Tags

Type your tag names separated by a space and hit enter

Topological Analysis for Sequence Variability: Case Study on more than 2K SARS-CoV-2 sequences of COVID-19 infected 54 countries in comparison with SARS-CoV-1 and MERS-CoV.
Infect Genet Evol. 2021 03; 88:104708.IG

Abstract

The pandemic due to novel coronavirus, SARS-CoV-2 is a serious global concern now. More than thousand new COVID-19 infections are getting reported daily for this virus across the globe. Thus, the medical research communities are trying to find the remedy to restrict the spreading of this virus, while the vaccine development work is still under research in parallel. In such critical situation, not only the medical research community, but also the scientists in different fields like microbiology, pharmacy, bioinformatics and data science are also sharing effort to accelerate the process of vaccine development, virus prediction, forecasting the transmissible probability and reproduction cases of virus for social awareness. With the similar context, in this article, we have studied sequence variability of the virus primarily focusing on three aspects: (a) sequence variability among SARS-CoV-1, MERS-CoV and SARS-CoV-2 in human host, which are in the same coronavirus family, (b) sequence variability of SARS-CoV-2 in human host for 54 different countries and (c) sequence variability between coronavirus family and country specific SARS-CoV-2 sequences in human host. For this purpose, as a case study, we have performed topological analysis of 2391 global genomic sequences of SARS-CoV-2 in association with SARS-CoV-1 and MERS-CoV using an integrated semi-alignment based computational technique. The results of the semi-alignment based technique are experimentally and statistically found similar to alignment based technique and computationally faster. Moreover, the outcome of this analysis can help to identify the nations with homogeneous SARS-CoV-2 sequences, so that same vaccine can be applied to their heterogeneous human population.

Links

PMC Free PDF

Authors+Show Affiliations

Sarkar JP
Larsen & Toubro Infotech Ltd., Pune, Maharashtra, India; Department of Computer Science and Engineering, Jadavpur University, Kolkata, West Bengal, India.
Saha I
Department of Computer Science and Engineering, National Institute of Technical Teachers' Training & Research, Kolkata, West Bengal, India. Electronic address: indrajit@nitttrkol.ac.in.
Seal A
Cognizant Technology Solutions, Kolkata, West Bengal, India.
Maity D
Department of Electronics and Communication Engineering, MCKV Institute of Engineering, Howrah, West Bengal, India.
Maulik U
Department of Computer Science and Engineering, Jadavpur University, Kolkata, West Bengal, India.

MeSH

AfricaAmericasAsiaAustraliaBase SequenceCOVID-19Computational BiologyCoronavirus InfectionsEuropeGenetic VariationGenome, ViralHost-Pathogen InteractionsHumansMiddle East Respiratory Syndrome CoronavirusPandemicsSevere acute respiratory syndrome-related coronavirusSARS-CoV-2Sequence AlignmentSevere Acute Respiratory Syndrome

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Review

Language

eng

PubMed ID

33421654

Citation

Sarkar, Jnanendra Prasad, et al. "Topological Analysis for Sequence Variability: Case Study On More Than 2K SARS-CoV-2 Sequences of COVID-19 Infected 54 Countries in Comparison With SARS-CoV-1 and MERS-CoV." Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, vol. 88, 2021, p. 104708.
Sarkar JP, Saha I, Seal A, et al. Topological Analysis for Sequence Variability: Case Study on more than 2K SARS-CoV-2 sequences of COVID-19 infected 54 countries in comparison with SARS-CoV-1 and MERS-CoV. Infect Genet Evol. 2021;88:104708.
Sarkar, J. P., Saha, I., Seal, A., Maity, D., & Maulik, U. (2021). Topological Analysis for Sequence Variability: Case Study on more than 2K SARS-CoV-2 sequences of COVID-19 infected 54 countries in comparison with SARS-CoV-1 and MERS-CoV. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 88, 104708. https://doi.org/10.1016/j.meegid.2021.104708
Sarkar JP, et al. Topological Analysis for Sequence Variability: Case Study On More Than 2K SARS-CoV-2 Sequences of COVID-19 Infected 54 Countries in Comparison With SARS-CoV-1 and MERS-CoV. Infect Genet Evol. 2021;88:104708. PubMed PMID: 33421654.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Topological Analysis for Sequence Variability: Case Study on more than 2K SARS-CoV-2 sequences of COVID-19 infected 54 countries in comparison with SARS-CoV-1 and MERS-CoV. AU - Sarkar,Jnanendra Prasad, AU - Saha,Indrajit, AU - Seal,Arijit, AU - Maity,Debasree, AU - Maulik,Ujjwal, Y1 - 2021/01/06/ PY - 2020/07/28/received PY - 2020/10/27/revised PY - 2020/12/31/accepted PY - 2021/1/10/pubmed PY - 2021/2/23/medline PY - 2021/1/9/entrez KW - COVID-19 KW - Coronavirsus KW - Genomic sequences KW - Global health KW - MERS-CoV KW - SARS-CoV-2 KW - Sequence alignment free technique SP - 104708 EP - 104708 JF - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JO - Infect Genet Evol VL - 88 N2 - The pandemic due to novel coronavirus, SARS-CoV-2 is a serious global concern now. More than thousand new COVID-19 infections are getting reported daily for this virus across the globe. Thus, the medical research communities are trying to find the remedy to restrict the spreading of this virus, while the vaccine development work is still under research in parallel. In such critical situation, not only the medical research community, but also the scientists in different fields like microbiology, pharmacy, bioinformatics and data science are also sharing effort to accelerate the process of vaccine development, virus prediction, forecasting the transmissible probability and reproduction cases of virus for social awareness. With the similar context, in this article, we have studied sequence variability of the virus primarily focusing on three aspects: (a) sequence variability among SARS-CoV-1, MERS-CoV and SARS-CoV-2 in human host, which are in the same coronavirus family, (b) sequence variability of SARS-CoV-2 in human host for 54 different countries and (c) sequence variability between coronavirus family and country specific SARS-CoV-2 sequences in human host. For this purpose, as a case study, we have performed topological analysis of 2391 global genomic sequences of SARS-CoV-2 in association with SARS-CoV-1 and MERS-CoV using an integrated semi-alignment based computational technique. The results of the semi-alignment based technique are experimentally and statistically found similar to alignment based technique and computationally faster. Moreover, the outcome of this analysis can help to identify the nations with homogeneous SARS-CoV-2 sequences, so that same vaccine can be applied to their heterogeneous human population. SN - 1567-7257 UR - https://www.unboundmedicine.com/medline/citation/33421654/Topological_Analysis_for_Sequence_Variability:_Case_Study_on_more_than_2K_SARS_CoV_2_sequences_of_COVID_19_infected_54_countries_in_comparison_with_SARS_CoV_1_and_MERS_CoV_ DB - PRIME DP - Unbound Medicine ER -