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Liu Y, Ye Q. The Key Site Variation and Immune Challenges in SARS-CoV-2 Evolution. Vaccines (Basel) 2023; 11:1472. [PMID: 37766148 PMCID: PMC10537874 DOI: 10.3390/vaccines11091472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a worldwide public health and economic threat, and virus variation amplifies the difficulty in epidemic prevention and control. The structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been studied extensively and is now well defined. The S protein is the most distinguishing feature in terms of infection and immunity, mediating virus entrance and inducing neutralizing antibodies. The S protein and its essential components are also the most promising target to develop vaccines and antibody-based drugs. Therefore, the key site mutation in the S gene is of high interest. Among them, RBD, NTD, and furin cleavage sites are the most mutable regions with the most mutation sites and the most serious consequences for SARS-CoV-2 biological characteristics, including infectivity, pathogenicity, natural immunity, vaccine efficacy, and antibody therapeutics. We are also aware that this outbreak may not be the last. Therefore, in this narrative review, we summarized viral variation and prevalence condition, discussed specific amino acid replacement and associated immune challenges and attempted to sum up some prevention and control strategies by reviewing the literature on previously published research about SARS-CoV-2 variation to assist in clarifying the mutation pathway and consequences of SARS-CoV-2 for developing countermeasures against such viruses as soon as possible.
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Affiliation(s)
| | - Qing Ye
- Department of ‘A’, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China;
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2
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Cooney DB, Levin SA, Mori Y, Plotkin JB. Evolutionary dynamics within and among competing groups. Proc Natl Acad Sci U S A 2023; 120:e2216186120. [PMID: 37155901 PMCID: PMC10193939 DOI: 10.1073/pnas.2216186120] [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: 09/22/2022] [Accepted: 03/22/2023] [Indexed: 05/10/2023] Open
Abstract
Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible for profound transitions in evolutionary history, including the origin of cellular life, multicellular life, and even societies. Here, we synthesize a growing literature that extends evolutionary game theory to describe multilevel evolutionary dynamics, using nested birth-death processes and partial differential equations to model natural selection acting on competition within and among groups of individuals. We analyze how mechanisms known to promote cooperation within a single group-including assortment, reciprocity, and population structure-alter evolutionary outcomes in the presence of competition among groups. We find that population structures most conducive to cooperation in multiscale systems can differ from those most conducive within a single group. Likewise, for competitive interactions with a continuous range of strategies we find that among-group selection may fail to produce socially optimal outcomes, but it can nonetheless produce second-best solutions that balance individual incentives to defect with the collective incentives for cooperation. We conclude by describing the broad applicability of multiscale evolutionary models to problems ranging from the production of diffusible metabolites in microbes to the management of common-pool resources in human societies.
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Affiliation(s)
- Daniel B Cooney
- Department of Mathematics, University of Pennsylvania, Philadelphia, PA 19104
- Center for Mathematical Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Simon A Levin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | - Yoichiro Mori
- Department of Mathematics, University of Pennsylvania, Philadelphia, PA 19104
- Center for Mathematical Biology, University of Pennsylvania, Philadelphia, PA 19104
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Joshua B Plotkin
- Department of Mathematics, University of Pennsylvania, Philadelphia, PA 19104
- Center for Mathematical Biology, University of Pennsylvania, Philadelphia, PA 19104
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
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Abstract
OBJECTIVE Interindividual variability in the clinical progression of COVID-19 may be explained by host genetics. Emerging literature supports a potential inherited predisposition to severe forms of COVID-19. Demographic and inflammatory characteristics of COVID-19 suggest that acquired hematologic mutations leading to clonal hematopoiesis (CH) may further increase vulnerability to adverse sequelae. This review summarizes the available literature examining genetic predispositions to severe COVID-19 and describes how these findings could eventually be used to improve its clinical management. DATA SOURCES A PubMed literature search was performed. STUDY SELECTION Studies examining the significance of inherited genetic variation or acquired CH mutations in severe COVID-19 were selected for inclusion. DATA EXTRACTION Relevant genetic association data and aspects of study design were qualitatively assessed and narratively synthesized. DATA SYNTHESIS Genetic variants affecting inflammatory responses may increase susceptibility to severe COVID-19. Genome-wide association studies and candidate gene approaches have identified a list of inherited mutations, which likely alter cytokine and interferon secretion, and lung-specific mechanisms of immunity in COVID-19. The potential role of CH in COVID-19 is more uncertain at present; however, the available evidence suggests that the various types of acquired mutations and their differential influence on immune cell function must be carefully considered. CONCLUSIONS The current literature supports the hypothesis that host genetic factors affect vulnerability to severe COVID-19. Further research is required to confirm the full scope of relevant variants and the causal mechanisms underlying these associations. Clinical approaches, which consider the genetic basis of interindividual variability in COVID-19 and potentially other causes of critical illness, could optimize hospital resource allocation, predict responsiveness to treatment, identify more efficacious drug targets, and ultimately improve outcomes.
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Kim BK, Choi WS, Jeong JH, Oh S, Park JH, Yun YS, Min SC, Kang DH, Kim EG, Ryu H, Kim HK, Baek YH, Choi YK, Song MS. A Rapid Method for Generating Infectious SARS-CoV-2 and Variants Using Mutagenesis and Circular Polymerase Extension Cloning. Microbiol Spectr 2023; 11:e0338522. [PMID: 36877070 PMCID: PMC10100849 DOI: 10.1128/spectrum.03385-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 02/12/2023] [Indexed: 03/07/2023] Open
Abstract
The appearance of SARS-CoV-2 variants in late 2020 raised alarming global public health concerns. Despite continued scientific progress, the genetic profiles of these variants bring changes in viral properties that threaten vaccine efficacy. Thus, it is critically important to investigate the biologic profiles and significance of these evolving variants. In this study, we demonstrate the application of circular polymerase extension cloning (CPEC) to the generation of full-length clones of SARS-CoV-2. We report that, combined with a specific primer design scheme, this yields a simpler, uncomplicated, and versatile approach for engineering SARS-CoV-2 variants with high viral recovery efficiency. This new strategy for genomic engineering of SARS-CoV-2 variants was implemented and evaluated for its efficiency in generating point mutations (K417N, L452R, E484K, N501Y, D614G, P681H, P681R, Δ69-70, Δ157-158, E484K+N501Y, and Ins-38F) and multiple mutations (N501Y/D614G and E484K/N501Y/D614G), as well as a large truncation (ΔORF7A) and insertion (GFP). The application of CPEC to mutagenesis also allows the inclusion of a confirmatory step prior to assembly and transfection. This method could be of value in the molecular characterization of emerging SARS-CoV-2 variants as well as the development and testing of vaccines, therapeutic antibodies, and antivirals. IMPORTANCE Since the first emergence of the SARS-CoV-2 variant in late 2020, novel variants have been continuously introduced to the human population, causing severe public health threats. In general, because these variants acquire new genetic mutation/s, it is critical to analyze the biological function of viruses that such mutations can confer. Therefore, we devised a method that can construct SARS-CoV-2 infectious clones and their variants rapidly and efficiently. The method was developed based on a PCR-based circular polymerase extension cloning (CPEC) combined with a specific primer design scheme. The efficiency of the newly designed method was evaluated by generating SARS-CoV-2 variants with single point mutations, multiple point mutations, and a large truncation and insertion. This method could be of value for the molecular characterization of emerging SARS-CoV-2 variants and the development and testing of vaccines and antiviral agents.
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Affiliation(s)
- Beom Kyu Kim
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Won-Suk Choi
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Ju Hwan Jeong
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Sol Oh
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Ji-Hyun Park
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Yu Soo Yun
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Seong Cheol Min
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Da Hyeon Kang
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Eung-Gook Kim
- Department of Biochemistry, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Hojin Ryu
- Department of Biological Sciences and Biotechnology, College of Natural Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Hye Kwon Kim
- Department of Biological Sciences and Biotechnology, College of Natural Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Yun Hee Baek
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
| | - Young Ki Choi
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Min-Suk Song
- Department of Microbiology, Chungbuk National University, College of Medicine and Medical Research Institute, Cheongju, Chungbuk, Republic of Korea
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Cooney DB. Assortment and Reciprocity Mechanisms for Promotion of Cooperation in a Model of Multilevel Selection. Bull Math Biol 2022; 84:126. [PMID: 36136162 DOI: 10.1007/s11538-022-01082-8] [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: 05/04/2022] [Accepted: 09/05/2022] [Indexed: 11/26/2022]
Abstract
In the study of the evolution of cooperation, many mechanisms have been proposed to help overcome the self-interested cheating that is individually optimal in the Prisoners' Dilemma game. These mechanisms include assortative or networked social interactions, other-regarding preferences considering the payoffs of others, reciprocity rules to establish cooperation as a social norm, and multilevel selection involving simultaneous competition between individuals favoring cheaters and competition between groups favoring cooperators. In this paper, we build on recent work studying PDE replicator equations for multilevel selection to understand how within-group mechanisms of assortment, other-regarding preferences, and both direct and indirect reciprocity can help to facilitate cooperation in concert with evolutionary competition between groups. We consider a group-structured population in which interactions between individuals consist of Prisoners' Dilemma games and study the dynamics of multilevel competition determined by the payoffs individuals receive when interacting according to these within-group mechanisms. We find that the presence of each of these mechanisms acts synergistically with multilevel selection for the promotion of cooperation, decreasing the strength of between-group competition required to sustain long-time cooperation and increasing the collective payoff achieved by the population. However, we find that only other-regarding preferences allow for the achievement of socially optimal collective payoffs for Prisoners' Dilemma games in which average payoff is maximized by an intermediate mix of cooperators and defectors. For the other three mechanisms, the multilevel dynamics remain susceptible to a shadow of lower-level selection, as the collective outcome fails to exceed the payoff of the all-cooperator group.
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Affiliation(s)
- Daniel B Cooney
- Department of Mathematics and Center for Mathematical Biology, University of Pennsylvania, Philadelphia, PA, USA.
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Cooney DB, Mori Y. Long-time behavior of a PDE replicator equation for multilevel selection in group-structured populations. J Math Biol 2022; 85:12. [PMID: 35864421 DOI: 10.1007/s00285-022-01776-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/11/2022] [Accepted: 05/04/2022] [Indexed: 11/26/2022]
Abstract
In many biological systems, natural selection acts simultaneously on multiple levels of organization. This scenario typically presents an evolutionary conflict between the incentive of individuals to cheat and the collective incentive to establish cooperation within a group. Generalizing previous work on multilevel selection in evolutionary game theory, we consider a hyperbolic PDE model of a group-structured population, in which members within a single group compete with each other for individual-level replication; while the group also competes against other groups for group-level replication. We derive a threshold level of the relative strength of between-group competition such that defectors take over the population below the threshold while cooperation persists in the long-time population above the threshold. Under stronger assumptions on the initial distribution of group compositions, we further prove that the population converges to a steady state density supporting cooperation for between-group selection strength above the threshold. We further establish long-time bounds on the time-average of the collective payoff of the population, showing that the long-run population cannot outperform the payoff of a full-cooperator group even in the limit of infinitely-strong between-group competition. When the group replication rate is maximized by an intermediate level of within-group cooperation, individual-level selection casts a long shadow on the dynamics of multilevel selection: no level of between-group competition can erase the effects of the individual incentive to defect. We further extend our model to study the case of multiple types of groups, showing how the games that groups play can coevolve with the level of cooperation.
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Affiliation(s)
- Daniel B Cooney
- Department of Mathematics and Center for Mathematical Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Yoichiro Mori
- Department of Mathematics, Department of Biology, and Center for Mathematical Biology, University of Pennsylvania, Philadelphia, PA, USA
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7
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SeyedAlinaghi S, Mirzapour P, Dadras O, Pashaei Z, Karimi A, MohsseniPour M, Soleymanzadeh M, Barzegary A, Afsahi AM, Vahedi F, Shamsabadi A, Behnezhad F, Saeidi S, Mehraeen E, Shayesteh Jahanfar. Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. Eur J Med Res 2021; 26:51. [PMID: 34103090 PMCID: PMC8185313 DOI: 10.1186/s40001-021-00524-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/28/2021] [Indexed: 02/08/2023] Open
Abstract
INTRODUCTION Coronavirus Disease-2019 (SARS-CoV-2) started its devastating trajectory into a global pandemic in Wuhan, China, in December 2019. Ever since, several variants of SARS-CoV-2 have been identified. In the present review, we aimed to characterize the different variants of SARS-CoV-2 and explore the related morbidity and mortality. METHODS A systematic review including the current evidence related to different variants of SARS-CoV-2 and the related morbidity and mortality was conducted through a systematic search utilizing the keywords in the online databases including Scopus, PubMed, Web of Science, and Science Direct; we retrieved all related papers and reports published in English from December 2019 to September 2020. RESULTS A review of identified articles has shown three main genomic variants, including type A, type B, and type C. we also identified three clades including S, V, and G. Studies have demonstrated that the C14408T and A23403G alterations in the Nsp12 and S proteins are the most prominent alterations in the world, leading to life-threatening mutations.The spike D614G amino acid change has become the most common variant since December 2019. From missense mutations found from Gujarat SARS-CoV-2 genomes, C28854T, deleterious mutation in the nucleocapsid (N) gene was significantly associated with patients' mortality. The other significant deleterious variant (G25563T) is found in patients located in Orf3a and has a potential role in viral pathogenesis. CONCLUSION Overall, researchers identified several SARS-CoV-2 variants changing clinical manifestations and increasing the transmissibility, morbidity, and mortality of COVID-19. This should be considered in current practice and interventions to combat the pandemic and prevent related morbidity and mortality.
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Affiliation(s)
- SeyedAhmad SeyedAlinaghi
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran
| | - Pegah Mirzapour
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran
| | - Omid Dadras
- Department of Global Health and Socioepidemiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Zahra Pashaei
- Chronic Respiratory Disease Research Center, Masih Daneshvari Hospital, Tehran, Iran
| | - Amirali Karimi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehrzad MohsseniPour
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdi Soleymanzadeh
- Ophthalmology Resident at Farabi Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Amir Masoud Afsahi
- Department of Radiology, School of Medicine, University of California, San Diego, CA, USA
| | - Farzin Vahedi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmadreza Shamsabadi
- Department of Health Information Technology, Esfarayen Faculty of Medical Sciences, Esfarayen, Iran
| | - Farzane Behnezhad
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Solmaz Saeidi
- Department of Nursing, Khalkhal University of Medical Sciences, Khalkhal, Iran
| | - Esmaeil Mehraeen
- Department of Health Information Technology, Khalkhal University of Medical Sciences, 1419733141, Khalkhal, Iran.
| | - Shayesteh Jahanfar
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA, USA
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Cruceriu D, Baldasici O, Balacescu L, Gligor-Popa S, Flonta M, Man MA, Visan S, Vlad C, Trifa AP, Balacescu O, Achimas-Cadariu P. Critical Aspects Concerning the Development of a Pooling Approach for SARS-CoV-2 Diagnosis Using Large-Scale PCR Testing. Viruses 2021; 13:v13050902. [PMID: 34067983 PMCID: PMC8152296 DOI: 10.3390/v13050902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 01/01/2023] Open
Abstract
The primary approach to controlling the spread of the pandemic SARS-CoV-2 is to diagnose and isolate the infected people quickly. Our paper aimed to investigate the efficiency and the reliability of a hierarchical pooling approach for large-scale PCR testing for SARS-CoV-2 diagnosis. To identify the best conditions for the pooling approach for SARS-CoV-2 diagnosis by RT-qPCR, we investigated four manual methods for both RNA extraction and PCR assessment targeting one or more of the RdRp, N, S, and ORF1a genes, by using two PCR devices and an automated flux for SARS-CoV-2 detection. We determined the most efficient and accurate diagnostic assay, taking into account multiple parameters. The optimal pool size calculation included the prevalence of SARS-CoV-2, the assay sensitivity of 95%, an assay specificity of 100%, and a range of pool sizes of 5 to 15 samples. Our investigation revealed that the most efficient and accurate procedure for detecting the SARS-CoV-2 has a detection limit of 2.5 copies/PCR reaction. This pooling approach proved to be efficient and accurate in detecting SARS-CoV-2 for all samples with individual quantification cycle (Cq) values lower than 35, accounting for more than 94% of all positive specimens. Our data could serve as a comprehensive practical guide for SARS-CoV-2 diagnostic centers planning to address such a pooling strategy.
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Affiliation(s)
- Daniel Cruceriu
- Department of Genetics, Genomics and Experimental Pathology, The Oncology Institute “Prof. Dr. Ion Chiricuta”, 34-36, Republicii Street, 400015 Cluj-Napoca, Romania; (D.C.); (O.B.); (L.B.); (S.V.)
- Department of Molecular Biology and Biotechnology, “Babes-Bolyai” University, 1, M. Kogălniceanu Street, 400084 Cluj-Napoca, Romania
| | - Oana Baldasici
- Department of Genetics, Genomics and Experimental Pathology, The Oncology Institute “Prof. Dr. Ion Chiricuta”, 34-36, Republicii Street, 400015 Cluj-Napoca, Romania; (D.C.); (O.B.); (L.B.); (S.V.)
| | - Loredana Balacescu
- Department of Genetics, Genomics and Experimental Pathology, The Oncology Institute “Prof. Dr. Ion Chiricuta”, 34-36, Republicii Street, 400015 Cluj-Napoca, Romania; (D.C.); (O.B.); (L.B.); (S.V.)
| | - Stefana Gligor-Popa
- Department of Oncogenetics, The Oncology Institute “Prof. Dr. Ion Chiricuta”, 34-36, Republicii Street, 400015 Cluj-Napoca, Romania;
| | - Mirela Flonta
- Laboratory of Microbiology, Clinical Hospital of Infectious Diseases, 23, Iuliu Moldovan Street, 400348 Cluj-Napoca, Romania;
| | - Milena A. Man
- Department of Medical Sciences—Pulmonology, “Iuliu Hatieganu” University of Medicine and Pharmacy, 8, Victor Babes Street, 400012 Cluj-Napoca, Romania;
- Covid Department, “Leon Daniello” Clinical Hospital of Pulmonology, 6, Hasdeu Street, 400371 Cluj-Napoca, Romania
| | - Simona Visan
- Department of Genetics, Genomics and Experimental Pathology, The Oncology Institute “Prof. Dr. Ion Chiricuta”, 34-36, Republicii Street, 400015 Cluj-Napoca, Romania; (D.C.); (O.B.); (L.B.); (S.V.)
| | - Catalin Vlad
- Department of Surgery, The Oncology Institute “Prof. Dr. Ion Chiricuta”, 34-36, Republicii Street, 400015 Cluj-Napoca, Romania; (C.V.); (P.A.-C.)
- Department of Oncology, “Iuliu Hatieganu” University of Medicine and Pharmacy, 8, Victor Babes Street, 400012 Cluj-Napoca, Romania
| | - Adrian P. Trifa
- Department of Oncogenetics, The Oncology Institute “Prof. Dr. Ion Chiricuta”, 34-36, Republicii Street, 400015 Cluj-Napoca, Romania;
- Department of Genetics, “Iuliu Hatieganu” University of Medicine and Pharmacy, 8, Victor Babes Street, 400012 Cluj-Napoca, Romania
- Correspondence: (A.P.T.); (O.B.); Tel.: +40-264-598-362 (O.B.)
| | - Ovidiu Balacescu
- Department of Genetics, Genomics and Experimental Pathology, The Oncology Institute “Prof. Dr. Ion Chiricuta”, 34-36, Republicii Street, 400015 Cluj-Napoca, Romania; (D.C.); (O.B.); (L.B.); (S.V.)
- Department of Medical Oncology, “Iuliu Hatieganu” University of Medicine and Pharmacy, 8, Victor Babes Street, 400012 Cluj-Napoca, Romania
- Correspondence: (A.P.T.); (O.B.); Tel.: +40-264-598-362 (O.B.)
| | - Patriciu Achimas-Cadariu
- Department of Surgery, The Oncology Institute “Prof. Dr. Ion Chiricuta”, 34-36, Republicii Street, 400015 Cluj-Napoca, Romania; (C.V.); (P.A.-C.)
- Department of Oncology, “Iuliu Hatieganu” University of Medicine and Pharmacy, 8, Victor Babes Street, 400012 Cluj-Napoca, Romania
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Armero A, Berthet N, Avarre JC. Intra-Host Diversity of SARS-Cov-2 Should Not Be Neglected: Case of the State of Victoria, Australia. Viruses 2021; 13:133. [PMID: 33477885 PMCID: PMC7833370 DOI: 10.3390/v13010133] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/05/2021] [Accepted: 01/14/2021] [Indexed: 12/14/2022] Open
Abstract
Since the identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the etiological agent of the current COVID-19 pandemic, a rapid and massive effort has been made to obtain the genomic sequences of this virus to monitor (in near real time) the phylodynamic and diversity of this new pathogen. However, less attention has been given to the assessment of intra-host diversity. RNA viruses such as SARS-CoV-2 inhabit the host as a population of variants called quasispecies. We studied the quasispecies diversity in four of the main SARS-CoV-2 genes (ORF1a, ORF1b, S and N genes), using a dataset consisting of 210 next-generation sequencing (NGS) samples collected between January and early April of 2020 in the State of Victoria, Australia. We found evidence of quasispecies diversity in 68% of the samples, 76% of which was nonsynonymous variants with a higher density in the spike (S) glycoprotein and ORF1a genes. About one-third of the nonsynonymous intra-host variants were shared among the samples, suggesting host-to-host transmission. Quasispecies diversity changed over time. Phylogenetic analysis showed that some of the intra-host single-nucleotide variants (iSNVs) were restricted to specific lineages, highlighting their potential importance in the epidemiology of this virus. A greater effort must be made to determine the magnitude of the genetic bottleneck during transmission and the epidemiological and/or evolutionary factors that may play a role in the changes in the diversity of quasispecies over time.
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Affiliation(s)
- Alix Armero
- The Center for Microbes, Development and Health, Institut Pasteur of Shanghai—Chinese Academy of Sciences, Discovery and Molecular Characterization of Pathogens, Shanghai 200000, China;
| | - Nicolas Berthet
- The Center for Microbes, Development and Health, Institut Pasteur of Shanghai—Chinese Academy of Sciences, Discovery and Molecular Characterization of Pathogens, Shanghai 200000, China;
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