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Arbi M, Khedhiri M, Ayouni K, Souiai O, Dhouib S, Ghanmi N, Benkahla A, Triki H, Haddad-Boubaker S. Recombination Events Among SARS-CoV-2 Omicron Subvariants: Impact on Spike Interaction With ACE2 Receptor and Neutralizing Antibodies. Evol Bioinform Online 2024; 20:11769343241272415. [PMID: 39149136 PMCID: PMC11325312 DOI: 10.1177/11769343241272415] [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: 03/14/2024] [Accepted: 07/03/2024] [Indexed: 08/17/2024] Open
Abstract
The recombination plays a key role in promoting evolution of RNA viruses and emergence of potentially epidemic variants. Some studies investigated the recombination occurrence among SARS-CoV-2, without exploring its impact on virus-host interaction. In the aim to investigate the burden of recombination in terms of frequency and distribution, the occurrence of recombination was first explored in 44 230 Omicron sequences among BQ subvariants and the under investigation "ML" (Multiple Lineages) denoted sequences, using 3seq software. Second, the recombination impact on interaction between the Spike protein and ACE2 receptor as well as neutralizing antibodies (nAbs), was analyzed using docking tools. Recombination was detected in 56.91% and 82.20% of BQ and ML strains, respectively. It took place mainly in spike and ORF1a genes. For BQ recombinant strains, the docking analysis showed that the spike interacted strongly with ACE2 and weakly with nAbs. The mutations S373P, S375F and T376A constitute a residue network that enhances the RBD interaction with ACE2. Thirteen mutations in RBD (S373P, S375F, T376A, D405N, R408S, K417N, N440K, S477N, P494S, Q498R, N501Y, and Y505H) and NTD (Y240H) seem to be implicated in immune evasion of recombinants by altering spike interaction with nAbs. In conclusion, this "in silico" study demonstrated that the recombination mechanism is frequent among Omicron BQ and ML variants. It highlights new key mutations, that potentially implicated in enhancement of spike binding to ACE2 (F376A) and escape from nAbs (RBD: F376A, D405N, R408S, N440K, S477N, P494S, and Y505H; NTD: Y240H). Our findings present considerable insights for the elaboration of effective prophylaxis and therapeutic strategies against future SARS-CoV-2 waves.
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Affiliation(s)
- Marwa Arbi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Marwa Khedhiri
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
- Research Laboratory: "Virus, Vector and Host" (LR20IPT02), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Kaouther Ayouni
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
- Research Laboratory: "Virus, Vector and Host" (LR20IPT02), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
- Higher Institute of Medical Technologies of Tunis, Tunis Al Manar University, Tunis, Tunisia
| | - Samar Dhouib
- High School of Statistics and Analysis of Information (ESSAI), University of Carthage, Tunis, Tunisia
| | - Nidhal Ghanmi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
- Research Laboratory: "Virus, Vector and Host" (LR20IPT02), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Sondes Haddad-Boubaker
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
- Research Laboratory: "Virus, Vector and Host" (LR20IPT02), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
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2
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Aldeguer-Riquelme B, Conrad RE, Antón J, Rossello-Mora R, Konstantinidis KT. A natural ANI gap that can define intra-species units of bacteriophages and other viruses. mBio 2024; 15:e0153624. [PMID: 39037288 PMCID: PMC11323488 DOI: 10.1128/mbio.01536-24] [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: 06/11/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024] Open
Abstract
Despite the importance of intra-species variants of viruses for causing disease and/or disrupting ecosystem functioning, there is no universally applicable standard to define these. A (natural) gap in whole-genome average nucleotide identity (ANI) values around 95% is commonly used to define species, especially for bacteriophages, but whether a similar gap exists within species that can be used to define intra-species units has not been evaluated yet. Whole-genome comparisons among members of 1,016 bacteriophage (Caudoviricetes) species revealed a region of low frequency of ANI values around 99.2%-99.8%, showing threefold or fewer pairs than expected for an even distribution. This second gap is prevalent in viruses infecting various cultured or uncultured hosts from a variety of environments, although a few exceptions to this pattern were also observed (3.7% of total species) and are likely attributed to cultivation biases or other factors. Similar results were observed for a limited set of eukaryotic viruses that are adequately sampled, including SARS-CoV-2, whose ANI-based clusters matched well with the WHO-defined variants of concern, indicating that our findings from bacteriophages might be more broadly applicable and the ANI-based clusters may represent functionally and/or ecologically distinct units. These units appear to be predominantly driven by (high) ecological cohesiveness coupled to either frequent recombination for bacteriophages or selection and clonal evolution for other viruses such as SARS-CoV-2, indicating that fundamentally different underlying mechanisms could lead to similar diversity patterns. Accordingly, we propose the ANI gap approach outlined above for defining viral intra-species units, for which we propose the term genomovars. IMPORTANCE Viral species are composed of an ensemble of intra-species variants whose individual dynamics may have major implications for human and animal health and/or ecosystem functioning. However, the lack of universally accepted standards to define these intra-species variants has led researchers to use different approaches for this task, creating inconsistent intra-species units across different viral families and confusion in communication. By comparing hundreds of mostly bacteriophage genomes, we show that there is a widely distributed natural gap in whole-genome average nucleotide identity values in most, but not all, of these species that can be used to define intra-species units. Therefore, these results advance the molecular toolbox for tracking viral intra-species units and should facilitate future epidemiological and environmental studies.
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Affiliation(s)
- Borja Aldeguer-Riquelme
- School of Civil & Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Roth E. Conrad
- School of Civil & Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, San Vicente del Raspeig, Spain
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Konstantinos T. Konstantinidis
- School of Civil & Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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3
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Ryder R, Smith E, Borthwick D, Elder J, Panditrao M, Morales C, Wadford DA. Emergence of Recombinant SARS-CoV-2 Variants in California from 2020 to 2022. Viruses 2024; 16:1209. [PMID: 39205183 PMCID: PMC11359944 DOI: 10.3390/v16081209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/17/2024] [Accepted: 07/24/2024] [Indexed: 09/04/2024] Open
Abstract
The detection, characterization, and monitoring of SARS-CoV-2 recombinant variants constitute a challenge for public health authorities worldwide. Recombinant variants, composed of two or more SARS-CoV-2 lineages, often have unknown impacts on transmission, immune escape, and virulence in the early stages of emergence. We examined 4213 SARS-CoV-2 recombinant SARS-CoV-2 genomes collected between 2020 and 2022 in California to describe regional and statewide trends in prevalence. Many of these recombinant genomes, such as those belonging to the XZ lineage or novel recombinant lineages, likely originated within the state of California. We discuss the challenges and limitations surrounding Pango lineage assignments, the use of publicly available sequence data, and adequate sample sizes for epidemiologic analyses. Although these challenges will continue as SARS-CoV-2 sequencing volumes decrease globally, this study enhances our understanding of SARS-CoV-2 recombinant genomes to date while providing a foundation for future insights into emerging recombinant lineages.
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Affiliation(s)
- Rahil Ryder
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
| | - Emily Smith
- Theiagen Genomics, Highlands Ranch, CO 80129, USA;
| | - Deva Borthwick
- COVID Control Branch, Division of Communicable Disease Control, CDPH, Richmond, CA 94804, USA
| | - Jesse Elder
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
| | - Mayuri Panditrao
- COVID Control Branch, Division of Communicable Disease Control, CDPH, Richmond, CA 94804, USA
| | - Christina Morales
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
| | - Debra A. Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
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4
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Wong Y, Ignatieva A, Koskela J, Gorjanc G, Wohns AW, Kelleher J. A general and efficient representation of ancestral recombination graphs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.03.565466. [PMID: 37961279 PMCID: PMC10635123 DOI: 10.1101/2023.11.03.565466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
As a result of recombination, adjacent nucleotides can have different paths of genetic inheritance and therefore the genealogical trees for a sample of DNA sequences vary along the genome. The structure capturing the details of these intricately interwoven paths of inheritance is referred to as an ancestral recombination graph (ARG). Classical formalisms have focused on mapping coalescence and recombination events to the nodes in an ARG. This approach is out of step with modern developments, which do not represent genetic inheritance in terms of these events or explicitly infer them. We present a simple formalism that defines an ARG in terms of specific genomes and their intervals of genetic inheritance, and show how it generalises these classical treatments and encompasses the outputs of recent methods. We discuss nuances arising from this more general structure, and argue that it forms an appropriate basis for a software standard in this rapidly growing field.
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Affiliation(s)
- Yan Wong
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK
| | - Anastasia Ignatieva
- School of Mathematics and Statistics, University of Glasgow, UK
- Department of Statistics, University of Oxford, UK
| | - Jere Koskela
- School of Mathematics, Statistics and Physics, Newcastle University, UK
- Department of Statistics, University of Warwick, UK
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, UK
| | - Anthony W. Wohns
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, USA
| | - Jerome Kelleher
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK
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5
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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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6
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Emad R, Naga IS. Comparative genotyping of SARS-CoV-2 among Egyptian patients: near-full length genomic sequences versus selected spike and nucleocapsid regions. Med Microbiol Immunol 2023; 212:437-446. [PMID: 37789185 PMCID: PMC10618331 DOI: 10.1007/s00430-023-00783-8] [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: 07/10/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023]
Abstract
Several tools have been developed for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genotyping based on either whole genome or spike sequencing. We aimed to highlight the molecular epidemiological landscape of SARS-CoV-2 in Egypt since the start of the pandemic, to describe discrepancies between the 3 typing tools: Global Initiative on Sharing Avian Influenza Data (GISAID), Nextclade, and Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) and to assess the fitness of spike and nucleocapsid regions for lineage assignment compared to the whole genome. A total of 3935 sequences isolated from Egypt (March 2020-2023) were retrieved from the GISAID database. A subset of data (n = 1212) with high coverage whole genome was used for tool discrimination and agreement analyses. Among 1212 sequences, the highest discriminatory power was 0.895 for PANGOLIN, followed by GISAID (0.872) and Nextclade (0.866). There was a statistically significant difference (p = 0.0418) between lineages assigned via spike (30%) and nucleocapsid (46%) compared to their whole genome-assigned lineages. The first 3 pandemic waves were dominated by B.1, followed by C.36 and then C.36.3, while the fourth to sixth waves were dominated by the B.1.617.2, BA, and BA.5.2 lineages, respectively. Current shift in lineage typing to recombinant forms. The 3 typing tools showed comparable discrimination among SARS-CoV-2 lineages. The nucleocapsid region could be used for lineage assignment.
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Affiliation(s)
- Rasha Emad
- Alexandria Main University Hospital, Alexandria, Egypt.
| | - Iman S Naga
- Department of Microbiology, Medical Research Institute, Alexandria University, Alexandria, Egypt
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7
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Chaves-Blanco L, de Salazar A, Fuentes A, Viñuela L, Perez-Florido J, Dopazo J, García F. Evaluation of a combined detection of SARS-CoV-2 and its variants using real-time allele-specific PCR strategy: an advantage for clinical practice. Epidemiol Infect 2023; 151:e201. [PMID: 37997654 PMCID: PMC10753446 DOI: 10.1017/s095026882300184x] [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: 08/03/2023] [Revised: 10/08/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023] Open
Abstract
This study aimed to assess the ability of a real-time reverse transcription polymerase chain reaction (RT-PCR) with multiple targets to detect SARS-CoV-2 and its variants in a single test. Nasopharyngeal specimens were collected from patients in Granada, Spain, between January 2021 and December 2022. Five allele-specific RT-PCR kits were used sequentially, with each kit designed to detect a predominant variant at the time. When the Alpha variant was dominant, the kit included the HV69/70 deletion, E and N genes. When Delta replaced Alpha, the kit incorporated the L452R mutation in addition to E and N genes. When Omicron became dominant, L452R was replaced with the N679K mutation. Before incorporating each variant kit, a comparative analysis was carried out with SARS-CoV-2 whole genome sequencing (WGS). The results demonstrated that RT-PCR with multiple targets can provide rapid and effective detection of SARS-CoV-2 and its variants in a single test. A very high degree of agreement (96.2%) was obtained between the comparison of RT-PCR and WGS. Allele-specific RT-PCR assays make it easier to implement epidemiological surveillance systems for effective public health decision making.
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Affiliation(s)
- Lucía Chaves-Blanco
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
| | - Adolfo de Salazar
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Ana Fuentes
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Laura Viñuela
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Javier Perez-Florido
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Sevilla, Sevilla, Spain
| | - Joaquín Dopazo
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Sevilla, Sevilla, Spain
- FPS/ELIXIR-ES, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, Sevilla, Spain
| | - Federico García
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
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8
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Rouzine IM, Rozhnova G. Evolutionary implications of SARS-CoV-2 vaccination for the future design of vaccination strategies. COMMUNICATIONS MEDICINE 2023; 3:86. [PMID: 37336956 PMCID: PMC10279745 DOI: 10.1038/s43856-023-00320-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/07/2023] [Indexed: 06/21/2023] Open
Abstract
Once the first SARS-CoV-2 vaccine became available, mass vaccination was the main pillar of the public health response to the COVID-19 pandemic. It was very effective in reducing hospitalizations and deaths. Here, we discuss the possibility that mass vaccination might accelerate SARS-CoV-2 evolution in antibody-binding regions compared to natural infection at the population level. Using the evidence of strong genetic variation in antibody-binding regions and taking advantage of the similarity between the envelope proteins of SARS-CoV-2 and influenza, we assume that immune selection pressure acting on these regions of the two viruses is similar. We discuss the consequences of this assumption for SARS-CoV-2 evolution in light of mathematical models developed previously for influenza. We further outline the implications of this phenomenon, if our assumptions are confirmed, for the future design of SARS-CoV-2 vaccination strategies.
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Affiliation(s)
- Igor M Rouzine
- Immunogenetics, Sechenov Institute of Evolutionary Physiology and Biochemistry of Russian Academy of Sciences, Saint-Petersburg, Russia.
| | - Ganna Rozhnova
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
- Center for Complex Systems Studies (CCSS), Utrecht University, Utrecht, The Netherlands.
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9
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Lenguiya LH, Fritz M, De Fonclare DDR, Corbet S, Becquart P, Mbou C, Nguie RJ, Mouellet WS, Demboux JEL, Issamou Mayengue P, Koukouikila-Koussounda F, Ar Gouilh M, Leroy EM, Niama FR. Whole-Genome Characterization of SARS-CoV-2 Reveals Simultaneous Circulation of Three Variants and a Putative Recombination (20B/20H) in Pets, Brazzaville, Republic of the Congo. Viruses 2023; 15:v15040933. [PMID: 37112914 PMCID: PMC10142050 DOI: 10.3390/v15040933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Following the emergence of SARS-CoV-2, cases of pets infected with variants circulating among humans were reported. In order to evaluate the occurrence of SARS-CoV-2 circulation among pets in the Republic of the Congo, we conducted a ten-month study of dogs and cats living in COVID-19-positive households in Brazzaville and neighboring localities. Real-time PCR and the Luminex platform were used to detect SARS-CoV-2 RNA and antibodies to SARS-CoV-2 RBD and S proteins, respectively. Our results show for the first time the simultaneous circulation of several variants of SARS-CoV-2, including viruses from clades 20A and 20H and a putative recombinant variant between viruses from clades 20B and 20H. We found a high seroprevalence of 38.6%, with 14% of tested pets positive for SARS-CoV-2 RNA. Thirty-four percent of infected pets developed mild clinical signs, including respiratory and digestive signs, and shed the virus for about one day to two weeks. These results highlight the potential risk of SARS-CoV-2 interspecies transmission and the benefits of a "One Health" approach that includes SARS-CoV-2 diagnosis and surveillance of viral diversity in pets. This approach aims to prevent transmission to surrounding wildlife as well as spillback to humans.
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Affiliation(s)
| | - Matthieu Fritz
- Institut de Recherche pour le Développement, Unité Mixte de Recherche Mivegec, BP34090 Montpellier, France
| | - Daphné de Riols De Fonclare
- UNICAEN, Department of Viroloy, University of Rouen Normandie, Inserm Dynamicure UMR 1311, BP14000 Caen, France
| | - Sandrine Corbet
- UNICAEN, Department of Viroloy, University of Rouen Normandie, Inserm Dynamicure UMR 1311, BP14000 Caen, France
| | - Pierre Becquart
- Institut de Recherche pour le Développement, Unité Mixte de Recherche Mivegec, BP34090 Montpellier, France
| | | | | | | | | | - Pembe Issamou Mayengue
- Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville BP69, Congo
- Laboratoire National de Santé Publique, Brazzaville BP120, Congo
| | - Félix Koukouikila-Koussounda
- Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville BP69, Congo
- Laboratoire National de Santé Publique, Brazzaville BP120, Congo
| | - Meriadeg Ar Gouilh
- UNICAEN, Department of Viroloy, University of Rouen Normandie, Inserm Dynamicure UMR 1311, BP14000 Caen, France
| | - Eric M Leroy
- Institut de Recherche pour le Développement, Unité Mixte de Recherche Mivegec, BP34090 Montpellier, France
| | - Fabien Roch Niama
- Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville BP69, Congo
- Laboratoire National de Santé Publique, Brazzaville BP120, Congo
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10
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Pacchiarini N, Cronin M, Sawyer C, Williams C, Beazer A, Cottrell S, Morgan M, Saunders V, Moore C, Connor TR, Williams C. Novel recombinant SARS-CoV-2 lineage detected through genomic surveillance in Wales, UK. Microb Genom 2023; 9. [PMID: 37052600 DOI: 10.1099/mgen.0.000984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Recombination, the process whereby a segment of genetic material from one genome is inserted into another, producing a new chimeric genome, is an important evolutionary mechanism frequently observed in coronaviruses. The risks posed by recombination include the shuffling of advantageous mutations that may increase transmissibility, severity or vaccine escape. We present a genomic and epidemiological description of a new recombinant lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), XR, first identified in Wales. The Pathogen Genomics Unit (Public Health Wales, UK) sequences positive SARS-CoV-2 PCR tests using the ARTIC SARS-CoV-2 sequencing protocol. Recombinants were detected using an in-house pipeline and the epidemiological data analysed in R. Nosocomial cases were defined as those with samples taken after >7 days in hospital. Between February and March 2022, we identified 78 samples with highly similar genomes, comprising a BA.1-like 5' end, a BA.2-like 3' end and a BA.2-like spike protein. This signature is consistent with recombination and was defined as XR by Pangolin (PANGO v1.8). A total of 50 % of cases had a sample collected whilst in hospital and the first three cases were immunocompromised patients. The patient median age was 58 years (range: 4-95 years) and most of the patients were fully vaccinated against SARS-CoV-2 (74 % third dose/booster). Three patients died within 28 days of their sample collection date, one of whom had COVID-19 listed amongst ICD10 (International Classification of Diseases 10) coded causes of death. Our integrated system enabled real-time monitoring of recombinant SARS-CoV-2 for early detection, in order to rapidly risk assess and respond. This work highlights the importance of setting-based surveillance of recombinant SARS-CoV-2, as well as the need to monitor immunocompromised populations through repeat testing and sequencing.
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Affiliation(s)
- Nicole Pacchiarini
- Communicable Disease Surveillance Centre (CDSC), Public Health Wales, Cardiff, Wales, UK
| | - Michelle Cronin
- Communicable Disease Surveillance Centre (CDSC), Public Health Wales, Cardiff, Wales, UK
| | - Clare Sawyer
- Communicable Disease Surveillance Centre (CDSC), Public Health Wales, Cardiff, Wales, UK
| | - Catie Williams
- Pathogen Genomics Unit, Public Health Wales, Cardiff, Wales, UK
| | - Andrew Beazer
- Pathogen Genomics Unit, Public Health Wales, Cardiff, Wales, UK
| | - Simon Cottrell
- Communicable Disease Surveillance Centre (CDSC), Public Health Wales, Cardiff, Wales, UK
| | - Mari Morgan
- Communicable Disease Surveillance Centre (CDSC), Public Health Wales, Cardiff, Wales, UK
| | - Vince Saunders
- Cardiff and Vale University Health Board, Cardiff, Wales, UK
| | - Catherine Moore
- Wales Specialist Virology Centre, Microbiology, Public Health Wales, Cardiff, Wales, UK
| | - Thomas R Connor
- Pathogen Genomics Unit, Public Health Wales, Cardiff, Wales, UK
- Cardiff University School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Christopher Williams
- Communicable Disease Surveillance Centre (CDSC), Public Health Wales, Cardiff, Wales, UK
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11
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Shiraz R, Tripathi S. Enhanced recombination among Omicron subvariants of SARS-CoV-2 contributes to viral immune escape. J Med Virol 2023; 95:e28519. [PMID: 36691935 DOI: 10.1002/jmv.28519] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/14/2022] [Accepted: 01/19/2023] [Indexed: 01/25/2023]
Abstract
Genetic recombination is an important driver of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution, which requires the coinfection of a single host cell with different SARS-CoV-2 strains. To understand the emergence and prevalence of recombinant SARS-CoV-2 lineages through time and space, we analyzed SARS-CoV-2 genome sequences collected from November 2019 to July 2022. We observed an extraordinary increase in the emergence of SARS-CoV-2 recombinant lineages during the Omicron wave, particularly in Northern America and Europe. This phenomenon was independent of the sequencing frequency or genetic diversity of circulating SARS-CoV-2 strains. The recombination breakpoints were more prevalent in the 3'-untranslated region of the viral genome. Importantly, we noted the enrichment of certain amino acids in the Spike protein of recombinant lineages, which have been reported to confer immune escape from neutralizing antibodies and increase angiotensin-converting enzyme 2 receptor binding in some cases. We also observed I42V amino acid change genetically fixated in the NSP14 of the Omicron lineage, which needs further characterization for its potential role in enhanced recombination. Overall, we report the important and timely observation of accelerated recombination in the currently circulating SARS-CoV-2 Omicron variants and explore their potential contribution to viral fitness, particularly immune escape.
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Affiliation(s)
- Rishad Shiraz
- Microbiology and Cell Biology Department, Indian Institute of Science, Bengaluru, India.,Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Shashank Tripathi
- Microbiology and Cell Biology Department, Indian Institute of Science, Bengaluru, India.,Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
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12
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Correlated substitutions reveal SARS-like coronaviruses recombine frequently with a diverse set of structured gene pools. Proc Natl Acad Sci U S A 2023; 120:e2206945119. [PMID: 36693089 PMCID: PMC9945976 DOI: 10.1073/pnas.2206945119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Quantifying SARS-like coronavirus (SL-CoV) evolution is critical to understanding the origins of SARS-CoV-2 and the molecular processes that could underlie future epidemic viruses. While genomic analyses suggest recombination was a factor in the emergence of SARS-CoV-2, few studies have quantified recombination rates among SL-CoVs. Here, we infer recombination rates of SL-CoVs from correlated substitutions in sequencing data using a coalescent model with recombination. Our computationally-efficient, non-phylogenetic method infers recombination parameters of both sampled sequences and the unsampled gene pools with which they recombine. We apply this approach to infer recombination parameters for a range of positive-sense RNA viruses. We then analyze a set of 191 SL-CoV sequences (including SARS-CoV-2) and find that ORF1ab and S genes frequently undergo recombination. We identify which SL-CoV sequence clusters have recombined with shared gene pools, and show that these pools have distinct structures and high recombination rates, with multiple recombination events occurring per synonymous substitution. We find that individual genes have recombined with different viral reservoirs. By decoupling contributions from mutation and recombination, we recover the phylogeny of non-recombined portions for many of these SL-CoVs, including the position of SARS-CoV-2 in this clonal phylogeny. Lastly, by analyzing >400,000 SARS-CoV-2 whole genome sequences, we show current diversity levels are insufficient to infer the within-population recombination rate of the virus since the pandemic began. Our work offers new methods for inferring recombination rates in RNA viruses with implications for understanding recombination in SARS-CoV-2 evolution and the structure of clonal relationships and gene pools shaping its origins.
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13
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Perez-Florido J, Casimiro-Soriguer CS, Ortuño F, Fernandez-Rueda JL, Aguado A, Lara M, Riazzo C, Rodriguez-Iglesias MA, Camacho-Martinez P, Merino-Diaz L, Pupo-Ledo I, de Salazar A, Viñuela L, Fuentes A, Chueca N, García F, Dopazo J, Lepe JA. Detection of High Level of Co-Infection and the Emergence of Novel SARS CoV-2 Delta-Omicron and Omicron-Omicron Recombinants in the Epidemiological Surveillance of Andalusia. Int J Mol Sci 2023; 24:2419. [PMID: 36768752 PMCID: PMC9916856 DOI: 10.3390/ijms24032419] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Recombination is an evolutionary strategy to quickly acquire new viral properties inherited from the parental lineages. The systematic survey of the SARS-CoV-2 genome sequences of the Andalusian genomic surveillance strategy has allowed the detection of an unexpectedly high number of co-infections, which constitute the ideal scenario for the emergence of new recombinants. Whole genome sequence of SARS-CoV-2 has been carried out as part of the genomic surveillance programme. Sample sources included the main hospitals in the Andalusia region. In addition to the increase of co-infections and known recombinants, three novel SARS-CoV-2 delta-omicron and omicron-omicron recombinant variants with two break points have been detected. Our observations document an epidemiological scenario in which co-infection and recombination are detected more frequently. Finally, we describe a family case in which co-infection is followed by the detection of a recombinant made from the two co-infecting variants. This increased number of recombinants raises the risk of emergence of recombinant variants with increased transmissibility and pathogenicity.
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Affiliation(s)
- Javier Perez-Florido
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Sevilla, 41013 Sevilla, Spain
| | - Carlos S. Casimiro-Soriguer
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Sevilla, 41013 Sevilla, Spain
| | - Francisco Ortuño
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Department of Computer Architecture and Computer Technology, University of Granada, 18071 Granada, Spain
| | - Jose L. Fernandez-Rueda
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
| | - Andrea Aguado
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
| | - María Lara
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
| | - Cristina Riazzo
- Unit of Microbiology, University Hospital Reina Sofia, 14004 Cordoba, Spain
| | - Manuel A. Rodriguez-Iglesias
- Servicio de Microbiología, Hospital Universitario Puerta del Mar, INIBICA, Universidad de Cádiz, 11003 Cádiz, Spain
| | - Pedro Camacho-Martinez
- Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
| | - Laura Merino-Diaz
- Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
| | - Inmaculada Pupo-Ledo
- Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
| | - Adolfo de Salazar
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
| | - Laura Viñuela
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
| | - Ana Fuentes
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
| | - Natalia Chueca
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
| | | | - Federico García
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, 28046 Madrid, Spain
- Instituto de Investigación Biosanitaria, ibs.GRANADA, 18012 Granada, Spain
| | - Joaquín Dopazo
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Sevilla, 41013 Sevilla, Spain
- FPS/ELIXIR-ES, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, 41013 Sevilla, Spain
| | - Jose A. Lepe
- Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
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14
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Sargsyan K, Mazmanian K, Lim C. A strategy for evaluating potential antiviral resistance to small molecule drugs and application to SARS-CoV-2. Sci Rep 2023; 13:502. [PMID: 36627366 PMCID: PMC9831016 DOI: 10.1038/s41598-023-27649-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Alterations in viral fitness cannot be inferred from only mutagenesis studies of an isolated viral protein. To-date, no systematic analysis has been performed to identify mutations that improve virus fitness and reduce drug efficacy. We present a generic strategy to evaluate which viral mutations might diminish drug efficacy and applied it to assess how SARS-CoV-2 evolution may affect the efficacy of current approved/candidate small-molecule antivirals for Mpro, PLpro, and RdRp. For each drug target, we determined the drug-interacting virus residues from available structures and the selection pressure of the virus residues from the SARS-CoV-2 genomes. This enabled the identification of promising drug target regions and small-molecule antivirals that the virus can develop resistance. Our strategy of utilizing sequence and structural information from genomic sequence and protein structure databanks can rapidly assess the fitness of any emerging virus variants and can aid antiviral drug design for future pathogens.
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Affiliation(s)
- Karen Sargsyan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan.
| | - Karine Mazmanian
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan.
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan.
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15
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Jankowiak M, Obermeyer FH, Lemieux JE. Inferring selection effects in SARS-CoV-2 with Bayesian Viral Allele Selection. PLoS Genet 2022; 18:e1010540. [PMID: 36508459 PMCID: PMC9779722 DOI: 10.1371/journal.pgen.1010540] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 12/22/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
The global effort to sequence millions of SARS-CoV-2 genomes has provided an unprecedented view of viral evolution. Characterizing how selection acts on SARS-CoV-2 is critical to developing effective, long-lasting vaccines and other treatments, but the scale and complexity of genomic surveillance data make rigorous analysis challenging. To meet this challenge, we develop Bayesian Viral Allele Selection (BVAS), a principled and scalable probabilistic method for inferring the genetic determinants of differential viral fitness and the relative growth rates of viral lineages, including newly emergent lineages. After demonstrating the accuracy and efficacy of our method through simulation, we apply BVAS to 6.9 million SARS-CoV-2 genomes. We identify numerous mutations that increase fitness, including previously identified mutations in the SARS-CoV-2 Spike and Nucleocapsid proteins, as well as mutations in non-structural proteins whose contribution to fitness is less well characterized. In addition, we extend our baseline model to identify mutations whose fitness exhibits strong dependence on vaccination status as well as pairwise interaction effects, i.e. epistasis. Strikingly, both these analyses point to the pivotal role played by the N501 residue in the Spike protein. Our method, which couples Bayesian variable selection with a diffusion approximation in allele frequency space, lays a foundation for identifying fitness-associated mutations under the assumption that most alleles are neutral.
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Affiliation(s)
- Martin Jankowiak
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Fritz H. Obermeyer
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Generate Biomedicines, Cambridge, Massachusetts, United States of America
| | - Jacob E. Lemieux
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Division of Infectious Diseases, Massachusetts General Hospital, Cambridge, Massachusetts, United States of America
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16
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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
| | - 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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17
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Zeng HL, Liu Y, Dichio V, Aurell E. Temporal epistasis inference from more than 3 500 000 SARS-CoV-2 genomic sequences. Phys Rev E 2022; 106:044409. [PMID: 36397507 DOI: 10.1103/physreve.106.044409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
We use direct coupling analysis (DCA) to determine epistatic interactions between loci of variability of the SARS-CoV-2 virus, segmenting genomes by month of sampling. We use full-length, high-quality genomes from the GISAID repository up to October 2021 for a total of over 3 500 000 genomes. We find that DCA terms are more stable over time than correlations but nevertheless change over time as mutations disappear from the global population or reach fixation. Correlations are enriched for phylogenetic effects, and in particularly statistical dependencies at short genomic distances, while DCA brings out links at longer genomic distance. We discuss the validity of a DCA analysis under these conditions in terms of a transient auasilinkage equilibrium state. We identify putative epistatic interaction mutations involving loci in spike.
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Affiliation(s)
- Hong-Li Zeng
- School of Science, Nanjing University of Posts and Telecommunications, New Energy Technology Engineering Laboratory of Jiangsu Province, Nanjing 210023, China
| | - Yue Liu
- School of Science, Nanjing University of Posts and Telecommunications, New Energy Technology Engineering Laboratory of Jiangsu Province, Nanjing 210023, China
| | - Vito Dichio
- Inria Paris, Aramis Project Team, Paris 75013, France
- Institut du Cerveau, ICM, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Paris, France
| | - Erik Aurell
- Department of Computational Science and Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
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18
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Turakhia Y, Thornlow B, Hinrichs A, McBroome J, Ayala N, Ye C, Smith K, De Maio N, Haussler D, Lanfear R, Corbett-Detig R. Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape. Nature 2022; 609:994-997. [PMID: 35952714 PMCID: PMC9519458 DOI: 10.1038/s41586-022-05189-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 08/03/2022] [Indexed: 11/29/2022]
Abstract
Accurate and timely detection of recombinant lineages is crucial for interpreting genetic variation, reconstructing epidemic spread, identifying selection and variants of interest, and accurately performing phylogenetic analyses1-4. During the SARS-CoV-2 pandemic, genomic data generation has exceeded the capacities of existing analysis platforms, thereby crippling real-time analysis of viral evolution5. Here, we use a new phylogenomic method to search a nearly comprehensive SARS-CoV-2 phylogeny for recombinant lineages. In a 1.6 million sample tree from May 2021, we identify 589 recombination events, which indicate that around 2.7% of sequenced SARS-CoV-2 genomes have detectable recombinant ancestry. Recombination breakpoints are inferred to occur disproportionately in the 3' portion of the genome that contains the spike protein. Our results highlight the need for timely analyses of recombination for pinpointing the emergence of recombinant lineages with the potential to increase transmissibility or virulence of the virus. We anticipate that this approach will empower comprehensive real-time tracking of viral recombination during the SARS-CoV-2 pandemic and beyond.
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Affiliation(s)
- Yatish Turakhia
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, USA.
| | - Bryan Thornlow
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Angie Hinrichs
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jakob McBroome
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Nicolas Ayala
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Cheng Ye
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, USA
| | - Kyle Smith
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - David Haussler
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Robert Lanfear
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
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19
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Müller NF, Kistler KE, Bedford T. A Bayesian approach to infer recombination patterns in coronaviruses. Nat Commun 2022; 13:4186. [PMID: 35859071 PMCID: PMC9297283 DOI: 10.1038/s41467-022-31749-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/30/2022] [Indexed: 02/06/2023] Open
Abstract
As shown during the SARS-CoV-2 pandemic, phylogenetic and phylodynamic methods are essential tools to study the spread and evolution of pathogens. One of the central assumptions of these methods is that the shared history of pathogens isolated from different hosts can be described by a branching phylogenetic tree. Recombination breaks this assumption. This makes it problematic to apply phylogenetic methods to study recombining pathogens, including, for example, coronaviruses. Here, we introduce a Markov chain Monte Carlo approach that allows inference of recombination networks from genetic sequence data under a template switching model of recombination. Using this method, we first show that recombination is extremely common in the evolutionary history of SARS-like coronaviruses. We then show how recombination rates across the genome of the human seasonal coronaviruses 229E, OC43 and NL63 vary with rates of adaptation. This suggests that recombination could be beneficial to fitness of human seasonal coronaviruses. Additionally, this work sets the stage for Bayesian phylogenetic tracking of the spread and evolution of SARS-CoV-2 in the future, even as recombinant viruses become prevalent.
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Affiliation(s)
- Nicola F Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Kathryn E Kistler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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20
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McLeod DV, Gandon S. Effects of epistasis and recombination between vaccine-escape and virulence alleles on the dynamics of pathogen adaptation. Nat Ecol Evol 2022; 6:786-793. [PMID: 35437006 DOI: 10.1038/s41559-022-01709-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 02/22/2022] [Indexed: 11/09/2022]
Abstract
Pathogen adaptation to public health interventions such as vaccination may take tortuous routes and involve multiple mutations at different locations in the pathogen genome, acting on distinct phenotypic traits. Yet how these multi-locus adaptations jointly evolve is poorly understood. Here we consider the joint evolution of two adaptations: pathogen escape from the vaccine-induced immune response and adjustments to pathogen virulence affecting transmission or clearance. We elucidate the role played by epistasis and recombination, with an emphasis on the different protective effects of vaccination. We show that vaccines blocking infection, reducing transmission and/or increasing clearance generate positive epistasis between the vaccine-escape and virulence alleles, favouring strains that carry both mutations, whereas vaccines reducing virulence mortality generate negative epistasis, favouring strains that carry either mutation but not both. High rates of recombination can affect these predictions. If epistasis is positive, frequent recombination can prevent the transient build-up of more virulent escape strains. If epistasis is negative, frequent recombination between loci can create an evolutionary bistability, favouring whichever adaptation is more accessible. Our work provides a timely alternative to the variant-centred perspective on pathogen adaptation and captures the effect of different types of vaccine on the interference between multiple adaptive mutations.
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Affiliation(s)
- David V McLeod
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France. .,Institute of Ecology and Evolution, Universität Bern, Bern, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Sylvain Gandon
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France.
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21
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Chrzastek K, Tennakoon C, Bialy D, Freimanis G, Flannery J, Shelton H. A random priming amplification method for whole genome sequencing of SARS-CoV-2 virus. BMC Genomics 2022; 23:406. [PMID: 35644636 PMCID: PMC9148844 DOI: 10.1186/s12864-022-08563-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 03/24/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Non-targeted whole genome sequencing is a powerful tool to comprehensively identify constituents of microbial communities in a sample. There is no need to direct the analysis to any identification before sequencing which can decrease the introduction of bias and false negatives results. It also allows the assessment of genetic aberrations in the genome (e.g., single nucleotide variants, deletions, insertions and copy number variants) including in noncoding protein regions. METHODS The performance of four different random priming amplification methods to recover RNA viral genetic material of SARS-CoV-2 were compared in this study. In method 1 (H-P) the reverse transcriptase (RT) step was performed with random hexamers whereas in methods 2-4 RT incorporating an octamer primer with a known tag. In methods 1 and 2 (K-P) sequencing was applied on material derived from the RT-PCR step, whereas in methods 3 (SISPA) and 4 (S-P) an additional amplification was incorporated before sequencing. RESULTS The SISPA method was the most effective and efficient method for non-targeted/random priming whole genome sequencing of SARS-CoV-2 that we tested. The SISPA method described in this study allowed for whole genome assembly of SARS-CoV-2 and influenza A(H1N1)pdm09 in mixed samples. We determined the limit of detection and characterization of SARS-CoV-2 virus which was 103 pfu/ml (Ct, 22.4) for whole genome assembly and 101 pfu/ml (Ct, 30) for metagenomics detection. CONCLUSIONS The SISPA method is predominantly useful for obtaining genome sequences from RNA viruses or investigating complex clinical samples as no prior sequence information is needed. It might be applied to monitor genomic virus changes, virus evolution and can be used for fast metagenomics detection or to assess the general picture of different pathogens within the sample.
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Affiliation(s)
| | | | - Dagmara Bialy
- The Pirbright Institute, Pirbright, Woking, Surrey, UK
| | | | - John Flannery
- The Pirbright Institute, Pirbright, Woking, Surrey, UK
| | - Holly Shelton
- The Pirbright Institute, Pirbright, Woking, Surrey, UK.
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22
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Dang S, Ren L, Wang J. Functional mutations of SARS-CoV-2: implications to viral transmission, pathogenicity and immune escape. Chin Med J (Engl) 2022; 135:1213-1222. [PMID: 35788093 PMCID: PMC9337262 DOI: 10.1097/cm9.0000000000002158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Indexed: 11/27/2022] Open
Abstract
ABSTRACT The pandemic of coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to major public health challenges globally. The increasing viral lineages identified indicate that the SARS-CoV-2 genome is evolving at a rapid rate. Viral genomic mutations may cause antigenic drift or shift, which are important ways by which SARS-CoV-2 escapes the human immune system and changes its transmissibility and virulence. Herein, we summarize the functional mutations in SARS-CoV-2 genomes to characterize its adaptive evolution to inform the development of vaccination, treatment as well as control and intervention measures.
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Affiliation(s)
- Shengyuan Dang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Lili Ren
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jianwei Wang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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23
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Nikolaidis M, Papakyriakou A, Chlichlia K, Markoulatos P, Oliver SG, Amoutzias GD. Comparative Analysis of SARS-CoV-2 Variants of Concern, Including Omicron, Highlights Their Common and Distinctive Amino Acid Substitution Patterns, Especially at the Spike ORF. Viruses 2022; 14:707. [PMID: 35458441 PMCID: PMC9025783 DOI: 10.3390/v14040707] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/25/2022] [Accepted: 03/27/2022] [Indexed: 12/13/2022] Open
Abstract
In order to gain a deeper understanding of the recently emerged and highly divergent Omicron variant of concern (VoC), a study of amino acid substitution (AAS) patterns was performed and compared with those of the other four successful variants of concern (Alpha, Beta, Gamma, Delta) and one closely related variant of interest (VoI-Lambda). The Spike ORF consistently emerges as an AAS hotspot in all six lineages, but in Omicron this enrichment is significantly higher. The progenitors of each of these VoC/VoI lineages underwent positive selection in the Spike ORF. However, once they were established, their Spike ORFs have been undergoing purifying selection, despite the application of global vaccination schemes from 2021 onwards. Our analyses reject the hypothesis that the heavily mutated receptor binding domain (RBD) of the Omicron Spike was introduced via recombination from another closely related Sarbecovirus. Thus, successive point mutations appear as the most parsimonious scenario. Intriguingly, in each of the six lineages, we observed a significant number of AAS wherein the new residue is not present at any homologous site among the other known Sarbecoviruses. Such AAS should be further investigated as potential adaptations to the human host. By studying the phylogenetic distribution of AAS shared between the six lineages, we observed that the Omicron (BA.1) lineage had the highest number (8/10) of recurrent mutations.
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Affiliation(s)
- Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Athanasios Papakyriakou
- Institute of Biosciences & Applications, National Centre for Scientific Research Demokritos, 15341 Agia Paraskevi, Greece;
| | - Katerina Chlichlia
- Laboratory of Molecular Immunology, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus-Dragana, 68100 Alexandroupolis, Greece;
| | - Panayotis Markoulatos
- Microbial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Stephen G. Oliver
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK;
| | - Grigorios D. Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
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24
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Francisco Junior RDS, de Almeida LGP, Lamarca AP, Cavalcante L, Martins Y, Gerber AL, Guimarães APDC, Salviano RB, dos Santos FL, de Oliveira TH, de Souza IV, de Carvalho EM, Ribeiro MS, Carvalho S, da Silva FD, Garcia MHDO, de Souza LM, da Silva CG, Ribeiro CLP, Cavalcanti AC, de Mello CMB, Tanuri A, Vasconcelos ATR. Emergence of Within-Host SARS-CoV-2 Recombinant Genome After Coinfection by Gamma and Delta Variants: A Case Report. Front Public Health 2022; 10:849978. [PMID: 35273945 PMCID: PMC8902039 DOI: 10.3389/fpubh.2022.849978] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/24/2022] [Indexed: 12/13/2022] Open
Abstract
In this study, we report the first case of intra-host SARS-CoV-2 recombination during a coinfection by the variants of concern (VOC) AY.33 (Delta) and P.1 (Gamma) supported by sequencing reads harboring a mosaic of lineage-defining mutations. By using next-generation sequencing reads intersecting regions that simultaneously overlap lineage-defining mutations from Gamma and Delta, we were able to identify a total of six recombinant regions across the SARS-CoV-2 genome within a sample. Four of them mapped in the spike gene and two in the nucleocapsid gene. We detected mosaic reads harboring a combination of lineage-defining mutations from each VOC. To our knowledge, this is the first report of intra-host RNA-RNA recombination between two lineages of SARS-CoV-2, which can represent a threat to public health management during the COVID-19 pandemic due to the possibility of the emergence of viruses with recombinant phenotypes.
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Affiliation(s)
| | - Luiz G. P. de Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Alessandra P. Lamarca
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Liliane Cavalcante
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Yasmmin Martins
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Alexandra L. Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | | | - Ricardo Barbosa Salviano
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda Leitão dos Santos
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thiago Henrique de Oliveira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | - Silvia Carvalho
- Secretaria Estadual de Saúde do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | | | | | | | - Amilcar Tanuri
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Ignatieva A, Hein J, Jenkins PA. Ongoing Recombination in SARS-CoV-2 Revealed through Genealogical Reconstruction. Mol Biol Evol 2022; 39:msac028. [PMID: 35106601 PMCID: PMC8841603 DOI: 10.1093/molbev/msac028] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The evolutionary process of genetic recombination has the potential to rapidly change the properties of a viral pathogen, and its presence is a crucial factor to consider in the development of treatments and vaccines. It can also significantly affect the results of phylogenetic analyses and the inference of evolutionary rates. The detection of recombination from samples of sequencing data is a very challenging problem and is further complicated for SARS-CoV-2 by its relatively slow accumulation of genetic diversity. The extent to which recombination is ongoing for SARS-CoV-2 is not yet resolved. To address this, we use a parsimony-based method to reconstruct possible genealogical histories for samples of SARS-CoV-2 sequences, which enables us to pinpoint specific recombination events that could have generated the data. We propose a statistical framework for disentangling the effects of recurrent mutation from recombination in the history of a sample, and hence provide a way of estimating the probability that ongoing recombination is present. We apply this to samples of sequencing data collected in England and South Africa and find evidence of ongoing recombination.
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Affiliation(s)
| | - Jotun Hein
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- The Alan Turing Institute, British Library, London, United Kingdom
| | - Paul A Jenkins
- Department of Statistics, University of Warwick, Coventry, United Kingdom
- Department of Computer Science, University of Warwick, Coventry, United Kingdom
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26
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Amoutzias GD, Nikolaidis M, Tryfonopoulou E, Chlichlia K, Markoulatos P, Oliver SG. The Remarkable Evolutionary Plasticity of Coronaviruses by Mutation and Recombination: Insights for the COVID-19 Pandemic and the Future Evolutionary Paths of SARS-CoV-2. Viruses 2022; 14:78. [PMID: 35062282 PMCID: PMC8778387 DOI: 10.3390/v14010078] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/22/2021] [Accepted: 12/31/2021] [Indexed: 12/13/2022] Open
Abstract
Coronaviruses (CoVs) constitute a large and diverse subfamily of positive-sense single-stranded RNA viruses. They are found in many mammals and birds and have great importance for the health of humans and farm animals. The current SARS-CoV-2 pandemic, as well as many previous epidemics in humans that were of zoonotic origin, highlights the importance of studying the evolution of the entire CoV subfamily in order to understand how novel strains emerge and which molecular processes affect their adaptation, transmissibility, host/tissue tropism, and patho non-homologous genicity. In this review, we focus on studies over the last two years that reveal the impact of point mutations, insertions/deletions, and intratypic/intertypic homologous and non-homologous recombination events on the evolution of CoVs. We discuss whether the next generations of CoV vaccines should be directed against other CoV proteins in addition to or instead of spike. Based on the observed patterns of molecular evolution for the entire subfamily, we discuss five scenarios for the future evolutionary path of SARS-CoV-2 and the COVID-19 pandemic. Finally, within this evolutionary context, we discuss the recently emerged Omicron (B.1.1.529) VoC.
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Affiliation(s)
- Grigorios D. Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Eleni Tryfonopoulou
- Laboratory of Molecular Immunology, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus-Dragana, 68100 Alexandroupolis, Greece; (E.T.); (K.C.)
| | - Katerina Chlichlia
- Laboratory of Molecular Immunology, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus-Dragana, 68100 Alexandroupolis, Greece; (E.T.); (K.C.)
| | - Panayotis Markoulatos
- Microbial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Stephen G. Oliver
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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27
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Arenas M. ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation. Bioinformatics 2021; 38:58-64. [PMID: 34450622 PMCID: PMC8696103 DOI: 10.1093/bioinformatics/btab617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/24/2021] [Accepted: 08/24/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION The evolutionary processes of mutation and recombination, upon which selection operates, are fundamental to understand the observed molecular diversity. Unlike nucleotide sequences, the estimation of the recombination rate in protein sequences has been little explored, neither implemented in evolutionary frameworks, despite protein sequencing methods are largely used. RESULTS In order to accommodate this need, here I present a computational framework, called ProteinEvolverABC, to jointly estimate recombination and substitution rates from alignments of protein sequences. The framework implements the approximate Bayesian computation approach, with and without regression adjustments and includes a variety of substitution models of protein evolution, demographics and longitudinal sampling. It also implements several nuisance parameters such as heterogeneous amino acid frequencies and rate of change among sites and, proportion of invariable sites. The framework produces accurate coestimation of recombination and substitution rates under diverse evolutionary scenarios. As illustrative examples of usage, I applied it to several viral protein families, including coronaviruses, showing heterogeneous substitution and recombination rates. AVAILABILITY AND IMPLEMENTATION ProteinEvolverABC is freely available from https://github.com/miguelarenas/proteinevolverabc, includes a graphical user interface for helping the specification of the input settings, extensive documentation and ready-to-use examples. Conveniently, the simulations can run in parallel on multicore machines. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Miguel Arenas
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Universidade de Vigo, Departamento de Bioquimica, Xenetica e Inmunoloxia, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310 Vigo, Spain
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