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Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses.
Kannan, Saathvik R; Spratt, Austin N; Cohen, Alisha R; Naqvi, S Hasan; Chand, Hitendra S; Quinn, Thomas P; Lorson, Christian L; Byrareddy, Siddappa N; Singh, Kamal.
  • Kannan SR; Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
  • Spratt AN; Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
  • Cohen AR; Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
  • Naqvi SH; Department of Medicine, University of Missouri, Columbia, MO, 65211, USA.
  • Chand HS; Department of Immunology and Nanomedicine, Florida International University, Miami, FL, USA.
  • Quinn TP; Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA.
  • Lorson CL; Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.
  • Byrareddy SN; Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68131, USA; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden. Electronic address: sid.byrareddy@unmc.edu.
  • Singh K; Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm,
J Autoimmun ; 124: 102715, 2021 11.
Article in English | MEDLINE | ID: covidwho-1437496
ABSTRACT
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been rapidly evolving in the form of new variants. At least eleven known variants have been reported. The objective of this study was to delineate the differences in the mutational profile of Delta and Delta Plus variants. High-quality sequences (n = 1756) of Delta (B.1.617.2) and Delta Plus (AY.1 or B.1.617.2.1) variants were used to determine the prevalence of mutations (≥20 %) in the entire SARS-CoV-2 genome, their co-existence, and change in prevalence over a period of time. Structural analysis was conducted to get insights into the impact of mutations on antibody binding. A Sankey diagram was generated using phylogenetic analysis coupled with sequence-acquisition dates to infer the migration of the Delta Plus variant and its presence in the United States. The Delta Plus variant had a significant number of high-prevalence mutations (≥20 %) than in the Delta variant. Signature mutations in Spike (G142D, A222V, and T95I) existed at a more significant percentage in the Delta Plus variant than the Delta variant. Three mutations in Spike (K417N, V70F, and W258L) were exclusively present in the Delta Plus variant. A new mutation was identified in ORF1a (A1146T), which was only present in the Delta Plus variant with ~58 % prevalence. Furthermore, five key mutations (T95I, A222V, G142D, R158G, and K417N) were significantly more prevalent in the Delta Plus than in the Delta variant. Structural analyses revealed that mutations alter the sidechain conformation to weaken the interactions with antibodies. Delta Plus, which first emerged in India, reached the United States through England and Japan, followed by its spread to more than 20 the United States. Based on the results presented here, it is clear that the Delta and Delta Plus variants have unique mutation profiles, and the Delta Plus variant is not just a simple addition of K417N to the Delta variant. Highly correlated mutations may have emerged to keep the structural integrity of the virus.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Evolution, Molecular / Mutation, Missense / SARS-CoV-2 / COVID-19 Type of study: Observational study / Randomized controlled trials Topics: Variants Limits: Humans Language: English Journal: J Autoimmun Journal subject: Allergy and Immunology Year: 2021 Document Type: Article Affiliation country: J.jaut.2021.102715

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Evolution, Molecular / Mutation, Missense / SARS-CoV-2 / COVID-19 Type of study: Observational study / Randomized controlled trials Topics: Variants Limits: Humans Language: English Journal: J Autoimmun Journal subject: Allergy and Immunology Year: 2021 Document Type: Article Affiliation country: J.jaut.2021.102715