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Rogozin IB, Saura A, Poliakov E, Bykova A, Roche-Lima A, Pavlov YI, Yurchenko V. Properties and Mechanisms of Deletions, Insertions, and Substitutions in the Evolutionary History of SARS-CoV-2. Int J Mol Sci 2024; 25:3696. [PMID: 38612505 PMCID: PMC11011937 DOI: 10.3390/ijms25073696] [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: 02/25/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
SARS-CoV-2 has accumulated many mutations since its emergence in late 2019. Nucleotide substitutions leading to amino acid replacements constitute the primary material for natural selection. Insertions, deletions, and substitutions appear to be critical for coronavirus's macro- and microevolution. Understanding the molecular mechanisms of mutations in the mutational hotspots (positions, loci with recurrent mutations, and nucleotide context) is important for disentangling roles of mutagenesis and selection. In the SARS-CoV-2 genome, deletions and insertions are frequently associated with repetitive sequences, whereas C>U substitutions are often surrounded by nucleotides resembling the APOBEC mutable motifs. We describe various approaches to mutation spectra analyses, including the context features of RNAs that are likely to be involved in the generation of recurrent mutations. We also discuss the interplay between mutations and natural selection as a complex evolutionary trend. The substantial variability and complexity of pipelines for the reconstruction of mutations and the huge number of genomic sequences are major problems for the analyses of mutations in the SARS-CoV-2 genome. As a solution, we advocate for the development of a centralized database of predicted mutations, which needs to be updated on a regular basis.
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Affiliation(s)
- Igor B. Rogozin
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Eugenia Poliakov
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anastassia Bykova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities—RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan 00936, Puerto Rico
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
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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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