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Maruyama S, Wada D, Kanayama S, Shimazu H, Miyano Y, Inoue A, Kashihara M, Okuda K, Saito F, Nakamori Y, Ishii K, Kuwagata Y. The evaluation of risk factors for prolonged viral shedding during anti-SARS-CoV-2 monoclonal antibodies and long-term administration of antivirals in COVID-19 patients with B-cell lymphoma treated by anti-CD20 antibody. BMC Infect Dis 2024; 24:715. [PMID: 39039440 PMCID: PMC11265166 DOI: 10.1186/s12879-024-09631-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 07/18/2024] [Indexed: 07/24/2024] Open
Abstract
BACKGROUND The global impact of the coronavirus disease 2019 (COVID-19) pandemic has resulted in significant morbidity and mortality. Immunocompromised patients, particularly those treated for B-cell lymphoma, have shown an increased risk of persistent infection with SARS-CoV-2 and severe outcomes and mortality. Multi-mutational SARS-CoV-2 variants can arise during the course of such persistent cases of COVID-19. No optimal, decisive strategy is currently available for patients with persistent infection that allows clinicians to sustain viral clearance, determine optimal timing to stop treatment, and prevent virus reactivation. We introduced a novel treatment combining antivirals, neutralizing antibodies, and genomic analysis with frequent monitoring of spike-specific antibody and viral load for immunocompromised patients with persistent COVID-19 infection. The aim of this retrospective study was to report and evaluate the efficacy of our novel treatment for immunocompromised B-cell lymphoma patients with persistent COVID-19 infection. METHODS This retrospective descriptive analysis had no controls. Patients with B-cell lymphoma previously receiving immunotherapy including anti-CD20 antibodies, diagnosed as having COVID-19 infection, and treated in our hospital after January 2022 were included. We selected anti-SARS-CoV-2 monoclonal antibodies according to subvariants. Every 5 days, viral load was tested by RT-PCR, with antivirals continued until viral shedding was confirmed. Primary outcome was virus elimination. Independent predictors of prolonged viral shedding time were determined by multivariate Cox regression. RESULTS Forty-four patients were included in this study. Thirty-five patients received rituximab, 19 obinutuzumab, and 26 bendamustine. Median treatment duration was 10 (IQR, 10-20) days; 22 patients received combination antiviral therapy. COVID-19 was severe in 16 patients, and critical in 2. All patients survived, with viral shedding confirmed at median 28 (IQR, 19-38) days. Bendamustine use or within 1 year of last treatment for B-cell lymphoma, and multiple treatment lines for B-cell lymphoma significantly prolonged time to viral shedding. CONCLUSIONS Among 44 consecutive patients treated, anti-SARS-CoV-2 monoclonal antibodies and long-term administration of antiviral drugs, switching, and combination therapy resulted in virus elimination and 100% survival. Bendamustine use, within 1 year of last treatment for B-cell lymphoma, and multiple treatment lines for B-cell lymphoma were the significant independent predictors of prolonged viral shedding time.
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Affiliation(s)
- Shuhei Maruyama
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-cho, Moriguchi, Osaka, 570-8507, Japan
| | - Daiki Wada
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-cho, Moriguchi, Osaka, 570-8507, Japan.
| | - Shuji Kanayama
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-cho, Moriguchi, Osaka, 570-8507, Japan
| | - Haruka Shimazu
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-cho, Moriguchi, Osaka, 570-8507, Japan
| | - Yumiko Miyano
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-cho, Moriguchi, Osaka, 570-8507, Japan
| | - Akira Inoue
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-cho, Moriguchi, Osaka, 570-8507, Japan
| | - Masami Kashihara
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-cho, Moriguchi, Osaka, 570-8507, Japan
| | - Kazuyuki Okuda
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-cho, Moriguchi, Osaka, 570-8507, Japan
| | - Fukuki Saito
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-cho, Moriguchi, Osaka, 570-8507, Japan
| | - Yasushi Nakamori
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-cho, Moriguchi, Osaka, 570-8507, Japan
| | - Kazuyoshi Ishii
- Department of Hematology and Oncology, Kansai Medical University General Medical Center, 10-15 Fumizono-cho, Moriguchi, Osaka, 570-8507, Japan
| | - Yasuyuki Kuwagata
- Department of Emergency and Critical Care Medicine, Kansai Medical University Hospital, 2-3-1 Shinmachi, Hirakata, Osaka, 573-1191, Japan
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Sayama Y, Sakagami A, Okamoto M, Sakamoto M, Koizumi H, Kimura Y, Dapat C, Saito M, Suzuki Y, Sasaki M, Sugawara N, Oshitani H. Identification of Various Recombinants in a Patient Coinfected With the Different SARS-CoV-2 Variants. Influenza Other Respir Viruses 2024; 18:e13340. [PMID: 38890805 PMCID: PMC11187932 DOI: 10.1111/irv.13340] [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: 10/12/2023] [Revised: 03/18/2024] [Accepted: 05/30/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Viral recombination that occurs by exchanging genetic materials between two viral genomes coinfecting the same host cells is associated with the emergence of new viruses with different virulence. Herein, we detected a patient coinfected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta and Omicron variants and identified various recombinants in the SARS-CoV-2 full-length spike gene using long-read and Sanger sequencing. METHODS Samples from five patients in Japan with household transmission of coronavirus disease 2019 (COVID-19) were analyzed using molecular assays for detection and identification of SARS-CoV-2. Whole-genome sequencing was conducted using multiplex PCR with short-read sequencing. RESULTS Among the five SARS-CoV-2-positive patients, the mutation-specific assay identified the Delta variant in three, the Omicron variant in one, and an undetermined in one. The undermined patient was identified as Delta using whole-genome sequencing, but samples showed a mixed population of Delta and Omicron variants. This patient was analyzed for viral quasispecies by long-read and Sanger sequencing using a full-length spike gene amplicon. In addition to the Delta and Omicron sequences, the viral quasispecies analysis identified nine different genetic recombinant sequences with various breakpoints between Delta and Omicron sequences. The nine detected recombinant sequences in the spike gene showed over 99% identity with viruses that were detected during the Delta and Omicron cocirculation period from the United States and Europe. CONCLUSIONS This study demonstrates that patients coinfected with different SARS-CoV-2 variants can generate various viral recombinants and that various recombinant viruses may be produced during the cocirculation of different variants.
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Affiliation(s)
- Yusuke Sayama
- Department of VirologyTohoku University of Graduate School of MedicineSendaiMiyagiJapan
| | - Akie Sakagami
- Department of MicrobiologyMiyagi Prefectural Institute of Public Health and EnvironmentSendaiMiyagiJapan
| | - Michiko Okamoto
- Department of VirologyTohoku University of Graduate School of MedicineSendaiMiyagiJapan
| | - Masahiro Sakamoto
- Department of VirologyTohoku University of Graduate School of MedicineSendaiMiyagiJapan
| | - Hikari Koizumi
- Department of MicrobiologyMiyagi Prefectural Institute of Public Health and EnvironmentSendaiMiyagiJapan
| | - Yoko Kimura
- Department of MicrobiologyMiyagi Prefectural Institute of Public Health and EnvironmentSendaiMiyagiJapan
| | - Clyde Dapat
- Department of VirologyTohoku University of Graduate School of MedicineSendaiMiyagiJapan
| | - Mayuko Saito
- Department of VirologyTohoku University of Graduate School of MedicineSendaiMiyagiJapan
| | - Yuko Suzuki
- Department of MicrobiologyMiyagi Prefectural Institute of Public Health and EnvironmentSendaiMiyagiJapan
| | - Mie Sasaki
- Department of MicrobiologyMiyagi Prefectural Institute of Public Health and EnvironmentSendaiMiyagiJapan
| | - Naoko Sugawara
- Department of MicrobiologyMiyagi Prefectural Institute of Public Health and EnvironmentSendaiMiyagiJapan
| | - Hitoshi Oshitani
- Department of VirologyTohoku University of Graduate School of MedicineSendaiMiyagiJapan
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Wu H, Zhou HY, Zheng H, Wu A. Towards Understanding and Identification of Human Viral Co-Infections. Viruses 2024; 16:673. [PMID: 38793555 PMCID: PMC11126107 DOI: 10.3390/v16050673] [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: 04/05/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Viral co-infections, in which a host is infected with multiple viruses simultaneously, are common in the human population. Human viral co-infections can lead to complex interactions between the viruses and the host immune system, affecting the clinical outcome and posing challenges for treatment. Understanding the types, mechanisms, impacts, and identification methods of human viral co-infections is crucial for the prevention and control of viral diseases. In this review, we first introduce the significance of studying human viral co-infections and summarize the current research progress and gaps in this field. We then classify human viral co-infections into four types based on the pathogenic properties and species of the viruses involved. Next, we discuss the molecular mechanisms of viral co-infections, focusing on virus-virus interactions, host immune responses, and clinical manifestations. We also summarize the experimental and computational methods for the identification of viral co-infections, emphasizing the latest advances in high-throughput sequencing and bioinformatics approaches. Finally, we highlight the challenges and future directions in human viral co-infection research, aiming to provide new insights and strategies for the prevention, control, diagnosis, and treatment of viral diseases. This review provides a comprehensive overview of the current knowledge and future perspectives on human viral co-infections and underscores the need for interdisciplinary collaboration to address this complex and important topic.
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Affiliation(s)
- Hui Wu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211100, China;
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Hang-Yu Zhou
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211100, China;
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
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Falkenberg SM, Buckley A, Boggiatto P. Evaluation of the PrimeFlow RNA assay as a method of detection of SARS-CoV-2 single and dual Infections. Cytotechnology 2024; 76:191-196. [PMID: 38495292 PMCID: PMC10940553 DOI: 10.1007/s10616-023-00608-9] [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: 06/20/2023] [Accepted: 11/06/2023] [Indexed: 03/19/2024] Open
Abstract
Given the implications of increased transmissibility, virulence, host range, and immune escapes of emerging variants of SARS-CoV-2, developing in vitro models that allow for detection of variants and differences in infection dynamics is important. The objective of this study, was to evaluate the PrimeFlow RNA in-situ assay as a method of detection for multiple strains of SARS-CoV-2. Evaluation of detection and infection statuses included single infections with an Alpha, Delta, or Omicron variants and dual infections with Alpha/Omicron or Delta/Omicron. RNA probes specific for the Spike protein coding region, were designed (omicron or non-omicron specific). SARS-CoV-2 RNA was detected in greater frequency in the Vero E6 and minimally in the fetal deer testicle cell lines by flow cytometry using this approach for viral detection of multiple variants. Most evident in the Vero E6 cells, 24 h post infection both Alpha and Delta predominated over Omicron in dual infections. This is the first report using the PrimeFlow assay for the detection of SARS-CoV-2 at the single-cell level and as a potential model for competition of variants utilizing infection dynamics in cell culture.
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Affiliation(s)
- Shollie M. Falkenberg
- Ruminant Disease and Immunology Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA USA
- College of Veterinary Medicine, Department of Pathobiology, Auburn University, Auburn, AL USA
| | - Alexa Buckley
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA USA
| | - Paola Boggiatto
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA USA
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García-López R, Taboada B, Zárate S, Muñoz-Medina JE, Salas-Lais AG, Herrera-Estrella A, Boukadida C, Vazquez-Perez JA, Gómez-Gil B, Sanchez-Flores A, Arias CF. Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover. Microb Genom 2024; 10:001220. [PMID: 38512312 PMCID: PMC11004493 DOI: 10.1099/mgen.0.001220] [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: 11/03/2023] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
A total of 14 973 alleles in 29 661 sequenced samples collected between March 2021 and January 2023 by the Mexican Consortium for Genomic Surveillance (CoViGen-Mex) and collaborators were used to construct a thorough map of mutations of the Mexican SARS-CoV-2 genomic landscape containing Intra-Patient Minor Allelic Variants (IPMAVs), which are low-frequency alleles not ordinarily present in a genomic consensus sequence. This additional information proved critical in identifying putative coinfecting variants included alongside the most common variants, B.1.1.222, B.1.1.519, and variants of concern (VOCs) Alpha, Gamma, Delta, and Omicron. A total of 379 coinfection events were recorded in the dataset (a rate of 1.28 %), resulting in the first such catalogue in Mexico. The most common putative coinfections occurred during the spread of Delta or after the introduction of Omicron BA.2 and its descendants. Coinfections occurred constantly during periods of variant turnover when more than one variant shared the same niche and high infection rate was observed, which was dependent on the local variants and time. Coinfections might occur at a higher frequency than customarily reported, but they are often ignored as only the consensus sequence is reported for lineage identification.
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Affiliation(s)
- Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Angel Gustavo Salas-Lais
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Joel Armando Vazquez-Perez
- Laboratorio de Biología Molecular de Enfermedades Emergentes y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Unidad Mazatlán, Mazatlán, Sinaloa, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Aguayo-Acosta A, Oyervides-Muñoz MA, Rodriguez-Aguillón KO, Ovalle-Carcaño A, Romero-Castillo KD, Robles-Zamora A, Johnson M, Parra-Saldívar R, Sosa-Hernández JE. Omicron and Delta variant prevalence detection and identification during the fourth COVID-19 wave in Mexico using wastewater-based epidemiology. IJID REGIONS 2024; 10:44-51. [PMID: 38149263 PMCID: PMC10750064 DOI: 10.1016/j.ijregi.2023.11.005] [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: 08/31/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 12/28/2023]
Abstract
Objectives To identify the SARS-CoV-2 variants Delta and Omicron during the fourth wave of the COVID-19 pandemic in Mexico using samples taken from 19 locations in 18 out of the 32 states. Methods The genetic material concentration was done with PEG/NaCl precipitation, SARS-CoV-2 presence was confirmed by reverse transcriptase-quantitative polymerase chain reaction assay, the variant detection was carried out using a commercial mutation detection panel kit, and variant/mutation confirmation was done by amplicon sequencing of receptor-binding domain target region. The study used 41 samples. Results The Delta variant was confirmed in two samples during August 2021 (Querétaro and CDMX) and in three samples during November 2021 (Aguascalientes, Ciudad Juárez campuses, and Nuevo Leon). In December 2021, another sample with the Delta variant was confirmed in Nuevo Leon. Between January to March 2022 only the presence of Omicron was confirmed, (variant BA.1). Additionally, in this period six samples were identified with the status "Variant Not Determined". Conclusion To our knowledge, this study is one of the first to identify Omicron and Delta variants with polymerase chain reaction in Mexico and Latin America and its distribution across the country with 56% Mexican states making it a viable alternative for variant detection without conducting a large quantity of sequencing of clinical tests.
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Affiliation(s)
- Alberto Aguayo-Acosta
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Mariel Araceli Oyervides-Muñoz
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Kassandra O. Rodriguez-Aguillón
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Antonio Ovalle-Carcaño
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | | | | | - Marc Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, USA
| | - Roberto Parra-Saldívar
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
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Pipek OA, Medgyes-Horváth A, Stéger J, Papp K, Visontai D, Koopmans M, Nieuwenhuijse D, Oude Munnink BB, Csabai I. Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples. Nat Commun 2024; 15:517. [PMID: 38225254 PMCID: PMC10789779 DOI: 10.1038/s41467-023-43391-z] [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: 07/11/2023] [Accepted: 11/06/2023] [Indexed: 01/17/2024] Open
Abstract
Systematic monitoring of SARS-CoV-2 co-infections between different lineages and assessing the risk of intra-host recombinant emergence are crucial for forecasting viral evolution. Here we present a comprehensive analysis of more than 2 million SARS-CoV-2 raw read datasets submitted to the European COVID-19 Data Portal to identify co-infections and intra-host recombination. Co-infection was observed in 0.35% of the investigated cases. Two independent procedures were implemented to detect intra-host recombination. We show that sensitivity is predominantly determined by the density of lineage-defining mutations along the genome, thus we used an expanded list of mutually exclusive defining mutations of specific variant combinations to increase statistical power. We call attention to multiple challenges rendering recombinant detection difficult and provide guidelines for the reduction of false positives arising from chimeric sequences produced during PCR amplification. Additionally, we identify three recombination hotspots of Delta - Omicron BA.1 intra-host recombinants.
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Affiliation(s)
- Orsolya Anna Pipek
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Anna Medgyes-Horváth
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary.
| | - József Stéger
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Krisztián Papp
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Dávid Visontai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Marion Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - David Nieuwenhuijse
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
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Peñas-Utrilla D, Muñóz P, Pérez-Lago L, García de Viedma D. Mining genomic repositories to further our knowledge of the extent of SARS-CoV-2 co-infections. Microb Genom 2024; 10:001158. [PMID: 38226969 PMCID: PMC10868610 DOI: 10.1099/mgen.0.001158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/30/2023] [Indexed: 01/17/2024] Open
Abstract
Recombination events between Delta and Omicron SARS-CoV-2 lineages highlight the need for co-infection research. Existing studies focus on late-phase co-infections, with few examining earlier pandemic stages. This new study aims to globally identify and characterize co-infections using a bioinformatic pipeline to analyse genomic data from diverse locations and pandemic phases. Among 26988 high-quality SARS-CoV-2 isolates from 11 diverse project databases, we identified 141 potential co-infection cases (0.52%), surpassing previous prevalence estimates. These co-infections were observed throughout the pandemic timeline, with an increase noted after the emergence of the Omicron variant. Co-infections involving the Omicron variant were the most prevalent, potentially influenced by the high level of diversity within this lineage and its impact on the viral landscape. Additionally, we found co-infections involving the pre-Alpha/Alpha lineages, which have been rarely described, raising possibilities of contributing to new lineage emergence through recombination events. The analysis revealed co-infection cases involving both different and the same lineages/sublineages. Our study showcases the potential of our pipeline to leverage valuable information stored in global sequence repositories, advancing our understanding of SARS-CoV-2 co-infections. The prevalence of co-infections highlights the importance of monitoring viral diversity and its potential implications on disease dynamics. Integrating clinical data with genomic findings can further shed light on the clinical implications and outcomes of co-infections.
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Affiliation(s)
- Daniel Peñas-Utrilla
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Escuela de Doctorado, Universidad de Alcalá, Plaza de San Diego, s/n, 28801 Alcalá de Henares, Madrid, Spain
| | - Patricia Muñóz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias-CIBERES, 28029 Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias-CIBERES, 28029 Madrid, Spain
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Zhao J, Kang M, Wu H, Sun B, Baele G, He WT, Lu M, Suchard MA, Ji X, He N, Su S, Veit M. Risk assessment of SARS-CoV-2 replicating and evolving in animals. Trends Microbiol 2024; 32:79-92. [PMID: 37541811 DOI: 10.1016/j.tim.2023.07.002] [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: 03/16/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
The retransmissions of SARS-CoV-2 from several mammals - primarily mink and white-tailed deer - to humans have raised concerns for the emergence of a new animal-derived SARS-CoV-2 variant to worsen the pandemic. Here, we discuss animal species that are susceptible to natural or experimental infection with SARS-CoV-2 and can transmit the virus to mates or humans. We describe cutting-edge techniques to assess the impact of a mutation in the viral spike (S) protein on its receptor and on antibody binding. Our review of spike sequences of animal-derived viruses identified nine unique amino acid exchanges in the receptor-binding domain (RBD) that are not present in any variant of concern (VOC). These mutations are present in SARS-CoV-2 found in companion animals such as dogs and cats, and they exhibit a higher frequency in SARS-CoV-2 found in mink and white-tailed deer, suggesting that sustained transmissions may contribute to maintaining novel mutations. Four of these exchanges, such as Leu452Met, could undermine acquired immune protection in humans while maintaining high affinity for the human angiotensin-converting enzyme 2 (ACE2) receptor. Finally, we discuss important avenues of future research into animal-derived viruses with public health risks.
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Affiliation(s)
- Jin Zhao
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Mei Kang
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China; Clinical Research Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongyan Wu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Bowen Sun
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Guy Baele
- Department of Microbiology, Immunology, and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Wan-Ting He
- School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Meng Lu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA; Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | - Na He
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Shuo Su
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China.
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin, Germany.
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10
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Chen Q, Qin S, Zhou HY, Deng YQ, Shi PD, Zhao H, Li XF, Huang XY, Wu YR, Guo Y, Pei GQ, Wang YF, Sun SQ, Du ZM, Cui YJ, Fan H, Qin CF. Competitive fitness and homologous recombination of SARS-CoV-2 variants of concern. J Med Virol 2023; 95:e29278. [PMID: 38088537 DOI: 10.1002/jmv.29278] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/26/2023] [Accepted: 11/11/2023] [Indexed: 12/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to emerge and cocirculate in humans and wild animals. The factors driving the emergence and replacement of novel variants and recombinants remain incompletely understood. Herein, we comprehensively characterized the competitive fitness of SARS-CoV-2 wild type (WT) and three variants of concern (VOCs), Alpha, Beta and Delta, by coinfection and serial passaging assays in different susceptible cells. Deep sequencing analyses revealed cell-specific competitive fitness: the Beta variant showed enhanced replication fitness during serial passage in Caco-2 cells, whereas the WT and Alpha variant showed elevated fitness in Vero E6 cells. Interestingly, a high level of neutralizing antibody sped up competition and completely reshaped the fitness advantages of different variants. More importantly, single clone purification identified a significant proportion of homologous recombinants that emerged during the passage history, and immune pressure reduced the frequency of recombination. Interestingly, a recombination hot region located between nucleotide sites 22,995 and 28,866 of the viral genomes could be identified in most of the detected recombinants. Our study not only profiled the variable competitive fitness of SARS-CoV-2 under different conditions, but also provided direct experimental evidence of homologous recombination between SARS-CoV-2 viruses, as well as a model for investigating SARS-CoV-2 recombination.
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Affiliation(s)
- Qi Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Si Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Hang-Yu Zhou
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yong-Qiang Deng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Pan-Deng Shi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Hui Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Xiao-Feng Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Xing-Yao Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Ya-Rong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Yan Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Guang-Qian Pei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Yun-Fei Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Si-Qi Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Zong-Min Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Yu-Jun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Hang Fan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
| | - Cheng-Feng Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing, China
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, China
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11
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Al-Shuhaib MBS, Hashim HO. Mastering DNA chromatogram analysis in Sanger sequencing for reliable clinical analysis. J Genet Eng Biotechnol 2023; 21:115. [PMID: 37955813 PMCID: PMC10643650 DOI: 10.1186/s43141-023-00587-6] [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: 10/04/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND Sanger dideoxy sequencing is vital in clinical analysis due to its accuracy, ability to analyze genetic markers like SNPs and STRs, capability to generate reliable DNA profiles, and its role in resolving complex clinical cases. The precision and robustness of Sanger sequencing contribute significantly to the scientific basis of clinical investigations. Though the reading of chromatograms seems to be a routine step, many errors conducted in PCR may lead to consequent limitations in the readings of AGCT peaks. These errors are possibly associated with improper DNA amplification and its subsequent interpretation of DNA sequencing files, such as noisy peaks, artifacts, and confusion between double-peak technical errors, heterozygosity, and double infection potentials. Thus, it is not feasible to read nucleic acid sequences without giving serious attention to these technical problems. To ensure the accuracy of DNA sequencing outcomes, it is also imperative to detect and rectify technical challenges that may lead to misinterpretation of the DNA sequence, resulting in errors and incongruities in subsequent analyses. SHORT CONCLUSION This overview sheds light on prominent technical concerns that can emerge prior to and during the interpretation of DNA chromatograms in Sanger sequencing, along with offering strategies to address them effectively. The significance of identifying and tackling these technical limitations during the chromatogram analysis is underscored in this review. Recognizing these concerns can aid in enhancing the quality of downstream analyses for Sanger sequencing results, which holds notable improvement in accuracy, reliability, and ability to provide crucial genetic information in clinical analysis.
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Affiliation(s)
- Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim 8, Babil, 51001, Iraq.
| | - Hayder O Hashim
- Department of Clinical Laboratory Sciences, College of Pharmacy, University of Babylon, Babil, 51001, Iraq
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12
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Hu S, Luo D, Zhu Q, Pan J, Chen B, Furian M, Harkare HV, Sun S, Fansa A, Wu X, Yu B, Ma T, Wang F, Shi S. An updated meta-analysis of Chinese herbal medicine for the prevention of COVID-19 based on Western-Eastern medicine. Front Pharmacol 2023; 14:1257345. [PMID: 38044944 PMCID: PMC10693348 DOI: 10.3389/fphar.2023.1257345] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/13/2023] [Indexed: 12/05/2023] Open
Abstract
Background and aims: Chinese herbal medicine (CHM) was used to prevent and treat coronavirus disease 2019 (COVID-19) in clinical practices. Many studies have demonstrated that the combination of CHM and Western medicine can be more effective in treating COVID-19 compared to Western medicine alone. However, evidence-based studies on the prevention in undiagnosed or suspected cases remain scarce. This systematic review and meta-analysis aimed to investigate the effectiveness of CHM in preventing recurrent, new, or suspected COVID-19 diseases. Methods: We conducted a comprehensive search using ten databases including articles published between December 2019 and September 2023. This search aimed to identify studies investigating the use of CHM to prevent COVID-19. Heterogeneity was assessed by a random-effects model. The relative risk (RR) and mean differences were calculated using 95% confidence intervals (CI). The modified Jadad Scale and the Newcastle-Ottawa Scale (NOS) were employed to evaluate the quality of randomized controlled trials and cohort studies, respectively. Results: Seventeen studies with a total of 47,351 patients were included. Results revealed that CHM significantly reduced the incidence of COVID-19 (RR = 0.24, 95% CI = 0.11-0.53, p = 0.0004), influenza (RR = 0.37, 95% CI = 0.18-0.76, p = 0.007), and severe pneumonia exacerbation rate (RR = 0.17, 95% CI = 0.05-0.64, p = 0.009) compared to non-treatment or conventional control group. Evidence evaluation indicated moderate quality evidence for COVID-19 incidence and serum complement components C3 and C4 in randomized controlled trials. For the incidence of influenza and severe pneumonia in RCTs as well as the ratio of CD4+/CD8+ lymphocytes, the evidence quality was low. The remaining outcomes including the disappearance rate of symptoms and adverse reactions were deemed to be of very low quality. Conclusion: CHM presents a promising therapeutic option for the prevention of COVID-19. However, additional high-quality clinical trials are needed to further strengthen evidential integrity.
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Affiliation(s)
- Siying Hu
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dan Luo
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qikui Zhu
- Department of Biomedical Engineering and Computer and Data Science, Case Western Reserve University, Cleveland, OH, United States
| | - Jie Pan
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Bonan Chen
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Michael Furian
- Research Department, Swiss University of Traditional Chinese Medicine, Bad Zurzach, Switzerland
| | - Harsh Vivek Harkare
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Shoukai Sun
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Adel Fansa
- Charité Universitätsmedizin Berlin, Berlin, Germany
- Faculty of Medicine, University of Basel, Basel, Switzerland
| | - Xiaoping Wu
- National Clinical Research Center for Chinese Medicine Cardiology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Baili Yu
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tianhong Ma
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Fei Wang
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shihua Shi
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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13
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Alisoltani A, Simons LM, Agnes MFR, Heald-Sargent TA, Muller WJ, Kociolek LK, Hultquist JF, Lorenzo-Redondo R, Ozer EA. Resurgence of SARS-CoV-2 Delta after Omicron variant superinfection in an immunocompromised pediatric patient. Virol J 2023; 20:246. [PMID: 37891657 PMCID: PMC10604949 DOI: 10.1186/s12985-023-02186-w] [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: 06/30/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Persistent SARS-CoV-2 infection in immunocompromised hosts is thought to contribute to viral evolution by facilitating long-term natural selection and viral recombination in cases of viral co-infection or superinfection. However, there are limited data on the longitudinal intra-host population dynamics of SARS-CoV-2 co-infection/superinfection, especially in pediatric populations. Here, we report a case of Delta-Omicron superinfection in a hospitalized, immunocompromised pediatric patient. METHODS We conducted Illumina whole genome sequencing (WGS) for longitudinal specimens to investigate intra-host dynamics of SARS-CoV-2 strains. Topoisomerase PCR cloning of Spike open-reading frame and Sanger sequencing of samples was performed for four specimens to validate the findings. Analysis of publicly available SARS-CoV-2 sequence data was performed to investigate the co-circulation and persistence of SARS-CoV-2 variants. RESULTS Results of WGS indicate the patient was initially infected with the SARS-CoV-2 Delta variant before developing a SARS-CoV-2 Omicron variant superinfection, which became predominant. Shortly thereafter, viral loads decreased below the level of detection before resurgence of the original Delta variant with no residual trace of Omicron. After 54 days of persistent infection, the patient tested negative for SARS-CoV-2 but ultimately succumbed to a COVID-19-related death. Despite protracted treatment with remdesivir, no antiviral resistance mutations emerged. These results indicate a unique case of persistent SARS-CoV-2 infection with the Delta variant interposed by a transient superinfection with the Omicron variant. Analysis of publicly available sequence data suggests the persistence and ongoing evolution of Delta subvariants despite the global predominance of Omicron, potentially indicative of continued transmission in an unknown population or niche. CONCLUSION A better understanding of SARS-CoV-2 intra-host population dynamics, persistence, and evolution during co-infections and/or superinfections will be required to continue optimizing patient care and to better predict the emergence of new variants of concern.
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Affiliation(s)
- Arghavan Alisoltani
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Lacy M Simons
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Maria Francesca Reyes Agnes
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | | | - William J Muller
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Larry K Kociolek
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA.
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14
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Nimsamer P, Sawaswong V, Klomkliew P, Kaewsapsak P, Puenpa J, Poovorawan Y, Payungporn S. "Nano COVID-19": Nanopore sequencing of spike gene to identify SARS-CoV-2 variants of concern. Exp Biol Med (Maywood) 2023; 248:1841-1849. [PMID: 37702217 DOI: 10.1177/15353702231190931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a worldwide pandemic infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). World Health Organization (WHO) has defined the viral variants of concern (VOC) which cause more severe disease, higher transmissibility, and reduced vaccine efficacy. In this study, the "Nano COVID-19" workflow based on Oxford nanopore sequencing of the full-length spike gene combined with flexible data analysis options was developed to identify SARS-CoV-2 VOCs. The primers were designed to cover the full-length spike gene and can amplify all VOC strains. The results of VOC identification based on phylogenetic analysis of the full-length spike gene were comparable to the whole genome sequencing (WGS). Compared to the standard VOC identification pipeline, the fast analysis based on Read Assignment, Mapping, and Phylogenetic Analysis in Real Time (RAMPART) and the user-friendly method based on EPI2ME yielded 89.3% and 97.3% accuracy, respectively. The EPI2ME pipeline is recommended for researchers without bioinformatic skills, whereas RAMPART is more suitable for bioinformaticians. This workflow provides a cost-effective, simplified pipeline with a rapid turnaround time. Furthermore, it is portable to point-of-care SARS-CoV-2 VOC identification and compatible with large-scale analysis. Therefore, "Nano COVID-19" is an alternative viral epidemic screening and transmission tracking workflow.
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Affiliation(s)
- Pattaraporn Nimsamer
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Vorthon Sawaswong
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pavit Klomkliew
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pornchai Kaewsapsak
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jiratchaya Puenpa
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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15
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Trémeaux P, Latour J, Ranger N, Ferrer V, Harter A, Carcenac R, Boyer P, Demmou S, Nicot F, Raymond S, Izopet J. SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing. Microbiol Spectr 2023; 11:e0049323. [PMID: 37260377 PMCID: PMC10434069 DOI: 10.1128/spectrum.00493-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/09/2023] [Indexed: 06/02/2023] Open
Abstract
Co-infection with at least 2 strains of virus is the prerequisite for recombination, one of the means of genetic diversification. Little is known about the prevalence of these events in SARS-CoV-2, partly because it is difficult to detect them. We used long-read PacBio single-molecule real-time (SMRT) sequencing technology to sequence whole genomes and targeted regions for haplotyping. We identified 17 co-infections with SARS-CoV-2 strains belonging to different clades in 6829 samples sequenced between January and October, 2022 (prevalence 0.25%). There were 3 Delta/Omicron co-infections and 14 Omicron/Omicron co-infections (4 cases of 21K/21L, 1 case of 21L/22A, 2 cases of 21L/22B, 4 cases of 22A/22B, 2 cases of 22B/22C and 1 case of 22B/22E). Four of these patients (24%) also harbored recombinant minor haplotypes, including one with a recombinant virus that was selected in the viral quasispecies over the course of his chronic infection. While co-infections remain rare among SARS-CoV-2-infected individuals, long-read SMRT sequencing is a useful tool for detecting them as well as recombinant events, providing the basis for assessing their clinical impact, and a precise indicator of epidemic evolution. IMPORTANCE SARS-CoV-2 variants have been responsible for the successive waves of infection over the 3 years of pandemic. While co-infection followed by recombination is one driver of virus evolution, there have been few reports of co-infections, mainly between Delta and Omicron variants or between the first 2 Omicron variants 21K_BA.1 and 21L_BA.2. The 17 co-infections we detected during 2022 included cases with the recent clades of Omicron 22A, 22B, 22C, and 22E; 24% harbored recombinant variants. This study shows that long-read SMRT sequencing is well suited to SARS-CoV-2 genomic surveillance.
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Affiliation(s)
- Pauline Trémeaux
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Justine Latour
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Noémie Ranger
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Vénicia Ferrer
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Agnès Harter
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Romain Carcenac
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Pauline Boyer
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Sofia Demmou
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Florence Nicot
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Stéphanie Raymond
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291 – CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Jacques Izopet
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291 – CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
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16
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Deroche L, Bellecave P, David R, Ouattara E, Garcia M, Roblot F, Boinot L, Faucher JF, Rejasse A, Gschwind G, Malvy D, Filleul L, Rogez S, Lévêque N, Lafon ME. One year of SARS-CoV-2 circulation in the Nouvelle-Aquitaine region, February 2021-2022, France. Front Microbiol 2023; 14:1176575. [PMID: 37577437 PMCID: PMC10420073 DOI: 10.3389/fmicb.2023.1176575] [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: 02/28/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023] Open
Abstract
Background Since 2021, 3 variants of concern (VOC) have spread to France, causing successive epidemic waves. Objectives To describe the features of Alpha, Delta and Omicron VOC circulation in the Nouvelle-Aquitaine region, France, between February 2021 and February 2022. Study design Data from the three university hospitals (UH) of Nouvelle-Aquitaine were used to describe regional SARS-CoV-2 circulation (RT-PCR positive rates and identified VOC) as well as its consequences (total number of hospitalizations and admissions in intensive care unit). They were analyzed according to the predominant variant and compared with national data. Results A total of 611,106 SARS-CoV-2 RT-PCR tests were performed in the 3 Nouvelle-Aquitaine UH during the study period. The 37,750 positive samples were analyzed by variant-specific RT-PCR or whole-genome sequencing. In 2021, Alpha VOC was detected from week 5 until week 35. Delta became the most prevalent variant (77.3%) in week 26, reaching 100% in week 35. It was replaced by Omicron, which was initially detected week 48, represented 77% of positive samples in week 52 and was still predominant in February 2022. The RT-PCR positive rates were 4.3, 4.2, and 21.9% during the Alpha, Delta and Omicron waves, respectively. The ratio between intensive care unit admissions and total hospitalizations was lower during the Omicron wave than during the two previous waves due to the Alpha and Delta variants. Conclusion This study highlighted the need for strong regional cooperation to achieve effective SARS-CoV-2 epidemiological surveillance, in close association with the public health authorities.
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Affiliation(s)
- Luc Deroche
- Virology Laboratory, CHU Poitiers, Poitiers, France
| | | | - Romain David
- Virology Laboratory, CHU Bordeaux, Bordeaux, France
| | - Eric Ouattara
- Medical Information Analysis and Coordination Unit (UCAIM-DIM), Medical Information Department, Bordeaux University Hospital, Bordeaux, France
| | - Magali Garcia
- Virology Laboratory, CHU Poitiers, Poitiers, France
- LITEC UR15560, Université de Poitiers, Poitiers, France
| | - France Roblot
- Tropical Infectious Diseases Department, Poitiers University Hospital, Poitiers, France
- INSERM U1070, Université de Poitiers, Poitiers, France
| | - Laurence Boinot
- Service d’Information Médicale, CHU Poitiers, Poitiers, France
| | - Jean-François Faucher
- Tropical Infectious Diseases Department, Limoges University Hospital, Limoges, France
| | - Aurélie Rejasse
- Medical Information Department, Limoges University Hospital, Limoges, France
| | - Guillaume Gschwind
- Medical Information Department, Limoges University Hospital, Limoges, France
| | - Denis Malvy
- Department of Infectious and Tropical Diseases, CHU Bordeaux, Bordeaux, France
- UMR Inserm 1219/IRD, University of Bordeaux, Bordeaux, France
| | - Laurent Filleul
- Regional Office-Nouvelle Aquitaine, Santé publique France, Bordeaux, France
| | - Sylvie Rogez
- Virology Laboratory, CHU Limoges, Limoges, France
| | - Nicolas Lévêque
- Virology Laboratory, CHU Poitiers, Poitiers, France
- LITEC UR15560, Université de Poitiers, Poitiers, France
| | - Marie-Edith Lafon
- Virology Laboratory, CHU Bordeaux, Bordeaux, France
- CNRS UMR 5234, University of Bordeaux, Bordeaux, France
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17
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Peñas-Utrilla D, Pérez-Lago L, Molero-Salinas A, Estévez A, Sanz A, Herranz M, Martínez-Laperche C, Andrés-Zayas C, Veintimilla C, Catalán P, Alonso R, Muñoz P, García de Viedma D. Systematic genomic analysis of SARS-CoV-2 co-infections throughout the pandemic and segregation of the strains involved. Genome Med 2023; 15:57. [PMID: 37488638 PMCID: PMC10367318 DOI: 10.1186/s13073-023-01198-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/30/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND SARS-CoV-2 recombinants involving the divergent Delta and Omicron lineages have been described, and one of them, "Kraken" (XBB.1.5), has recently been a matter of concern. Recombination requires the coexistence of two SARS-CoV-2 strains in the same individual. Only a limited number of studies have focused on the identification of co-infections and are restricted to co-infections involving the Delta/Omicron lineages. METHODS We performed a systematic identification of SARS-CoV-2 co-infections throughout the pandemic (7609 different patients sequenced), not biassed towards the involvement of highly divergent lineages. Through a comprehensive set of validations based on the distribution of allelic frequencies, phylogenetic consistency, re-sequencing, host genetic analysis and contextual epidemiological analysis, these co-infections were robustly assigned. RESULTS Fourteen (0.18%) co-infections with ≥ 8 heterozygous calls (8-85 HZs) were identified. Co-infections were identified throughout the pandemic and involved an equal proportion of strains from different lineages/sublineages (including pre-Alpha variants, Delta and Omicron) or strains from the same lineage. Co-infected cases were mainly unvaccinated, with mild or asymptomatic clinical presentation, and most were at risk of overexposure associated with the healthcare environment. Strain segregation enabled integration of sequences to clarify nosocomial outbreaks where analysis had been impaired due to co-infection. CONCLUSIONS Co-infection cases were identified throughout the pandemic, not just in the time periods when highly divergent lineages were co-circulating. Co-infections involving different lineages or strains from the same lineage were occurring in the same proportion. Most cases were mild, did not require medical assistance and were not vaccinated, and a large proportion were associated with the hospital environment.
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Affiliation(s)
- Daniel Peñas-Utrilla
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Escuela de Doctorado, Universidad de Alcalá, Plaza de San Diego, S/N, Alcalá de Henares, Madrid, 28801, Spain
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain.
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.
| | - Andrea Molero-Salinas
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Agustín Estévez
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Amadeo Sanz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Marta Herranz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Carolina Martínez-Laperche
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Servicio de Oncohematología, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Cristina Andrés-Zayas
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Genomics Unit, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Cristina Veintimilla
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Pilar Catalán
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Roberto Alonso
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain.
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
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18
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Pernet O, Weisenhaus M, Stafylis C, Williams C, Campan M, Pettersson J, Green N, Lee DM, Thomas PD, Ward P, Hu H, Klausner JD, Kovacs AAZ. SARS-CoV-2 viral variants can rapidly be identified for clinical decision making and population surveillance using a high-throughput digital droplet PCR assay. Sci Rep 2023; 13:7612. [PMID: 37165019 PMCID: PMC10170421 DOI: 10.1038/s41598-023-34188-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 04/25/2023] [Indexed: 05/12/2023] Open
Abstract
Epidemiologic surveillance of circulating SARS-CoV-2 variants is essential to assess impact on clinical outcomes and vaccine efficacy. Whole genome sequencing (WGS), the gold-standard to identify variants, requires significant infrastructure and expertise. We developed a digital droplet polymerase chain reaction (ddPCR) assay that can rapidly identify circulating variants of concern/interest (VOC/VOI) using variant-specific mutation combinations in the Spike gene. To validate the assay, 800 saliva samples known to be SARS-CoV-2 positive by RT-PCR were used. During the study (July 2020-March 2022) the assay was easily adaptable to identify not only existing circulating VAC/VOI, but all new variants as they evolved. The assay can discriminate nine variants (Alpha, Beta, Gamma, Delta, Eta, Epsilon, Lambda, Mu, and Omicron) and sub-lineages (Delta 417N, Omicron BA.1, BA.2). Sequence analyses confirmed variant type for 124/124 samples tested. This ddPCR assay is an inexpensive, sensitive, high-throughput assay that can easily be adapted as new variants are identified.
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Affiliation(s)
- Olivier Pernet
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, University of Southern California, Los Angeles, CA, USA.
| | - Maia Weisenhaus
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, University of Southern California, Los Angeles, CA, USA
| | - Chrysovalantis Stafylis
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Christopher Williams
- Department of Preventive Medicine, Division of Bioinformatics, University of Southern California, Los Angeles, CA, USA
| | - Mihaela Campan
- Department of Pathology & Laboratory Medicine in Keck, University of Southern California, Los Angeles, CA, USA
| | - Jonas Pettersson
- Department of Pathology & Laboratory Medicine in Keck, University of Southern California, Los Angeles, CA, USA
| | - Nicole Green
- Los Angeles County Department of Public Health, Los Angeles, CA, USA
| | - David M Lee
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, University of Southern California, Los Angeles, CA, USA
| | - Paul D Thomas
- Department of Preventive Medicine, Division of Bioinformatics, University of Southern California, Los Angeles, CA, USA
| | - Pamela Ward
- Department of Pathology & Laboratory Medicine in Keck, University of Southern California, Los Angeles, CA, USA
| | - Howard Hu
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jeffrey D Klausner
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Andrea A Z Kovacs
- Department of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, University of Southern California, Los Angeles, CA, USA
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Pathology & Laboratory Medicine in Keck, University of Southern California, Los Angeles, CA, USA
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19
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González-Vázquez LD, Arenas M. Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic. Genes (Basel) 2023; 14:407. [PMID: 36833334 PMCID: PMC9956206 DOI: 10.3390/genes14020407] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) produced diverse molecular variants during its recent expansion in humans that caused different transmissibility and severity of the associated disease as well as resistance to monoclonal antibodies and polyclonal sera, among other treatments. In order to understand the causes and consequences of the observed SARS-CoV-2 molecular diversity, a variety of recent studies investigated the molecular evolution of this virus during its expansion in humans. In general, this virus evolves with a moderate rate of evolution, in the order of 10-3-10-4 substitutions per site and per year, which presents continuous fluctuations over time. Despite its origin being frequently associated with recombination events between related coronaviruses, little evidence of recombination was detected, and it was mostly located in the spike coding region. Molecular adaptation is heterogeneous among SARS-CoV-2 genes. Although most of the genes evolved under purifying selection, several genes showed genetic signatures of diversifying selection, including a number of positively selected sites that affect proteins relevant for the virus replication. Here, we review current knowledge about the molecular evolution of SARS-CoV-2 in humans, including the emergence and establishment of variants of concern. We also clarify relationships between the nomenclatures of SARS-CoV-2 lineages. We conclude that the molecular evolution of this virus should be monitored over time for predicting relevant phenotypic consequences and designing future efficient treatments.
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Affiliation(s)
- Luis Daniel González-Vázquez
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Miguel Arenas
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310 Vigo, Spain
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20
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Nicot F, Trémeaux P, Latour J, Carcenac R, Demmou S, Jeanne N, Ranger N, De Smet C, Raymond S, Dimeglio C, Izopet J. Whole-genome single molecule real-time sequencing of SARS-CoV-2 Omicron. J Med Virol 2023; 95:e28564. [PMID: 36756931 DOI: 10.1002/jmv.28564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
New variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome can only be identified using accurate sequencing methods. Single molecule real-time (SMRT) sequencing has been used to characterize Alpha and Delta variants, but not Omicron variants harboring numerous mutations in the SARS-CoV-2 genome. This study assesses the performance of a target capture SMRT sequencing protocol for whole genome sequencing (WGS) of SARS-CoV-2 Omicron variants and compared it to that of an amplicon SMRT sequencing protocol optimized for Omicron variants. The failure rate of the target capture protocol (6%) was lower than that of the amplicon protocol (34%, p < 0.001) on our data set, and the median genome coverage with the target capture protocol (98.6% [interquartile range (IQR): 86-99.4]) was greater than that with the amplicon protocol (76.6% [IQR: 66-89.6], [p < 0.001]). The percentages of samples with >95% whole genome coverage were 64% with the target capture protocol and 19% with the amplicon protocol (p < 0.05). The clades of 96 samples determined with both protocols were 93% concordant and the lineages of 59 samples were 100% concordant. Thus, target capture SMRT sequencing appears to be an efficient method for WGS, genotyping and detecting mutations of SARS-CoV-2 Omicron variants.
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Affiliation(s)
- Florence Nicot
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Pauline Trémeaux
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Justine Latour
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Romain Carcenac
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Sofia Demmou
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Nicolas Jeanne
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Noémie Ranger
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | | | - Stéphanie Raymond
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Chloé Dimeglio
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Jacques Izopet
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
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21
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Salimović-Bešić I, Dedeić-Ljubović A, Zahirović E, Hasanović M, Šehić M, Vukovikj M, Boshevska G, Vegar-Zubović S, Mehmedika-Suljić E, Izetbegović S. The SARS-CoV-2 Delta (B.1.617.2) variant with spike N501Y mutation in the shadow of Omicron emergence. Heliyon 2022; 8:e12650. [PMID: 36590492 PMCID: PMC9789543 DOI: 10.1016/j.heliyon.2022.e12650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 10/05/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
Circulation of the Omicron variant with the reemergence of the N501Y mutation along with many others in the spike protein has once again stirred the academic community. Interestingly, tracing the genetic diversity of SARS-CoV-2 shed light on a less frequent N501Y + Delta variant which has been in the global circulation for some time before the Omicron appearance. This paper aims to present the molecular characteristics of the SARS-CoV-2 Spike_N501Y + Delta variant detected in Bosnia and Herzegovina. The study was conducted during November and December 2021. All patients were tested using real-time RT-PCR for detection of SARS-CoV-2. A representative number of SARS-CoV-2 positive samples was pre-screened using VirSNiP SARS-CoV-2 Spike N501Y kit. The characterization of the viruses was carried out with Illumina RNA Prep with enrichment and the Respiratory Virus Oligo Panel kit. Among the analyzed sequences, we found two isolates of the Delta variant that differ from their most related clade- GK AY.4.3 in additional mutations N501Y and L54F. In this study, we described the presence of a rare form of Delta variant with Spike_N501Y mutation in the shadow of the Omicron emergence. Despite the set of mutations in the Spike protein, this form of Delta variant does not indicate the large-scale consequences for the general population. Further functional studies of this form could provide more information about its antigenicity and infectivity.
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Affiliation(s)
- Irma Salimović-Bešić
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina,Corresponding author.
| | - Amela Dedeić-Ljubović
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Edina Zahirović
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Medina Hasanović
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Merima Šehić
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Maja Vukovikj
- Institute of Public Health of Republic of North Macedonia, 50-ta Divizija 6, 1000, Skopje, Macedonia
| | - Golubinka Boshevska
- Faculty for Medical Sciences, University Goce Delchev, Krste Misirkov No.10-A P.O. Box 201, 2000, Shtip, Macedonia
| | - Sandra Vegar-Zubović
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Enra Mehmedika-Suljić
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Sebija Izetbegović
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
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22
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Focosi D, McConnell S, Casadevall A. The Omicron variant of concern: Diversification and convergent evolution in spike protein, and escape from anti-Spike monoclonal antibodies. Drug Resist Updat 2022; 65:100882. [PMID: 36260961 PMCID: PMC9528072 DOI: 10.1016/j.drup.2022.100882] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 01/17/2023]
Abstract
WHO-defined SARS-CoV-2 variants of concern (VOC) drive therapeutics and vaccine development. The Omicron VOC is dominating the arena since November 2021, but the number of its sublineages is growing in complexity. Omicron represent a galaxy with a myriad of stars that suddenly rise and expand before collapsing into apparent extinction when a more fit sublineage appears. This has already happened with BA.1, BA.2, and BA.4/5 and is happening with BA.2.75. We review here the current PANGO phylogeny, focusing on sublineages with Spike mutations, and show how frequently xxxxxxxx convergent evolution has occurred in these sublineages. We finally summarize how Omicron evolution has progressively defeated the anti-Spike monoclonal antibodies authorized so far, leaving clinicians to again fall back on COVID19 convalescent plasma from vaccinated donors as the only antibody-based therapy available.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy.
| | - Scott McConnell
- Department of Medicine, Johns Hopkins School of Public Health and School of Medicine, Baltimore, MD, USA
| | - Arturo Casadevall
- Department of Medicine, Johns Hopkins School of Public Health and School of Medicine, Baltimore, MD, USA
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23
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Sarkar P, Banerjee S, Chakrabarti S, Chakrabarti P, Bandyopadhyay A, Mitra AG, Saha S, Roy A, Sarkar S. Genome characterization, phylogenomic assessment and spatio-temporal dynamics study of highly mutated BA variants from India. Indian J Med Microbiol 2022; 43:66-72. [PMID: 36400646 PMCID: PMC9664238 DOI: 10.1016/j.ijmmb.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/08/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022]
Abstract
Purpose The emergence of highly mutated and transmissible BA variants has caused an unprecedented surge in COVID-19 infections worldwide. Thorough analysis of its genome structure and phylogenomic evolutionary details will serve as scientific reference for future research. Method Here, we have analyzed the BA variants from India using whole-genome sequencing, spike protein mutation study, spatio-temporal surveillance, phylogenomic assessment and epitope mapping. Results The predominance of BA.2/BA.2-like was observed in India during COVID-19 third wave. Genome analysis and mutation study highlighted the existence of 2128 amino acid changes within BA as compared to NC_045512.2. Presence of 23 unknown mutation sites (spanning region 61–831) were observed among the Indian BA variants as compared to the global BA strains. Unassigned probable Omicron showed the highest number of mutations (370) followed by BA.1 (104), BA.2.3 (56), and BA.2 (27). Presence of mutations ‘Q493R + Q498R + N501Y’, and ‘K417 N + E484A + N501Y’ remained exclusive to BA.2 as well as unassigned probable Omicron. The time-tree and phylogenomic network assessed the evolutionary relationship of the BA variants. Existence of 424 segregating sites and 113 parsimony informative sites within BA genomes were observed through haplotype network analysis. Epitope mapping depicted the presence of unique antigenic sites within the receptor binding domain of the BA variants that could be exploited for robust vaccine development. Conclusion These findings provide important scientific insights about the nature, diversity, and evolution of Indian BA variants. The study further divulges in the avenues of therapeutic upgradation for better management and eventual eradication of COVID-19.
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Affiliation(s)
- Poulomi Sarkar
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India
| | - Sarthak Banerjee
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India
| | - Saikat Chakrabarti
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India
| | - Partha Chakrabarti
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India
| | - Arun Bandyopadhyay
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India
| | | | - Soumen Saha
- MEDICA Super-specialty Hospital, Kolkata, India
| | - Aviral Roy
- MEDICA Super-specialty Hospital, Kolkata, India
| | - Siddik Sarkar
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India,Corresponding author. CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB-700032, India
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24
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Farahat RA. Omicron B.1.1.529 subvariant: Brief evidence and future prospects. Ann Med Surg (Lond) 2022; 83:104808. [PMID: 36339920 PMCID: PMC9621621 DOI: 10.1016/j.amsu.2022.104808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022] Open
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25
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Genomic Analysis of SARS-CoV-2 Alpha, Beta and Delta Variants of Concern Uncovers Signatures of Neutral and Non-Neutral Evolution. Viruses 2022; 14:v14112375. [PMID: 36366473 PMCID: PMC9695218 DOI: 10.3390/v14112375] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 01/31/2023] Open
Abstract
Due to the emergence of new variants of the SARS-CoV-2 coronavirus, the question of how the viral genomes evolved, leading to the formation of highly infectious strains, becomes particularly important. Three major emergent strains, Alpha, Beta and Delta, characterized by a significant number of missense mutations, provide a natural test field. We accumulated and aligned 4.7 million SARS-CoV-2 genomes from the GISAID database and carried out a comprehensive set of analyses. This collection covers the period until the end of October 2021, i.e., the beginnings of the Omicron variant. First, we explored combinatorial complexity of the genomic variants emerging and their timing, indicating very strong, albeit hidden, selection forces. Our analyses show that the mutations that define variants of concern did not arise gradually but rather co-evolved rapidly, leading to the emergence of the full variant strain. To explore in more detail the evolutionary forces at work, we developed time trajectories of mutations at all 29,903 sites of the SARS-CoV-2 genome, week by week, and stratified them into trends related to (i) point substitutions, (ii) deletions and (iii) non-sequenceable regions. We focused on classifying the genetic forces active at different ranges of the mutational spectrum. We observed the agreement of the lowest-frequency mutation spectrum with the Griffiths-Tavaré theory, under the Infinite Sites Model and neutrality. If we widen the frequency range, we observe the site frequency spectra much more consistently with the Tung-Durrett model assuming clone competition and selection. The coefficients of the fitting model indicate the possibility of selection acting to promote gradual growth slowdown, as observed in the history of the variants of concern. These results add up to a model of genomic evolution, which partly fits into the classical drift barrier ideas. Certain observations, such as mutation "bands" persistent over the epidemic history, suggest contribution of genetic forces different from mutation, drift and selection, including recombination or other genome transformations. In addition, we show that a "toy" mathematical model can qualitatively reproduce how new variants (clones) stem from rare advantageous driver mutations, and then acquire neutral or disadvantageous passenger mutations which gradually reduce their fitness so they can be then outcompeted by new variants due to other driver mutations.
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26
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Detection and prevalence of SARS-CoV-2 co-infections during the Omicron variant circulation in France. Nat Commun 2022; 13:6316. [PMID: 36274062 PMCID: PMC9588762 DOI: 10.1038/s41467-022-33910-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
From December 2021-February 2022, an intense and unprecedented co-circulation of SARS-CoV-2 variants with high genetic diversity raised the question of possible co-infections between variants and how to detect them. Using 11 mixes of Delta:Omicron isolates at different ratios, we evaluated the performance of 4 different sets of primers used for whole-genome sequencing and developed an unbiased bioinformatics method for the detection of co-infections involving genetically distinct SARS-CoV-2 lineages. Applied on 21,387 samples collected between December 6, 2021 to February 27, 2022 from random genomic surveillance in France, we detected 53 co-infections between different lineages. The prevalence of Delta and Omicron (BA.1) co-infections and Omicron lineages BA.1 and BA.2 co-infections were estimated at 0.18% and 0.26%, respectively. Among 6,242 hospitalized patients, the intensive care unit (ICU) admission rates were 1.64%, 4.81% and 15.38% in Omicron, Delta and Delta/Omicron patients, respectively. No BA.1/BA.2 co-infections were reported among ICU admitted patients. Among the 53 co-infected patients, a total of 21 patients (39.6%) were not vaccinated. Although SARS-CoV-2 co-infections were rare in this study, their proper detection is crucial to evaluate their clinical impact and the risk of the emergence of potential recombinants.
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Chaqroun A, Hartard C, Josse T, Taverniers A, Jeulin H, Gantzer C, Murray JM, Bertrand I, Schvoerer E. SARS-CoV-2 Variability in Patients and Wastewaters—Potential Immuno-Modulation during the Shift from Delta to Omicron. Biomedicines 2022; 10:biomedicines10092080. [PMID: 36140181 PMCID: PMC9496010 DOI: 10.3390/biomedicines10092080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/16/2022] Open
Abstract
The continuous emergence of SARS-CoV-2 variants favors potential co-infections and/or viral mutation events, leading to possible new biological properties. The aim of this work was to characterize SARS-CoV-2 genetic variability during the Delta–Omicron shift in patients and in a neighboring wastewater treatment plant (WWTP) in the same urban area. The surveillance of SARS-CoV-2 was performed by routine screening of positive samples by single nucleotide polymorphism analysis within the S gene. Moreover, additionally to national systematic whole genome sequencing (WGS) once a week in SARS-CoV-2-positive patients, WGS was also applied when mutational profiles were difficult to interpret by routine screening. Thus, WGS was performed on 414 respiratory samples and on four wastewater samples, northeastern France. This allowed us to report (i) the temporally concordant Delta to Omicron viral shift in patients and wastewaters; (ii) the characterization of 21J (Delta) and 21K (Omicron)/BA.1-21L (Omicron)/BA.2-BA.4 mixtures from humans or environmental samples; (iii) the mapping of composite mutations and the predicted impact on immune properties in the viral Spike protein.
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Affiliation(s)
- Ahlam Chaqroun
- CNRS, LCPME, Université de Lorraine, F-54000 Nancy, France
- Laboratoire de Virologie-Microbiologie, Hôpital Universitaire de Nancy, Université de Lorraine, F-54000 Nancy, France
| | - Cédric Hartard
- CNRS, LCPME, Université de Lorraine, F-54000 Nancy, France
- Laboratoire de Virologie-Microbiologie, Hôpital Universitaire de Nancy, Université de Lorraine, F-54000 Nancy, France
| | - Thomas Josse
- Laboratoire de Virologie-Microbiologie, Hôpital Universitaire de Nancy, Université de Lorraine, F-54000 Nancy, France
| | - Audrey Taverniers
- Laboratoire de Virologie-Microbiologie, Hôpital Universitaire de Nancy, Université de Lorraine, F-54000 Nancy, France
| | - Hélène Jeulin
- CNRS, LCPME, Université de Lorraine, F-54000 Nancy, France
- Laboratoire de Virologie-Microbiologie, Hôpital Universitaire de Nancy, Université de Lorraine, F-54000 Nancy, France
| | | | - John M. Murray
- School of Mathematics and Statistics, UNSW Sydney, Sydney, NSW 2052, Australia
| | | | | | - Evelyne Schvoerer
- CNRS, LCPME, Université de Lorraine, F-54000 Nancy, France
- Laboratoire de Virologie-Microbiologie, Hôpital Universitaire de Nancy, Université de Lorraine, F-54000 Nancy, France
- Correspondence: or
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