1
|
Gupta S, Gupta D, Bhatnagar S. Analysis of SARS-CoV-2 genome evolutionary patterns. Microbiol Spectr 2024; 12:e0265423. [PMID: 38197644 PMCID: PMC10846092 DOI: 10.1128/spectrum.02654-23] [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: 06/26/2023] [Accepted: 11/20/2023] [Indexed: 01/11/2024] Open
Abstract
The spread of SARS-CoV-2 virus accompanied by public availability of abundant sequence data provides a window for the determination of viral evolutionary patterns. In this study, SARS-CoV-2 genome sequences were collected from seven countries in the period January 2020-December 2022. The sequences were classified into three phases, namely, pre-vaccination, post-vaccination, and recent period. Comparison was performed between these phases based on parameters like mutation rates, selection pressure (dN/dS ratio), and transition to transversion ratios (Ti/Tv). Similar comparisons were performed among SARS-CoV-2 variants. Statistical significance was tested using Graphpad unpaired t-test. The analysis showed an increase in the percent genomic mutation rates post-vaccination and in recent periods across all countries from the pre-vaccination sequences. Mutation rates were highest in NSP3, S, N, and NSP12b before and increased further after vaccination. NSP4 showed the largest change in mutation rates after vaccination. The dN/dS ratios showed purifying selection that shifted toward neutral selection after vaccination. N, ORF8, ORF3a, and ORF10 were under highest positive selection before vaccination. Shift toward neutral selection was driven by E, NSP3, and ORF7a in the after vaccination set. In recent sequences, the largest dN/dS change was observed in E, NSP1, and NSP13. The Ti/Tv ratios decreased with time. C→U and G→U were the most frequent transitions and transversions. However, U→G was the most frequent transversion in recent period. The Omicron variant had the highest genomic mutation rates, while Delta showed the highest dN/dS ratio. Protein-wise dN/dS ratio was also seen to vary across the different variants.IMPORTANCETo the best of our knowledge, there exists no other large-scale study of the genomic and protein-wise mutation patterns during the time course of evolution in different countries. Analyzing the SARS-CoV-2 evolutionary patterns in view of the varying spatial, temporal, and biological signals is important for diagnostics, therapeutics, and pharmacovigilance of SARS-CoV-2.
Collapse
Affiliation(s)
- Shubhangi Gupta
- Department of Biological Sciences and Engineering, Computational and Structural Biology Laboratory, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Deepanshu Gupta
- Division of Biotechnology, Computational and Structural Biology Laboratory, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
| | - Sonika Bhatnagar
- Department of Biological Sciences and Engineering, Computational and Structural Biology Laboratory, Netaji Subhas University of Technology, Dwarka, New Delhi, India
- Division of Biotechnology, Computational and Structural Biology Laboratory, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
| |
Collapse
|
2
|
Hakim MS, Gunadi, Rahayu A, Wibawa H, Eryvinka LS, Supriyati E, Vujira KA, Iskandar K, Afiahayati, Daniwijaya EW, Oktoviani FN, Annisa L, Utami FDT, Amadeus VC, Nurhidayah SS, Leksono TP, Halim FV, Arguni E, Nuryastuti T, Wibawa T. Sequence analysis of the Spike, RNA-dependent RNA polymerase, and protease genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia. Virus Genes 2024:10.1007/s11262-023-02048-1. [PMID: 38244104 DOI: 10.1007/s11262-023-02048-1] [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: 06/25/2023] [Accepted: 12/22/2023] [Indexed: 01/22/2024]
Abstract
During the Covid-19 pandemic, the resurgence of SARS-CoV-2 was due to the development of novel variants of concern (VOC). Thus, genomic surveillance is essential to monitor continuing evolution of SARS-CoV-2 and to track the emergence of novel variants. In this study, we performed phylogenetic, mutation, and selection pressure analyses of the Spike, nsp12, nsp3, and nsp5 genes of SARS-CoV-2 isolates circulating in Yogyakarta and Central Java provinces, Indonesia from May 2021 to February 2022. Various bioinformatics tools were employed to investigate the evolutionary dynamics of distinct SARS-CoV-2 isolates. During the study period, 213 and 139 isolates of Omicron and Delta variants were identified, respectively. Particularly in the Spike gene, mutations were significantly more abundant in Omicron than in Delta variants. Consistently, in all of four genes studied, the substitution rates of Omicron were higher than that of Delta variants, especially in the Spike and nsp12 genes. In addition, selective pressure analysis revealed several sites that were positively selected in particular genes, implying that these sites were functionally essential for virus evolution. In conclusion, our study demonstrated a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia.
Collapse
Affiliation(s)
- Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Gunadi
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ayu Rahayu
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center Wates, Directorate General of Livestok Services, Ministry of Agriculture, Yogyakarta, Indonesia
| | - Laudria Stella Eryvinka
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Khanza Adzkia Vujira
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Kristy Iskandar
- Department of Child Health and Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Afiahayati
- Department of Computer Science and Electronics, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwin Widyanto Daniwijaya
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Farida Nur Oktoviani
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Luthvia Annisa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Fadila Dyah Trie Utami
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Verrell Christopher Amadeus
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Setiani Silvy Nurhidayah
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tiara Putri Leksono
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Fiqih Vidiantoro Halim
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| |
Collapse
|
3
|
Nedaei F, Esmaeili Rastaghi AR, Goodarzi E, Haji Mullah Asadullah H, Mirhadi F, Fateh A. Introduction and effect of natural selection analysis at common mutations of SARS-CoV-2 spike gene in Iran. Virus Res 2023; 336:199202. [PMID: 37595664 PMCID: PMC10491845 DOI: 10.1016/j.virusres.2023.199202] [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: 07/27/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/20/2023]
Abstract
The epidemic of coronavirus disease 2019 (COVID-19) was caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike (S) protein of SARS-Cov-2 is composed of two subunits, S1 and S2. This study aimed to describe SARS-CoV-2 haplotypes in Iranians based on the S gene, which plays a key role in the receptor recognition and cell membrane fusion proses. 95 positive saliva samples for SARS-CoV-2 were amplified and sequenced for the S gene. The sequences were classified into 35 haplotypes, which 11 haplotypes were new (H1, H2, H3, H4, H6, H7, H11, H13, H15, H16, H25) and have not been reported so far. Amino acid substitutions were found at 40 positions that 23 were located at S1 subunit and 16 were at S2 subunit and one was at cleavage loop (P681H/R), thus polymorphisms at S1 subunit were found to be higher than S2. The neutrality index (NI) analyses showed a negative departure from the neutral substitution patterns (NI > 1) for S1 and S2 subunit in the studied sequences. The co-occurrence of B-cell epitopes and mutation sites were found in seven positions with more probably to be exposed the immune system pressure. In conclusion, the results provide the significant data to design an effective vaccine based on this protein.
Collapse
Affiliation(s)
- Fatemeh Nedaei
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | | | - Esmaeil Goodarzi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Fatemeh Mirhadi
- Department of Medical science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
4
|
Nagasawa N, Kimura R, Akagawa M, Shirai T, Sada M, Okayama K, Sato-Fujimoto Y, Saito M, Kondo M, Katayama K, Ryo A, Kuroda M, Kimura H. Molecular Evolutionary Analyses of the Spike Protein Gene and Spike Protein in the SARS-CoV-2 Omicron Subvariants. Microorganisms 2023; 11:2336. [PMID: 37764181 PMCID: PMC10537508 DOI: 10.3390/microorganisms11092336] [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: 07/28/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
To better understand the evolution of the SARS-CoV-2 Omicron subvariants, we performed molecular evolutionary analyses of the spike (S) protein gene/S protein using advanced bioinformatics technologies. First, time-scaled phylogenetic analysis estimated that a common ancestor of the Wuhan, Alpha, Beta, Delta variants, and Omicron variants/subvariants diverged in May 2020. After that, a common ancestor of the Omicron variant generated various Omicron subvariants over one year. Furthermore, a chimeric virus between the BM.1.1.1 and BJ.1 subvariants, known as XBB, diverged in July 2021, leading to the emergence of the prevalent subvariants XBB.1.5 and XBB.1.16. Next, similarity plot (SimPlot) data estimated that the recombination point (breakpoint) corresponded to nucleotide position 1373. As a result, XBB.1.5 subvariants had the 5' nucleotide side from the breakpoint as a strain with a BJ.1 sequence and the 3' nucleotide side as a strain with a BM.1.1.1 sequence. Genome network data showed that Omicron subvariants were genetically linked with the common ancestors of the Wuhan and Delta variants, resulting in many amino acid mutations. Selective pressure analysis estimated that the prevalent subvariants, XBB.1.5 and XBB.1.16, had specific amino acid mutations, such as V445P, G446S, N460K, and F486P, located in the RBD when compared with the BA.4 and BA.5 subvariants. Moreover, some representative immunogenicity-associated amino acid mutations, including L452R, F486V, R493Q, and V490S, were also found in these subvariants. These substitutions were involved in the conformational epitopes, implying that these mutations affect immunogenicity and vaccine evasion. Furthermore, these mutations were identified as positive selection sites. These results suggest that the S gene/S protein Omicron subvariants rapidly evolved, and mutations observed in the conformational epitopes may reduce the effectiveness of the current vaccine, including bivalent vaccines such as mRNA vaccines containing the BA.4/BA.5 subvariants.
Collapse
Affiliation(s)
- Norika Nagasawa
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, 1-7-1, Tonya-machi, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (K.O.)
- Department of Medical Technology, Gunma Paz University School of Medical Science and Technology, 1-7-1, Tonya-machi, Takasaki-shi 370-0006, Gunma, Japan;
| | - Ryusuke Kimura
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, 1338-4, Shibukawa, Shibukawa-shi 377-0008, Gunma, Japan; (R.K.); (T.S.)
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi-shi 371-8514, Gunma, Japan
| | - Mao Akagawa
- Department of Clinical Laboratory, Juntendo University Hospital, Bunkyo-ku, Tokyo 113-8431, Japan;
| | - Tatsuya Shirai
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, 1338-4, Shibukawa, Shibukawa-shi 377-0008, Gunma, Japan; (R.K.); (T.S.)
| | - Mitsuru Sada
- Department of Respiratory Medicine, Kyourin University School of Medicine, 6-20-2, Shinkawa, Mitaka-shi 181-8611, Tokyo, Japan;
| | - Kaori Okayama
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, 1-7-1, Tonya-machi, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (K.O.)
| | - Yuka Sato-Fujimoto
- Department of Medical Technology, Gunma Paz University School of Medical Science and Technology, 1-7-1, Tonya-machi, Takasaki-shi 370-0006, Gunma, Japan;
| | - Makoto Saito
- Department of Clinical Engineering, Gunma Paz University School of Medical Science and Technology, Takasaki-shi 370-0006, Gunma, Japan; (M.S.); (M.K.)
| | - Mayumi Kondo
- Department of Clinical Engineering, Gunma Paz University School of Medical Science and Technology, Takasaki-shi 370-0006, Gunma, Japan; (M.S.); (M.K.)
| | - Kazuhiko Katayama
- Laboratory of Viral Infection Control, Ōmura Satoshi Memorial Institute, Graduate School of Infection Control Sciences, Kitasato University, 5-9-1, Shirogane, Minato-ku, Tokyo 108-8641, Japan;
| | - Akihide Ryo
- Department of Virology III, National Institute of Infectious Diseases, 4-7-1, Gakuen, Musashimurayama-shi 208-0011, Tokyo, Japan;
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan;
| | - Hirokazu Kimura
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, 1-7-1, Tonya-machi, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (K.O.)
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, 1338-4, Shibukawa, Shibukawa-shi 377-0008, Gunma, Japan; (R.K.); (T.S.)
- Department of Clinical Engineering, Gunma Paz University School of Medical Science and Technology, Takasaki-shi 370-0006, Gunma, Japan; (M.S.); (M.K.)
| |
Collapse
|
5
|
Chakraborty C, Chatterjee S, Bhattacharya M, Chopra H, Bhattacharya P, Islam MA, Dhama K. The D614G mutation helps to increase the transmissibility and reduce the virulence of SARS-CoV-2 variants through natural selection. Int J Surg 2023; 109:171-174. [PMID: 36799841 PMCID: PMC10389482 DOI: 10.1097/js9.0000000000000155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 02/18/2023]
Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal
| | - Srijan Chatterjee
- Institute for Skeletal Aging and Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, Gangwon-do, Republic of Korea
| | | | - Hitesh Chopra
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Prosun Bhattacharya
- COVID-19 Research, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Teknikringen 10B, Stockholm, Sweden
| | - Md. Aminul Islam
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, Kishoreganj, Bangladesh
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| |
Collapse
|
6
|
Warger J, Gaudieri S. On the Evolutionary Trajectory of SARS-CoV-2: Host Immunity as a Driver of Adaptation in RNA Viruses. Viruses 2022; 15:70. [PMID: 36680110 PMCID: PMC9866609 DOI: 10.3390/v15010070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022] Open
Abstract
Host immunity can exert a complex array of selective pressures on a pathogen, which can drive highly mutable RNA viruses towards viral escape. The plasticity of a virus depends on its rate of mutation, as well as the balance of fitness cost and benefit of mutations, including viral adaptations to the host's immune response. Since its emergence, SARS-CoV-2 has diversified into genetically distinct variants, which are characterised often by clusters of mutations that bolster its capacity to escape human innate and adaptive immunity. Such viral escape is well documented in the context of other pandemic RNA viruses such as the human immunodeficiency virus (HIV) and influenza virus. This review describes the selection pressures the host's antiviral immunity exerts on SARS-CoV-2 and other RNA viruses, resulting in divergence of viral strains into more adapted forms. As RNA viruses obscure themselves from host immunity, they uncover weak points in their own armoury that can inform more comprehensive, long-lasting, and potentially cross-protective vaccine coverage.
Collapse
Affiliation(s)
- Jacob Warger
- School of Medicine and Pharmacology, University of Western Australia, Crawley, WA 6009, Australia
| | - Silvana Gaudieri
- School of Human Sciences, University of Western Australia, Crawley, WA 6009, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Mandurah, WA 6150, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| |
Collapse
|