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Comprehensive comparative genomic and microsatellite analysis of SARS, MERS, BAT-SARS, and COVID-19 coronaviruses.
J Med Virol. 2021 Jul; 93(7):4382-4391.JM

Abstract

The coronavirus disease 2019 (COVID-19) pandemic has spread around the globe very rapidly. Previously, the evolution pattern and similarity among the COVID-19 causative organism severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and causative organisms of other similar infections have been determined using a single type of genetic marker in different studies. Herein, the SARS-CoV-2 and related β coronaviruses Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV, bat coronavirus (BAT-CoV) were comprehensively analyzed using a custom-built pipeline that employed phylogenetic approaches based on multiple types of genetic markers including the whole genome sequences, mutations in nucleotide sequences, mutations in protein sequences, and microsatellites. The whole-genome sequence-based phylogeny revealed that the strains of SARS-CoV-2 are more similar to the BAT-CoV strains. The mutational analysis showed that on average MERS-CoV and BAT-CoV genomes differed at 134.21 and 136.72 sites, respectively, whereas the SARS-CoV genome differed at 26.64 sites from the reference genome of SARS-CoV-2. Furthermore, the microsatellite analysis highlighted a relatively higher number of average microsatellites for MERS-CoV and SARS-CoV-2 (106.8 and 107, respectively), and a lower number for SARS-CoV and BAT-CoV (95.8 and 98.5, respectively). Collectively, the analysis of multiple genetic markers of selected β viral genomes revealed that the newly born SARS-COV-2 is closely related to BAT-CoV, whereas, MERS-CoV is more distinct from the SARS-CoV-2 than BAT-CoV and SARS-CoV.

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Authors+Show Affiliations

Rehman HA
Intelligent Criminology Research Lab (ICRL), National Center of Artificial Intelligence (NCAI), Al-Khawarizmi Institute of Computer Science (KICS), University of Engineering and Technology (UET), Lahore, Pakistan.
Ramzan F
Department of Computer Science, University of Engineering and Technology (UET), Lahore, Pakistan.
Basharat Z
Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan.
Shakeel M
Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan.
Khan MUG
Intelligent Criminology Research Lab (ICRL), National Center of Artificial Intelligence (NCAI), Al-Khawarizmi Institute of Computer Science (KICS), University of Engineering and Technology (UET), Lahore, Pakistan. Department of Computer Science, University of Engineering and Technology (UET), Lahore, Pakistan.
Khan IA
Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan.

MeSH

AlphacoronavirusAnimalsBase SequenceChiropteraDNA Mutational AnalysisGenetic MarkersGenetic VariationGenome, ViralHumansMicrosatellite RepeatsMiddle East Respiratory Syndrome CoronavirusPhylogenySevere acute respiratory syndrome-related coronavirusSARS-CoV-2Sequence AlignmentSequence Homology, Nucleic AcidWhole Genome Sequencing

Pub Type(s)

Journal Article

Language

eng

PubMed ID

33782990

Citation

Rehman, Hafiz Abdul, et al. "Comprehensive Comparative Genomic and Microsatellite Analysis of SARS, MERS, BAT-SARS, and COVID-19 Coronaviruses." Journal of Medical Virology, vol. 93, no. 7, 2021, pp. 4382-4391.
Rehman HA, Ramzan F, Basharat Z, et al. Comprehensive comparative genomic and microsatellite analysis of SARS, MERS, BAT-SARS, and COVID-19 coronaviruses. J Med Virol. 2021;93(7):4382-4391.
Rehman, H. A., Ramzan, F., Basharat, Z., Shakeel, M., Khan, M. U. G., & Khan, I. A. (2021). Comprehensive comparative genomic and microsatellite analysis of SARS, MERS, BAT-SARS, and COVID-19 coronaviruses. Journal of Medical Virology, 93(7), 4382-4391. https://doi.org/10.1002/jmv.26974
Rehman HA, et al. Comprehensive Comparative Genomic and Microsatellite Analysis of SARS, MERS, BAT-SARS, and COVID-19 Coronaviruses. J Med Virol. 2021;93(7):4382-4391. PubMed PMID: 33782990.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Comprehensive comparative genomic and microsatellite analysis of SARS, MERS, BAT-SARS, and COVID-19 coronaviruses. AU - Rehman,Hafiz Abdul, AU - Ramzan,Farheen, AU - Basharat,Zarrin, AU - Shakeel,Muhammad, AU - Khan,Muhammad Usman Ghani, AU - Khan,Ishtiaq Ahmad, Y1 - 2021/04/08/ PY - 2021/03/02/revised PY - 2021/01/28/received PY - 2021/03/24/accepted PY - 2021/3/31/pubmed PY - 2021/6/9/medline PY - 2021/3/30/entrez KW - COVID-19 KW - MERS KW - SARS KW - SARS-CoV-2 KW - pandemic KW - phylogenetic SP - 4382 EP - 4391 JF - Journal of medical virology JO - J Med Virol VL - 93 IS - 7 N2 - The coronavirus disease 2019 (COVID-19) pandemic has spread around the globe very rapidly. Previously, the evolution pattern and similarity among the COVID-19 causative organism severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and causative organisms of other similar infections have been determined using a single type of genetic marker in different studies. Herein, the SARS-CoV-2 and related β coronaviruses Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV, bat coronavirus (BAT-CoV) were comprehensively analyzed using a custom-built pipeline that employed phylogenetic approaches based on multiple types of genetic markers including the whole genome sequences, mutations in nucleotide sequences, mutations in protein sequences, and microsatellites. The whole-genome sequence-based phylogeny revealed that the strains of SARS-CoV-2 are more similar to the BAT-CoV strains. The mutational analysis showed that on average MERS-CoV and BAT-CoV genomes differed at 134.21 and 136.72 sites, respectively, whereas the SARS-CoV genome differed at 26.64 sites from the reference genome of SARS-CoV-2. Furthermore, the microsatellite analysis highlighted a relatively higher number of average microsatellites for MERS-CoV and SARS-CoV-2 (106.8 and 107, respectively), and a lower number for SARS-CoV and BAT-CoV (95.8 and 98.5, respectively). Collectively, the analysis of multiple genetic markers of selected β viral genomes revealed that the newly born SARS-COV-2 is closely related to BAT-CoV, whereas, MERS-CoV is more distinct from the SARS-CoV-2 than BAT-CoV and SARS-CoV. SN - 1096-9071 UR - https://www.unboundmedicine.com/medline/citation/33782990/Comprehensive_comparative_genomic_and_microsatellite_analysis_of_SARS_MERS_BAT_SARS_and_COVID_19_coronaviruses_ DB - PRIME DP - Unbound Medicine ER -