Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline

doi:10.1111/tbed.13834

	Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline
	Rahman, Mohammed Shaminur 1; Islam, Mohammed Rafiul 1; Hoque, Mohammed Nazmul 1,2; Akther, Masuda 1; Puspo, Joynob Akter 1; Akter, Salma 1,4; Sultana, Munawar 1; Hossain, Mohammed Anwar 1; Alam, Abu Sayed Mohammad Rubayet Ul 3
	2020-10
发表期刊	TRANSBOUNDARY AND EMERGING DISEASES
ISSN	1865-1674
EISSN	1865-1682
摘要	Infecting millions of people, the SARS-CoV-2 is evolving at an unprecedented rate, demanding advanced and specified analytic pipeline to capture the mutational spectra. In order to explore mutations and deletions in the spike (S) protein - the most-discussed protein of SARS-CoV-2 - we comprehensively analyzed 35,750 complete S protein-coding sequences through a custom Python-based pipeline. This GISAID-collected dataset of until 24 June 2020 covered six continents and five major climate zones. We identified 27,801 (77.77% sequences) mutated strains compared to reference Wuhan-Hu-1 wherein 84.40% of these strains mutated by only a single amino acid (aa). An outlier strain (EPI_ISL_463893) from Bosnia and Herzegovina possessed six aa substitutions. We also identified 11 residues with high aa mutation frequency, and each contains four types of aa variations. The infamous D614G variant has spread worldwide with ever-rising dominance and across regions with different climatic conditions alongside L5F and D936Y mutants, which have been documented throughout all regions and climate zones, respectively. We also found 988 unique aa substitutions spanned across 660 residues, which differed significantly among different continents (p = .003) and climatic zones (p = .021) as inferred with the Kruskal-Wallis test. Besides, 17 in-frame deletions at four sites adjacent to receptor-binding-domain were determined that may have a possible impact on attenuation. This study provides a fast and accurate pipeline for identifying mutations and deletions from the large dataset for coding and also non-coding sequences as evidenced by the representative analysis on existing S protein data. By using separate multi-sequence alignment, removing ambiguous sequences and in-frame stop codons, and utilizing pairwise alignment, this method can derive both synonymous and non-synonymous mutations (strain_ID reference aa:mutation position:strain aa). We suggest that the pipeline will aid in the evolutionary surveillance of any SARS-CoV-2 encoded proteins and will prove to be crucial in tracking the ever-increasing variation of many other divergent RNA viruses in the future. The code is available at https://github.com/SShaminur/Mutation-Analysis.
关键词	Climate Geography Mutations SARS-CoV-2 Spike (S) protein \| COVID-19
DOI	10.1111/tbed.13834
WOS关键词	2019-NCOV ; GENETICS
WOS研究方向	Infectious Diseases ; Veterinary Sciences
WOS类目	Infectious Diseases ; Veterinary Sciences
出版者	WILEY
引用统计
文献类型	期刊论文
专题	新冠肺炎循证社会科学证据集成
作者单位	1.Univ Dhaka; 2.Bangabandhu Sheikh Mujibur Rahman Agr Univ; 3.Jashore Univ Sci & Technol; 4.Jahangirnagar Univ
推荐引用方式 GB/T 7714	Rahman, Mohammed Shaminur,Islam, Mohammed Rafiul,Hoque, Mohammed Nazmul,et al. Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline[J]. TRANSBOUNDARY AND EMERGING DISEASES,2020.
APA	Rahman, Mohammed Shaminur.,Islam, Mohammed Rafiul.,Hoque, Mohammed Nazmul.,Akther, Masuda.,Puspo, Joynob Akter.,...&Alam, Abu Sayed Mohammad Rubayet Ul.(2020).Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline.TRANSBOUNDARY AND EMERGING DISEASES.
MLA	Rahman, Mohammed Shaminur,et al."Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline".TRANSBOUNDARY AND EMERGING DISEASES (2020).

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