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Molecular insight into the genomic variation of SARS-CoV-2 strains from current outbreak.
Comput Biol Chem. 2021 Aug; 93:107533.CB

Abstract

Coronavirus disease 2019 (COVID-19) is the newly emerging viral disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The epidemic sparked in December 2019 at Wuhan city, China that causes a large global outbreak and a major public health catastrophe. Till now, more than 129 million positive cases have been reported in which more than 2.81 million were dead, surveyed by Johns Hopkins University, USA. The diverse symptoms of COVID-19 and an increased number of positive cases throughout the world hypothesize that this virus assembles more variants that are preventing the pursuit of its adequate treatment as well as the development of the vaccine. In this study, 715 SARS-CoV-2 genomes were retrieved from the gisaid and NCBI viral resources involving 39 countries and 164 different types of variants were identified based on 108 Single Nucleotide Polymorphisms (SNPs) in which the ancestral type of SARS-CoV-2 was found as the most frequent and the most prevalent in China. Moreover, variant type A104 was identified as the most frequent in the USA and A52 in Japan. The study also recognized the most common SNPs such as 241, 3037, 8782, 11083, 14408, 23403, and 28144 as well as variants regarding base-pair, C > T. A total of 65 non-synonymous SNPs were recognized which were mostly located in nucleocapsid phosphoprotein, Non-structural protein 3(Nsp3), and spike glycoprotein encoding gene. Molecular divergence analysis revealed that this virus was phylogenetically related to Yunnan 2013 bat strain. This study indicates SARS-CoV-2 frequently alters their genetic material, which mostly affects the nucleocapsid phosphoprotein, and spike glycoprotein-encoding gene and makes it very challenging to develop SARS-Cov-2 vaccine and antibody-mediated rapid diagnostic kit.

Authors+Show Affiliations

Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Khulna, Bangladesh. Electronic address: avizitdbmb@just.edu.bd.Laboratory of Gut-Brain Signaling, Laboratory Sciences and Services Division (LSSD), icddr,b, Dhaka, 1212, Bangladesh. Electronic address: sarah.khurshid99@gmail.com.Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Mymensingh, Bangladesh. Electronic address: aferdausi.gpb@bau.edu.bd.Upazilla Health Complex, Nazirpur, Pirojpur, Barishal, 8540, Barishal, Bangladesh. Electronic address: eshita.nipu@gmail.com.Gafargaon Islamia Govt. High School, Gafargaon, Mymensingh, Dhaka, 2230, Dhaka, Bangladesh. Electronic address: amitbau007@yahoo.com.Department of Mathematics, Jashore University of Science and Technology, Jashore, 7408, Bangladesh. Electronic address: ffa.math@just.edu.bd.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

34166886

Citation

Das, Avizit, et al. "Molecular Insight Into the Genomic Variation of SARS-CoV-2 Strains From Current Outbreak." Computational Biology and Chemistry, vol. 93, 2021, p. 107533.
Das A, Khurshid S, Ferdausi A, et al. Molecular insight into the genomic variation of SARS-CoV-2 strains from current outbreak. Comput Biol Chem. 2021;93:107533.
Das, A., Khurshid, S., Ferdausi, A., Nipu, E. S., Das, A., & Ahmed, F. F. (2021). Molecular insight into the genomic variation of SARS-CoV-2 strains from current outbreak. Computational Biology and Chemistry, 93, 107533. https://doi.org/10.1016/j.compbiolchem.2021.107533
Das A, et al. Molecular Insight Into the Genomic Variation of SARS-CoV-2 Strains From Current Outbreak. Comput Biol Chem. 2021;93:107533. PubMed PMID: 34166886.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Molecular insight into the genomic variation of SARS-CoV-2 strains from current outbreak. AU - Das,Avizit, AU - Khurshid,Sarah, AU - Ferdausi,Aleya, AU - Nipu,Eshita Sadhak, AU - Das,Amit, AU - Ahmed,Fee Faysal, Y1 - 2021/06/18/ PY - 2020/07/15/received PY - 2021/05/08/revised PY - 2021/06/16/accepted PY - 2021/6/25/pubmed PY - 2021/8/7/medline PY - 2021/6/24/entrez KW - COVID-19 KW - Nsp3 KW - Nucleocapsid phosphoprotein KW - SARS-CoV-2 KW - SNP KW - Spike glycoprotein SP - 107533 EP - 107533 JF - Computational biology and chemistry JO - Comput Biol Chem VL - 93 N2 - Coronavirus disease 2019 (COVID-19) is the newly emerging viral disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The epidemic sparked in December 2019 at Wuhan city, China that causes a large global outbreak and a major public health catastrophe. Till now, more than 129 million positive cases have been reported in which more than 2.81 million were dead, surveyed by Johns Hopkins University, USA. The diverse symptoms of COVID-19 and an increased number of positive cases throughout the world hypothesize that this virus assembles more variants that are preventing the pursuit of its adequate treatment as well as the development of the vaccine. In this study, 715 SARS-CoV-2 genomes were retrieved from the gisaid and NCBI viral resources involving 39 countries and 164 different types of variants were identified based on 108 Single Nucleotide Polymorphisms (SNPs) in which the ancestral type of SARS-CoV-2 was found as the most frequent and the most prevalent in China. Moreover, variant type A104 was identified as the most frequent in the USA and A52 in Japan. The study also recognized the most common SNPs such as 241, 3037, 8782, 11083, 14408, 23403, and 28144 as well as variants regarding base-pair, C > T. A total of 65 non-synonymous SNPs were recognized which were mostly located in nucleocapsid phosphoprotein, Non-structural protein 3(Nsp3), and spike glycoprotein encoding gene. Molecular divergence analysis revealed that this virus was phylogenetically related to Yunnan 2013 bat strain. This study indicates SARS-CoV-2 frequently alters their genetic material, which mostly affects the nucleocapsid phosphoprotein, and spike glycoprotein-encoding gene and makes it very challenging to develop SARS-Cov-2 vaccine and antibody-mediated rapid diagnostic kit. SN - 1476-928X UR - https://www.unboundmedicine.com/medline/citation/34166886/Molecular_insight_into_the_genomic_variation_of_SARS_CoV_2_strains_from_current_outbreak_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1476-9271(21)00100-6 DB - PRIME DP - Unbound Medicine ER -