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Comprehensive comparative genomic and microsatellite analysis of SARS, MERS, BAT-SARS, and COVID-19 coronaviruses.
Rehman, Hafiz Abdul; Ramzan, Farheen; Basharat, Zarrin; Shakeel, Muhammad; Khan, Muhammad Usman Ghani; Khan, Ishtiaq Ahmad.
  • 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.
  • Khan IA; Department of Computer Science, University of Engineering and Technology (UET), Lahore, Pakistan.
J Med Virol ; 93(7): 4382-4391, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1263102
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 ß 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 ß 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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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genome, Viral / Microsatellite Repeats / Severe acute respiratory syndrome-related coronavirus / Middle East Respiratory Syndrome Coronavirus / Alphacoronavirus / SARS-CoV-2 Type of study: Randomized controlled trials Limits: Animals / Humans Language: English Journal: J Med Virol Year: 2021 Document Type: Article Affiliation country: Jmv.26974

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genome, Viral / Microsatellite Repeats / Severe acute respiratory syndrome-related coronavirus / Middle East Respiratory Syndrome Coronavirus / Alphacoronavirus / SARS-CoV-2 Type of study: Randomized controlled trials Limits: Animals / Humans Language: English Journal: J Med Virol Year: 2021 Document Type: Article Affiliation country: Jmv.26974