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Ose NJ, Campitelli P, Modi T, Kazan IC, Kumar S, Ozkan SB. Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. eLife 2024; 12:RP92063. [PMID: 38713502 PMCID: PMC11076047 DOI: 10.7554/elife.92063] [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] [Indexed: 05/08/2024] Open
Abstract
We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 spike (S) protein. With this approach, we first identified candidate adaptive polymorphisms (CAPs) of the SARS-CoV-2 S protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.
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Affiliation(s)
- Nicholas James Ose
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - I Can Kazan
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple UniversityPhiladelphiaUnited States
- Department of Biology, Temple UniversityPhiladelphiaUnited States
- Center for Genomic Medicine Research, King Abdulaziz UniversityJeddahSaudi Arabia
| | - Sefika Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
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Ose NJ, Campitelli P, Modi T, Can Kazan I, Kumar S, Banu Ozkan S. Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557827. [PMID: 37745560 PMCID: PMC10515954 DOI: 10.1101/2023.09.14.557827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 Spike (S) protein. With this approach, we first identified Candidate Adaptive Polymorphisms (CAPs) of the SARS-CoV-2 Spike protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.
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Affiliation(s)
- Nicholas J. Ose
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - I. Can Kazan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - S. Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
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Li J, Li C, Xu W. Liver cancer-specific mutations in functional domains of ADAR2 lead to the elevation of coding and non-coding RNA editing in multiple tumor-related genes. Mol Genet Genomics 2024; 299:1. [PMID: 38170228 DOI: 10.1007/s00438-023-02091-5] [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: 08/24/2023] [Accepted: 10/17/2023] [Indexed: 01/05/2024]
Abstract
Mutation is the major cause of phenotypic innovations. Apart from DNA mutations, the alteration on RNA such as the ADAR-mediated A-to-I RNA editing could also shape the phenotype. These two layers of variations have not been systematically combined to study their collective roles in cancers. We collected the high-quality transcriptomes of ten hepatocellular carcinoma (HCC) and the matched control samples. We systematically identified HCC-specific mutations in the exonic regions and profiled the A-to-I RNA editome in each sample. All ten HCC samples had mutations in the CDS of ADAR2 gene (dsRNA-binding domain or catalytic domain). The consequence of these mutations converged to the elevation of ADAR2 efficiency as reflected by the global increase of RNA editing levels in HCC. The up-regulated editing sites (UES) were enriched in the CDS and UTR of oncogenes and tumor suppressor genes (TSG), indicating the possible roles of these target genes in HCC oncogenesis. We present the mutation-ADAR2-UES-oncogene/TSG-HCC axis that explains how mutations at different layers would finally lead to abnormal phenotype. In the light of central dogma, our work provides novel insights into how to fully take advantage of the transcriptome data to decipher the consequence of mutations.
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Affiliation(s)
- Jian Li
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Chaowei Li
- Department of PET/CT, The Second Clinical Medical College of Qingdao University (Qingdao Center Hospital), Qingdao, 266042, China
| | - Wengui Xu
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China.
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4
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Zhang K, Chen F, Shen HY, Zhang PP, Gao H, Peng H, Luo YS, Cheng ZS. Regulatory variants of APOBEC3 genes potentially associate with COVID-19 severity in populations with African ancestry. Sci Rep 2023; 13:22435. [PMID: 38105291 PMCID: PMC10725877 DOI: 10.1038/s41598-023-49791-x] [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: 07/14/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023] Open
Abstract
Since November 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused the worldwide pandemic of the coronavirus disease 2019 (COVID-19), the impact of which is huge to the lives of world populations. Many studies suggested that such situation will continue due to the endless mutations in SARS-CoV-2 genome that result in complexity of the efforts for the control of SARS-CoV-2, since the special enrichment of nucleotide substitution C>U in SARS-CoV-2 sequences were discovered mainly due to the editing by human host factors APOBEC3 genes. The observation of SARS-CoV-2 variants Beta (B.1.351) and Omicron (B.1.1.529) firstly spreading in South Africa promoted us to hypothesize that genetic variants of APOBEC3 special in African populations may be attributed to the higher mutation rate of SARS-CoV-2 variants in Africa. Current study was conducted to search for functional variants of APOBEC3 genes associate with COVID-19 hospitalization in African population. By integrating data from the 1000 Genomes Project, Genotype-Tissue Expression (GTEx), and Host Genetics Initiative (HGI) of COVID-19, we identified potential functional SNPs close to APOBEC3 genes that are associated with COVID-19 hospitalization in African but not with other populations. Our study provides new insights on the potential contribution of APOBEC3 genes on the evolution of SARS-CoV-2 mutations in African population, but further replication is needed to confirm our results.
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Affiliation(s)
- Ke Zhang
- The Key and Characteristic Laboratory of Modern Pathogenicity Biology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 561113, China
| | - Fang Chen
- The Key and Characteristic Laboratory of Modern Pathogenicity Biology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 561113, China
| | - Hu-Yan Shen
- The Key and Characteristic Laboratory of Modern Pathogenicity Biology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 561113, China
| | - Ping-Ping Zhang
- The Key and Characteristic Laboratory of Modern Pathogenicity Biology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 561113, China
| | - Han Gao
- The Department of Emergency ICU, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Hong Peng
- The Department of Emergency ICU, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Yu-Si Luo
- The Department of Emergency ICU, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China.
- The Department of Emergency, Liupanshui Hospital of The Affiliated Hospital of Guizhou Medical University, Liupanshui, 553000, China.
| | - Zhong-Shan Cheng
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Hospital, MS1122, Memphis, TN, 38105, USA.
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5
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Hou Q, Shang L, Chen X, Luo Q, Wei L, Zhang C. Convergent evolution of allele-specific gene expression that leads to non-small cell lung cancer in different human populations. J Appl Genet 2023:10.1007/s13353-023-00813-4. [PMID: 38036772 DOI: 10.1007/s13353-023-00813-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023]
Abstract
Phenotypical innovations during evolution are caused by novel mutations, which are usually heterozygous at the beginning. The gene expressions on two alleles of these mutation sites are not necessarily identical, leading to flexible allele-specific regulation in cell systems. We retrieve the transcriptome data of normal and non-small cell lung cancer (NSCLC) tissues from 47 African Americans (AA) and 50 European Americans (EA). We analyze the differentially expressed genes (DEGs) in NSCLC as well as the tumor-specific mutations. Expression and mutation profiles show convergent evolution in AA and EA populations. The tumor-specific mutations are poorly overlapped, but many of them are located in the same genes, mainly oncogenes and tumor suppressor genes. The DEGs in tumors are majorly caused by the mutated alleles rather than normal alleles. The relative expressions of mutated alleles are highly correlated between AA and EA. The differential expression in NSCLC is predominantly mediated by the mutated alleles on heterozygous sites. This molecular mechanism underlying NSCLC oncogenesis is conserved across different human populations, exhibiting convergent evolution. We present this novel angle that differential expression analysis should be performed separately for different alleles. Our ideas should greatly benefit the cancer community.
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Affiliation(s)
- Qiuyu Hou
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China
| | - Lifeng Shang
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China
| | - Xu Chen
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China
| | - Qiang Luo
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China
| | - Liang Wei
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China
| | - Chence Zhang
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China.
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Wang Y, Li Z, Wang X, Jiang W, Jiang W. SARS-CoV-2 continuously optimizes its codon usage to adapt to human lung environment. J Appl Genet 2023; 64:831-837. [PMID: 37740828 DOI: 10.1007/s13353-023-00790-8] [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: 03/27/2023] [Revised: 09/14/2023] [Accepted: 09/16/2023] [Indexed: 09/25/2023]
Abstract
Viruses need to utilize the resources from host cells to reproduce themselves. RNA translation rate, which is largely determined by codon usage, is the rate-limiting step across the life cycle of viruses. Adapting to the codon usage of hosts would help virus better proliferate. We retrieved the time-course mutation profile of millions of world-wide SARS-CoV-2 sequences. For synonymous mutations, we defined whether a mutation elevate or reduce the relative synonymous codon usage (RSCU). We found that if a synonymous mutation in SARS-CoV-2 increases the RSCU (calculated from human lungs), denoted as delta RSCU > 0, then this mutation is positively selected because the allele frequency (AF) of this mutation increases with time, and vice versa. The results suggest that in SARS-CoV-2, the synonymous mutations that increase codon optimality are beneficial to the virus and are favored by natural selection. For the first time, we used the dynamics of allele frequency to demonstrate that SARS-CoV-2 is continuously optimizing its codon usage to adapt to human lungs. Nevertheless, adaptation to other human tissues cannot be excluded. These results warn us that under this global pandemic, synonymous mutations in SARS-CoV-2 should not be automatically ignored since they indeed change the fitness of the virus.
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Affiliation(s)
- Yinglian Wang
- Institute of Integrated Medicine, Qingdao Medical College, Qingdao University, Qingdao, 266071, Shandong, China
- Changyi People's Hospital, Weifang, 261300, Shandong, China
| | - Zhenhua Li
- Pulmonary and Critical Care Medicine Department 2, Qingdao Municipal Hospital of Traditional Chinese Medicine (Qingdao Hiser Medical Group), Qingdao, 266033, China
- Department of Respiratory Diseases, The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao Haici Hospital, Qingdao, 266033, Shandong, China
| | - Xiuxiu Wang
- Department of Respiratory Medicine, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, 266035, Shandong, China
| | - Wen Jiang
- Pulmonary and Critical Care Medicine Department 2, Qingdao Municipal Hospital of Traditional Chinese Medicine (Qingdao Hiser Medical Group), Qingdao, 266033, China
- Department of Respiratory Diseases, The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao Haici Hospital, Qingdao, 266033, Shandong, China
| | - Wenqing Jiang
- Pulmonary and Critical Care Medicine Department 2, Qingdao Municipal Hospital of Traditional Chinese Medicine (Qingdao Hiser Medical Group), Qingdao, 266033, China.
- Department of Respiratory Diseases, The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao Haici Hospital, Qingdao, 266033, Shandong, China.
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7
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Ge F, Cao X, Jiang Y. A-to-I RNA editing shows dramatic up-regulation in osteosarcoma and broadly regulates tumor-related genes by altering microRNA target regions. J Appl Genet 2023; 64:493-505. [PMID: 37542613 DOI: 10.1007/s13353-023-00777-5] [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: 07/11/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/07/2023]
Abstract
A-to-I RNA editing is a prevalent type of RNA modification in animals. The dysregulation of RNA editing has led to multiple human cancers. However, the role of RNA editing has never been studied in osteosarcoma, a complex bone cancer with unknown molecular basis. We retrieved the RNA-sequencing data from 24 primary osteosarcoma patients and 3 healthy controls. We systematically profiled the RNA editomes in these samples and quantitatively identified reliable differential editing sites (DES) between osteosarcoma and normal samples. RNA editing efficiency is dramatically increased in osteosarcoma, presumably due to the significant up-regulation of editing enzymes ADAR1 and ADAR2. Up-regulated DES in osteosarcoma are enriched in 3'UTRs. Strikingly, such 3'UTR sites are further enriched in microRNA binding regions of gene EMP2 and other oncogenes, abolishing the microRNA suppression on target genes. Accordingly, the expression of these tumor-promoting genes is elevated in osteosarcoma. There might be an RNA editing-dependent pathway leading to osteosarcoma. We expanded our knowledge on the potential roles of RNA editing in oncogenesis. Based on these molecular features, our work is valuable for future prognosis and diagnosis of osteosarcoma.
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Affiliation(s)
- Fuqun Ge
- Department of Joint Surgery, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China
| | - Xinyue Cao
- School of Clinical Medicine, Qilu Medical University, Zibo, 255300, Shandong, China
| | - Yankai Jiang
- Department of Joint Surgery, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China.
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8
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Saldivar-Espinoza B, Garcia-Segura P, Novau-Ferré N, Macip G, Martínez R, Puigbò P, Cereto-Massagué A, Pujadas G, Garcia-Vallve S. The Mutational Landscape of SARS-CoV-2. Int J Mol Sci 2023; 24:ijms24109072. [PMID: 37240420 DOI: 10.3390/ijms24109072] [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: 03/28/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Mutation research is crucial for detecting and treating SARS-CoV-2 and developing vaccines. Using over 5,300,000 sequences from SARS-CoV-2 genomes and custom Python programs, we analyzed the mutational landscape of SARS-CoV-2. Although almost every nucleotide in the SARS-CoV-2 genome has mutated at some time, the substantial differences in the frequency and regularity of mutations warrant further examination. C>U mutations are the most common. They are found in the largest number of variants, pangolin lineages, and countries, which indicates that they are a driving force behind the evolution of SARS-CoV-2. Not all SARS-CoV-2 genes have mutated in the same way. Fewer non-synonymous single nucleotide variations are found in genes that encode proteins with a critical role in virus replication than in genes with ancillary roles. Some genes, such as spike (S) and nucleocapsid (N), show more non-synonymous mutations than others. Although the prevalence of mutations in the target regions of COVID-19 diagnostic RT-qPCR tests is generally low, in some cases, such as for some primers that bind to the N gene, it is significant. Therefore, ongoing monitoring of SARS-CoV-2 mutations is crucial. The SARS-CoV-2 Mutation Portal provides access to a database of SARS-CoV-2 mutations.
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Affiliation(s)
- Bryan Saldivar-Espinoza
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Pol Garcia-Segura
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Nil Novau-Ferré
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Guillem Macip
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | | | - Pere Puigbò
- Department of Biology, University of Turku, 20500 Turku, Finland
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, 43007 Tarragona, Spain
- Eurecat, Technology Centre of Catalonia, Unit of Nutrition and Health, 43204 Reus, Spain
| | - Adrià Cereto-Massagué
- EURECAT Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | - Gerard Pujadas
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Santiago Garcia-Vallve
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
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9
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Wei L. Retrospect of the Two-Year Debate: What Fuels the Evolution of SARS-CoV-2: RNA Editing or Replication Error? Curr Microbiol 2023; 80:151. [PMID: 36976379 PMCID: PMC10044072 DOI: 10.1007/s00284-023-03279-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/19/2023] [Indexed: 03/29/2023]
Abstract
Mutation is one of the mechanisms of the evolutionary divergence of an organism. Under this global COVID-19 pandemic, the fast evolution of SARS-CoV-2 became one of the most worrying issues. Some researchers believed that the hosts' RNA deamination systems (APOBECs and ADARs) are the major source of mutations and have driven the evolution of SARS-CoV-2. However, apart from RNA editing, the RDRP (RNA-dependent RNA polymerase)-mediated replication errors may also contribute to the mutation of SARS-CoV-2 (just like the single-nucleotide polymorphisms/variations in eukaryotes caused by DNA replication errors). Unfortunately, it is technically unable to distinguish RNA editing and replication errors (SNPs) in this RNA virus. Here comes a fundamental question: we indeed observed the fast evolution of SARS-CoV-2, but what exactly fuels its evolution: RNA editing or replication errors? This debate lasts for 2 years. In this piece, we will retrospect the 2-year debate on RNA editing versus SNPs.
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Affiliation(s)
- Lai Wei
- College of Life Sciences, Beijing Normal University, Beijing, China.
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Bian Z, Wu Z, Liu N, Jiang X. The efficacy and safety of SARS-CoV-2 vaccines mRNA1273 and BNT162b2 might be complicated by rampant C-to-U RNA editing. J Appl Genet 2023; 64:361-365. [PMID: 36943642 PMCID: PMC10028319 DOI: 10.1007/s13353-023-00756-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/14/2023] [Accepted: 03/12/2023] [Indexed: 03/23/2023]
Abstract
The SARS-CoV-2 RNA vaccines are smartly designed to increase the synonymous codon usage by introducing multiple U-to-C mutations. This design would elevate the translation efficiency of vaccine RNAs. However, we found evidence to reason that the designed cytidines might be converted to uridines again by C-to-U RNA deamination in host cells. This C-to-U mechanism might be a main factor that affects the efficacy and safety of RNA vaccines.
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Affiliation(s)
- Zhongzheng Bian
- Department of Emergency Medicine, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China
| | - Ziqian Wu
- Department of Emergency Medicine, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China
| | - Nan Liu
- Department of Emergency Medicine, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China
| | - Xiao Jiang
- Department of Emergency Intensive Care Unit, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China.
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11
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González-Vázquez LD, Arenas M. Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic. Genes (Basel) 2023; 14:407. [PMID: 36833334 PMCID: PMC9956206 DOI: 10.3390/genes14020407] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) produced diverse molecular variants during its recent expansion in humans that caused different transmissibility and severity of the associated disease as well as resistance to monoclonal antibodies and polyclonal sera, among other treatments. In order to understand the causes and consequences of the observed SARS-CoV-2 molecular diversity, a variety of recent studies investigated the molecular evolution of this virus during its expansion in humans. In general, this virus evolves with a moderate rate of evolution, in the order of 10-3-10-4 substitutions per site and per year, which presents continuous fluctuations over time. Despite its origin being frequently associated with recombination events between related coronaviruses, little evidence of recombination was detected, and it was mostly located in the spike coding region. Molecular adaptation is heterogeneous among SARS-CoV-2 genes. Although most of the genes evolved under purifying selection, several genes showed genetic signatures of diversifying selection, including a number of positively selected sites that affect proteins relevant for the virus replication. Here, we review current knowledge about the molecular evolution of SARS-CoV-2 in humans, including the emergence and establishment of variants of concern. We also clarify relationships between the nomenclatures of SARS-CoV-2 lineages. We conclude that the molecular evolution of this virus should be monitored over time for predicting relevant phenotypic consequences and designing future efficient treatments.
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Affiliation(s)
- Luis Daniel González-Vázquez
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Miguel Arenas
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310 Vigo, Spain
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12
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Pleiotropic Functions of Nitric Oxide Produced by Ascorbate for the Prevention and Mitigation of COVID-19: A Revaluation of Pauling's Vitamin C Therapy. Microorganisms 2023; 11:microorganisms11020397. [PMID: 36838362 PMCID: PMC9963342 DOI: 10.3390/microorganisms11020397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Linus Pauling, who was awarded the Nobel Prize in Chemistry, suggested that a high dose of vitamin C (l-ascorbic acid) might work as a prevention or treatment for the common cold. Vitamin C therapy was tested in clinical trials, but clear evidence was not found at that time. Although Pauling's proposal has been strongly criticized for a long time, vitamin C therapy has continued to be tested as a treatment for a variety of diseases, including coronavirus infectious disease 2019 (COVID-19). The pathogen of COVID-19, SARS-CoV-2, belongs to the β-coronavirus lineage, which includes human coronavirus, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS). This review intends to shed new light on vitamin C antiviral activity that may prevent SARS-CoV-2 infection through the chemical production of nitric oxide (NO). NO is a gaseous free radical that is largely produced by the enzyme NO synthase (NOS) in cells. NO produced by upper epidermal cells contributes to the inactivation of viruses and bacteria contained in air or aerosols. In addition to enzymatic production, NO can be generated by the chemical reduction of inorganic nitrite (NO2-), an alternative mechanism for NO production in living organisms. Dietary vitamin C, largely contained in fruits and vegetables, can reduce the nitrite in saliva to produce NO in the oral cavity when chewing foods. In the stomach, salivary nitrite can also be reduced to NO by vitamin C secreted from the epidermal cells of the stomach. The strong acidic pH of gastric juice facilitates the chemical reduction of salivary nitrite to produce NO. Vitamin C contributes in multiple ways to the host innate immune system as a first-line defense mechanism against pathogens. Highlighting chemical NO production by vitamin C, we suggest that controversies on the therapeutic effects of vitamin C in previous clinical trials may partly be due to less appreciation of the pleiotropic functions of vitamin C as a universal bioreductant.
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Li Y, Hou F, Zhou M, Yang X, Yin B, Jiang W, Xu H. C-to-U RNA deamination is the driving force accelerating SARS-CoV-2 evolution. Life Sci Alliance 2023; 6:6/1/e202201688. [PMID: 36347544 PMCID: PMC9644418 DOI: 10.26508/lsa.202201688] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022] Open
Abstract
Understanding the molecular mechanism underlying the rampant mutation of SARS-CoV-2 would help us control the COVID-19 pandemic. The APOBEC-mediated C-to-U deamination is a major mutation type in the SARS-CoV-2 genome. However, it is unclear whether the novel mutation rate u is higher for C-to-U than for other mutation types, and what the detailed driving force is. By analyzing the time course SARS-CoV-2 global population data, we found that C-to-U has the highest novel mutation rate u among all mutation types and that this u is still increasing with time (du/dt > 0). Novel C-to-U events, rather than other mutation types, have a preference over particular genomic regions. A less local RNA structure is correlated with a high novel C-to-U mutation rate. A cascade model nicely explains the du/dt > 0 for C-to-U deamination. In SARS-CoV-2, the RNA structure serves as the molecular basis of the extremely high and continuously accelerating C-to-U deamination rate. This mechanism is the driving force of the mutation, adaptation, and evolution of SARS-CoV-2. Our findings help us understand the dynamic evolution of the virus mutation rate.
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Affiliation(s)
- Yan Li
- Cardiovasology Department I, Qingdao Center Hospital, Qingdao, China
| | - Fanghua Hou
- Cardiovasology Department I, Qingdao Center Hospital, Qingdao, China
| | - Meili Zhou
- Emergency Department, Qingdao Center Hospital, Qingdao, China
| | - Xiaoping Yang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
| | - Bin Yin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
| | - Wenqing Jiang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
| | - Huiqing Xu
- Department of Pathology, Qingdao Haici Hospital, Qingdao, China
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Mechanistic investigation of the deamination reaction of 6-thioguanine: a theoretical study. Struct Chem 2022. [DOI: 10.1007/s11224-022-02121-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Zhang J, Zhao D, Hu J, Huang X, Gu Q, Tao Z. Hepatic dysfunctions in COVID-19 patients infected by the omicron variant of SARS-CoV-2. Front Public Health 2022; 10:1049006. [PMID: 36466505 PMCID: PMC9716022 DOI: 10.3389/fpubh.2022.1049006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/24/2022] [Indexed: 11/19/2022] Open
Abstract
Background Presently, the omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) dominates amid the coronavirus disease 2019 (COVID-19) pandemic, but its clinical characteristics with intrinsic severity and organ tropism remain understudied. Methods We reported 1,001 mild COVID-19 patients that were infected with the omicron variant of SARS-CoV-2 and hospitalized in China from February to June 2022, including their demographic information, medical/immunization history, clinical symptom, and hematological profile. Patients with one-, two- and three-dose vaccination were compared to assess the vaccine effectiveness. Importantly, liver damage caused by the omicron variant infection was evaluated, in comparison to that caused by the wild-type or the delta variant SARS-CoV-2 infection. Results For the reported COVID-19 patients infected by the omicron variant of SARS-CoV-2, their median age was 36.0 [interquartile range (IQR): 26.0-50.0] and 49.7% were female. Hypertension, diabetes, and bronchitis were the leading comorbidities, and asymptomatic patients took up a major portion (61.2%). While most hematological parameters revealed the alleviated pathogenicity, full vaccination or booster shot showed effective protection against clinical severity. Furthermore, liver damages caused by viral infection of the omicron variant were largely attenuated when compared to those by infection of the wild-type or the delta variant SARS-CoV-2. Conclusions Our results supported that the viremic effect of the omicron variant tended to be modest, while the liver damage caused by this strain became milder than the previous circulating variants.
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Affiliation(s)
- Jianguo Zhang
- Department of Emergency Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Daguo Zhao
- Department of Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jianhui Hu
- Department of Laboratory Medicine, Zhenjiang Hospital Affiliated to Nanjing University of Chinese Medicine, Zhenjiang Hospital of Traditional Chinese Medicine, Zhenjiang, China
| | - Xing Huang
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qingqing Gu
- Department of Infectious Diseases, The Affiliated Hospital of Kangda College of Nanjing Medical University, The Fourth People's Hospital of Lianyungang, Lianyungang, China
| | - Zhimin Tao
- Department of Emergency Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, China,Jiangsu Province Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China,*Correspondence: Zhimin Tao
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Hepatitis B virus (HBV) codon adapts well to the gene expression profile of liver cancer: an evolutionary explanation for HBV's oncogenic role. J Microbiol 2022; 60:1106-1112. [PMID: 36251120 PMCID: PMC9574796 DOI: 10.1007/s12275-022-2371-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/02/2022]
Abstract
Due to the evolutionary arms race between hosts and viruses, viruses must adapt to host translation systems to rapidly synthesize viral proteins. Highly expressed genes in hosts have a codon bias related to tRNA abundance, the primary RNA translation rate determinant. We calculated the relative synonymous codon usage (RSCU) of three hepatitis viruses (HAV, HBV, and HCV), SARS-CoV-2, 30 human tissues, and hepatocellular carcinoma (HCC). After comparing RSCU between viruses and human tissues, we calculated the codon adaptation index (CAI) of viral and human genes. HBV and HCV showed the highest correlations with HCC and the normal liver, while SARS-CoV-2 had the strongest association with lungs. In addition, based on HCC RSCU, the CAI of HBV and HCV genes was the highest. HBV and HCV preferentially adapt to the tRNA pool in HCC, facilitating viral RNA translation. After an initial trigger, rapid HBV/HCV translation and replication may change normal liver cells into HCC cells. Our findings reveal a novel perspective on virus-mediated oncogenesis.
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The Sponge Interaction Between Circular RNA and microRNA Serves as a Fast-Evolving Mechanism That Suppresses Non-small Cell Lung Cancer (NSCLC) in Humans. J Mol Evol 2022; 90:362-374. [PMID: 36036266 DOI: 10.1007/s00239-022-10067-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/19/2022] [Indexed: 10/15/2022]
Abstract
Non-small cell lung cancer (NSCLC) is one of the most lethal cancer types in the world. Currently, the molecular mechanisms and pathways underlying NSCLC oncogenesis are poorly understood. Using multiple Omics data, we systematically explored the differentially expressed circular RNAs (circRNAs) in NSCLC. We also investigated potential microRNA sponges (that absorb circRNAs) in NSCLC and downstream target genes with experimental verifications. hsa_circ_0003497 was down-regulated in NSCLC and played an inhibitory role in tumorigenesis. In contrast, miR-197-3p was up-regulated in NSCLC. hsa_circ_0003497 directly interacts with miR-197-3p and releases a target gene of miR-197-3p termed CTNND1 (a known tumor suppressor gene). Evolutionary analysis reveals fast evolution of this hsa_circ_0003497-miR-197-3p-CTNND1-NSCLC axis in mammals. This work clarified the biological functions and molecular mechanisms of how hsa_circ_0003497 suppresses NSCLC through miR-197-3p and CTNND1. We discovered molecular markers for the prognosis of NSCLC and provided potential intervention targets for its treatment.
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Xiao W, Sun Y, Xu J, Zhang N, Dong L. uORF-Mediated Translational Regulation of ATF4 Serves as an Evolutionarily Conserved Mechanism Contributing to Non-Small-Cell Lung Cancer (NSCLC) and Stress Response. J Mol Evol 2022; 90:375-388. [PMID: 35962830 PMCID: PMC9375200 DOI: 10.1007/s00239-022-10068-y] [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: 03/07/2022] [Accepted: 07/20/2022] [Indexed: 11/30/2022]
Abstract
Diseases and environmental stresses are two distinct challenges for virtually all living organisms. In light of evolution, cellular responses to diseases and stresses might share similar molecular mechanisms, but the detailed regulation pathway is not reported yet. We obtained the transcriptomes and translatomes from several NSCLC (non-small-cell lung cancer) patients as well as from different species under normal or stress conditions. We found that the translation level of gene ATF4 is remarkably enhanced in NSCLC due to the reduced number of ribosomes binding to its upstream open reading frames (uORFs). We also showed the evolutionary conservation of this uORF-ATF4 regulation in the stress response of other species. Molecular experiments showed that knockdown of ATF4 reduced the cell growth rate while overexpression of ATF4 enhanced cell growth, especially for the ATF4 allele with mutated uORFs. Population genetics analyses in multiple species verified that the mutations that abolish uATGs (start codon of uORFs) are highly deleterious, suggesting the functional importance of uORFs. Our study proposes an evolutionarily conserved pattern that enhances the ATF4 translation by uORFs upon stress or disease. We generalized the concept of cellular response to diseases and stresses. These two biological processes may share similar molecular mechanisms.
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Affiliation(s)
- Wenjing Xiao
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China.
| | - Yang Sun
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Jinpeng Xu
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Na Zhang
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Lina Dong
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
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Zhao M, Li C, Dong Y, Wang X, Jiang W, Chen Y. Nothing in SARS-CoV-2 makes sense except in the light of RNA modification? Future Virol 2022; 0. [PMID: 35873408 PMCID: PMC9302237 DOI: 10.2217/fvl-2022-0043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/04/2022] [Indexed: 01/03/2023]
Abstract
The expression pattern of RNA deaminases determines the mutation and evolution of SARS-CoV-2.
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Affiliation(s)
- Mingmei Zhao
- Department of Neurosurgery, Qingdao Center Hospital, Qingdao, Shandong, 266042, China
| | - Chunxiao Li
- Cardiovasology Department I, Qingdao Center Hospital, Qingdao, Shandong, 266042, China
| | - Yu Dong
- Interventional Catheterization Lab, Qingdao Center Hospital, Qingdao, Shandong, 266042, China
| | - Xuekun Wang
- Cardiovasology Department I, Qingdao Center Hospital, Qingdao, Shandong, 266042, China
| | - Wenqing Jiang
- Department of Respiratory Diseases, The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, 266033, China
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, 266033, China
| | - Yaogang Chen
- Department of Neurosurgery, Qingdao Center Hospital, Qingdao, Shandong, 266042, China
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Description of a One-Year Succession of Variants of Interest and Concern of SARS-CoV-2 in Venezuela. Viruses 2022; 14:v14071378. [PMID: 35891359 PMCID: PMC9317613 DOI: 10.3390/v14071378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 02/04/2023] Open
Abstract
Some of the lineages of SARS-CoV-2, the new coronavirus responsible for COVID-19, exhibit higher transmissibility or partial resistance to antibody-mediated neutralization and were designated by WHO as Variants of Interests (VOIs) or Concern (VOCs). The aim of this study was to monitor the dissemination of VOIs and VOCs in Venezuela from March 2021 to February 2022. A 614 nt genomic fragment was sequenced for the detection of some relevant mutations of these variants. Their presence was confirmed by complete genome sequencing, with a correlation higher than 99% between both methodologies. After the introduction of the Gamma VOC since the beginning of the year 2021, the variants Alpha VOC and Lambda VOI were detected as early as March 2021, at a very low frequency. In contrast, the Mu VOI, detected in May 2021, was able to circulate throughout the country. After the detection of the Delta VOC in June 2021, it became the predominant circulating variant. With the arrival of the Omicron VOC in December, this variant was able to displace the Delta one in less than one month.
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Cai H, Liu X, Zheng X. RNA editing detection in SARS-CoV-2 transcriptome should be different from traditional SNV identification. J Appl Genet 2022; 63:587-594. [PMID: 35661108 PMCID: PMC9166928 DOI: 10.1007/s13353-022-00706-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/24/2022] [Accepted: 05/31/2022] [Indexed: 10/31/2022]
Affiliation(s)
- Houhao Cai
- Shandong University of Traditional Chinese Medicine, Jinan, 250000, Shandong, China
| | - Xiantao Liu
- Pulmonary and Critical Care Medicine, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, China
| | - Xin Zheng
- Department of Respiratory and Critical Care Medicine, The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, 266000, Shandong, China.
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