (Sanger sequencing-based) screening methodology for SARS-CoV-2, performing PCR amplifications of a few target regions to detect diagnostic mutations between virus variants. Using the methodology developed in this work, we were able to discriminate between the following VoCs: Alpha, Beta, Gamma, Delta, and Omicron (BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5). This becomes important, especially in low-income countries where current methodologies like next-generation sequencing have prohibitive costs. Furthermore, rapid detection would allow sanitary authorities to take rapid measures to limit the spread of the virus and therefore reduce the probability of new virus dispersion. With this methodological approach, 13 previously unreported diagnostic mutations among several Omicron lineages were found.
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Affiliation(s)
- Germán Burgos
- Facultad de Medicina, Universidad de Las Américas (UDLA), Quito, Ecuador
- One Health Research Group, Faculty of Health Sciences, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Andrés Ambuludí
- Carrera de Ingeniería en Biotecnología, Facultad de Ingenierías y Ciencias Aplicadas, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - USFQ SARS-CoV-2 Consortium
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales (COCIBA), Universidad San Francisco de Quito (USFQ), Cumbaya, Ecuador
| | - Diana Morales-Jadán
- One Health Research Group, Faculty of Health Sciences, Universidad de Las Américas (UDLA), Quito, Ecuador
| | | | - Claire Muslin
- One Health Research Group, Faculty of Health Sciences, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Vinicio Armijos-Jaramillo
- Carrera de Ingeniería en Biotecnología, Facultad de Ingenierías y Ciencias Aplicadas, Universidad de Las Américas (UDLA), Quito, Ecuador
- Grupo de Bio-Quimioinformática, Universidad de Las Américas (UDLA), Quito, Ecuador
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Gupta J, Malik MZ, Chaturvedi M, Mishra M, Mishra SK, Grover A, Ray AK, Chaturvedi R. SARS CoV-2 spike protein variants exploit DC-SIGN/DC-SIGNR receptor for evolution and severity: an in-silico insight. Virusdisease 2023:1-19. [PMID: 37363363 PMCID: PMC10206574 DOI: 10.1007/s13337-023-00820-3] [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: 11/23/2022] [Accepted: 04/10/2023] [Indexed: 06/28/2023] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is related with the COVID-19 pandemic. Recent spike protein variations have had an effect on the transmission of the virus. In addition to ACE-2, spike proteins can employ DC-SIGN and its analogous receptor, DC-SIGNR, for host evasion. Spike variations in the DC-SIGN interaction region and role of DC-SIGN in immune evasion have not been well defined. To understand the spike protein variations and their binding mode, phylogenetic analysis of the complete GISAID (Global Initiative for Sharing Avian Influenza Data) data of the SARS-CoV-2 spike protein was considered. In addition, an in silico knockout network evaluation of the SARS-CoV-2 single-cell transcriptome was conducted to determine the key role of DC-SIGN/R in immunological dysregulation. Within the DC-SIGN-interacting region of the SARS-CoV spike protein, the spike protein of SARS-CoV-2 displayed remarkable similarity to the SARS-CoV spike protein. Surprisingly, the phylogenetic analysis revealed that the SARS-CoV-2's spike exhibited significantly diverse variants in the DC-SIGN interaction domain, which altered the frequency of these variants. The variation within the DC-SIGN-interacting domain of spike proteins affected the binding of a limited number of variants with DC-SIGN and DC-SIGNR and affected their evolution. MMGBSA binding free energies evaluation differed for variants from those of the wild type, suggesting the influence of substitution mutations on the interaction pattern. In silico knockout network analysis of the single-cell transcriptome of Bronchoalveolar Lavage and peripheral blood mononuclear cells revealed that SARS-CoV-2 altered DC-SIGN/R signaling. Early surveillance of diverse SARS-CoV-2 strains could preclude a worsening of the pandemic and facilitate the development of an optimum vaccine against variations. The spike Receptor Binding Domain genetic variants are thought to boost SARS CoV-2 immune evasion, resulting in its higher longevity. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-023-00820-3.
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Affiliation(s)
- Jyoti Gupta
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Md. Zubbair Malik
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, 15462 Kuwait
| | - Maya Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Mohit Mishra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Surbhi Kriti Mishra
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Ashwini Kumar Ray
- Department of Environmental Studies, University of Delhi, New Delhi, 11007 India
| | - Rupesh Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
- Special Center for Systems Medicine, Jawaharlal Nehru University, New Delhi, 110067 India
- Nanofludiks Research Pvt. Ltd., JNU-Atal Incubation Center, Jawaharlal Nehru University, New Delhi, 110067 India
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Mariani F, Morello R, Traini DO, La Rocca A, De Rose C, Valentini P, Buonsenso D. Risk Factors for Persistent Anosmia and Dysgeusia in Children with SARS-CoV-2 Infection: A Retrospective Study. CHILDREN (BASEL, SWITZERLAND) 2023; 10:children10030597. [PMID: 36980155 PMCID: PMC10047825 DOI: 10.3390/children10030597] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/05/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023]
Abstract
BACKGROUND Olfactory and gustative dysfunctions are two of the most common post-acute sequelae of SARS-CoV-2 infection in children, which can have a negative impact on the routines of children and families. As several children have had COVID-19 since the Omicron variant, it is important to investigate if this increase in infections is reflected in higher olfactory/taste disfunctions. The primary aim of this study was to characterize the presence of olfactory/gustative problems in a cohort of children, its evolution, and its association with risk factors such as COVID-19 variant, hospitalization, presence of olfactory/gustative dysfunction during the acute phase, and vaccination. METHODS This was a retrospective analysis of children with microbiologically confirmed SARS-CoV-2 infection evaluated in person at a referral pediatric post-COVID-19 clinic in Rome, Italy. We included children younger than 19 years old, evaluated from the beginning of the pandemic up to October 2022. At specific timepoints, we investigated the presence of olfactory/taste disfunctions and evaluated them according to the SARS-CoV-2 variants circulating at the time of infection. RESULTS A total of 1250 children (650 females; 52.0%) with a mean age of 6.77 (±4.12) years were included in the study. At 3, 6, 12, and 18 months, 12 (9.6%), 7 (5.6%), 2 (1.6%), and 1 (0.8%) of the children reported anosmia and dysgeusia post-COVID-19 infection, respectively. The presence of anosmia and dysgeusia during the acute phase of infection and being infected with a pre-Omicron variant were found to be significant risk factors for persistent olfactory and gustatory dysfunction during all follow-up periods. CONCLUSIONS anosmia and dysgeusia symptoms tended to decrease gradually over time, but not all children recovered quickly.
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Affiliation(s)
- Francesco Mariani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Rosa Morello
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | | | - Anna La Rocca
- Medicine and Surgery, Catholic University of Rome, 00168 Rome, Italy
| | - Cristina De Rose
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Piero Valentini
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Danilo Buonsenso
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Centro di Salute Globale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
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8
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Rasheed MK, Awrahman HA, Amin Al‐Jaf SM, Niranji SS. Identification of SARS CoV‐2 Omicron BA.1 and a novel Delta lineage by rapid methods and partial spike protein sequences in Sulaymaniyah Province, Iraq. Immun Inflamm Dis 2023; 11:e801. [PMID: 36988244 PMCID: PMC10022420 DOI: 10.1002/iid3.801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/22/2022] [Accepted: 02/09/2023] [Indexed: 03/19/2023] Open
Abstract
Background Five variants of concern (VOCs) of severe acute respiratory syndrome coronavirus 2 (SARS CoV‐2) have been globally recorded including Alpha, Beta, Gamma, Delta, and Omicron. The Omicron variant has outcompeted the other variants including the Delta variant. Molecular screenings of VOCs are important for surveillance, treatment, and vaccination programs. This study aimed to identify VOCs by using rapid inexpensive methods and partial sequencing of the virus's spike gene. Methods Mutation‐specific rRT PCR probes were used for both D614G and K417N mutations to potentially discriminate between Delta and Omicron variants. These were followed by sequencing of a fragment of spike gene (748 nucleotides), which covers the most notable VOC mutations in the receptor binding domain of SARS CoV‐2. Results Rapid methods showed that out of 24 SARS CoV‐2 positive samples, 19 carried the N417 mutation, which is present in the Omicron variant. Furthermore, 3 samples carried K417 wildtype, which is present in the Delta variant. Additionally, 2 samples containing both K417 and N417 suggested mixed infections between the two variants. The D614G mutation was present in all samples. Among the 4 samples sequenced, 3 samples carried 13 mutations, which are present in Omicron BA.1. The fourth sample contained the two common mutations (T478K and L452R) present in Delta, in addition to two more rare mutations (F456L and F490S), which are not commonly seen in Delta. Our data suggested that both Omicron variant BA.1 and a novel Delta variant might have circulated in this region that needs further investigations.
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Affiliation(s)
- Mariwan Kadir Rasheed
- College of Health ScienceUniversity of Human DevelopmentSulaymaniyahIraq,Sulaimani Veterinary DirectorateSulaimaniIraq
| | - Harem Abdalla Awrahman
- Hiwa Hospital, Sulaymaniyah General Directory of HealthMinistry of HealthSulaymaniyahIraq
| | - Sirwan M. Amin Al‐Jaf
- College of MedicineUniversity of GarmianKalarIraq,Coronavirus Research and Identification LabUniversity of GarmianKalarIraq
| | - Sherko S. Niranji
- College of MedicineUniversity of GarmianKalarIraq,Coronavirus Research and Identification LabUniversity of GarmianKalarIraq
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9
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Cancela F, Ramos N, Smyth DS, Etchebehere C, Berois M, Rodríguez J, Rufo C, Alemán A, Borzacconi L, López J, González E, Botto G, Thornhill SG, Mirazo S, Trujillo M. Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing. PLoS One 2023; 18:e0284483. [PMID: 37083889 PMCID: PMC10121012 DOI: 10.1371/journal.pone.0284483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 03/31/2023] [Indexed: 04/22/2023] Open
Abstract
SARS-CoV-2 surveillance of viral populations in wastewater samples is recognized as a useful tool for monitoring epidemic waves and boosting health preparedness. Next generation sequencing of viral RNA isolated from wastewater is a convenient and cost-effective strategy to understand the molecular epidemiology of SARS-CoV-2 and provide insights on the population dynamics of viral variants at the community level. However, in low- and middle-income countries, isolated groups have performed wastewater monitoring and data has not been extensively shared in the scientific community. Here we report the results of monitoring the co-circulation and abundance of variants of concern (VOCs) of SARS-CoV-2 in Uruguay, a small country in Latin America, between November 2020-July 2021 using wastewater surveillance. RNA isolated from wastewater was characterized by targeted sequencing of the Receptor Binding Domain region within the spike gene. Two computational approaches were used to track the viral variants. The results of the wastewater analysis showed the transition in the overall predominance of viral variants in wastewater from No-VOCs to successive VOCs, in agreement with clinical surveillance from sequencing of nasal swabs. The mutations K417T, E484K and N501Y, that characterize the Gamma VOC, were detected as early as December 2020, several weeks before the first clinical case was reported. Interestingly, a non-synonymous mutation described in the Delta VOC, L452R, was detected at a very low frequency since April 2021 when using a recently described sequence analysis tool (SAM Refiner). Wastewater NGS-based surveillance of SARS-CoV-2 is a reliable and complementary tool for monitoring the introduction and prevalence of VOCs at a community level allowing early public health decisions. This approach allows the tracking of symptomatic and asymptomatic individuals, who are generally under-reported in countries with limited clinical testing capacity. Our results suggests that wastewater-based epidemiology can contribute to improving public health responses in low- and middle-income countries.
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Affiliation(s)
- Florencia Cancela
- Sección Virología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Ramos
- Sección Virología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Davida S Smyth
- Department of Life Sciences, Texas A&M University-San Antonio, San Antonio, Texas, United States of America
| | - Claudia Etchebehere
- Departamento de Bioquímica y Genómica Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
| | - Mabel Berois
- Sección Virología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Jesica Rodríguez
- Laboratorio de Alimentos y Nutrición, Polo Tecnológico de Pando, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Caterina Rufo
- Laboratorio de Alimentos y Nutrición, Polo Tecnológico de Pando, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Alicia Alemán
- Departamento de Medicina Preventiva, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Liliana Borzacconi
- Instituto de Ingeniería Química, Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay
| | - Julieta López
- Departamento de Ingeniería Ambiental, Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay
| | - Elizabeth González
- Departamento de Ingeniería Ambiental, Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay
| | - Germán Botto
- Departamento de Métodos Cuantitativos, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Starla G Thornhill
- Department of Life Sciences, Texas A&M University-San Antonio, San Antonio, Texas, United States of America
| | - Santiago Mirazo
- Sección Virología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Mónica Trujillo
- Department of Biological Sciences and Geology, Queensborough Community College of The City University of New York, Queens, New York, United States of America
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Niranji SS, Amin Al‐Jaf SM. In response to: Disease severity and efficacy of homologous vaccination among patients infected with SARS-CoV-2 Delta or Omicron VOCs, compared to unvaccinated using main biomarkers. J Med Virol 2023; 95:e28213. [PMID: 36224626 PMCID: PMC9874565 DOI: 10.1002/jmv.28213] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 10/10/2022] [Indexed: 01/28/2023]
Affiliation(s)
- Sherko S. Niranji
- College of MedicineUniversity of GarmianKalarIraq,Coronavirus Research and Identification LabUniversity of GarmianKalarIraq
| | - Sirwan M. Amin Al‐Jaf
- College of MedicineUniversity of GarmianKalarIraq,Coronavirus Research and Identification LabUniversity of GarmianKalarIraq
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