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SARS-CoV-2 Pandemic Tracing in Italy Highlights Lineages with Mutational Burden in Growing Subsets.
Boccia, Angelo; Tufano, Rossella; Ferrucci, Veronica; Sepe, Leandra; Bianchi, Martina; Pascarella, Stefano; Zollo, Massimo; Paolella, Giovanni.
  • Boccia A; Ceinge Biotecnologie Avanzate, 80145 Naples, Italy.
  • Tufano R; Ceinge Biotecnologie Avanzate, 80145 Naples, Italy.
  • Ferrucci V; Ceinge Biotecnologie Avanzate, 80145 Naples, Italy.
  • Sepe L; Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Università degli Studi di Napoli Federico II, 80131 Naples, Italy.
  • Bianchi M; Ceinge Biotecnologie Avanzate, 80145 Naples, Italy.
  • Pascarella S; Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Università degli Studi di Napoli Federico II, 80131 Naples, Italy.
  • Zollo M; Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Rome, Italy.
  • Paolella G; Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Rome, Italy.
Int J Mol Sci ; 23(8)2022 Apr 09.
Article in English | MEDLINE | ID: covidwho-1785747
ABSTRACT
Tracing the appearance and evolution of virus variants is essential in the management of the COVID-19 pandemic. Here, we focus on SARS-CoV-2 spread in Italian patients by using viral sequences deposited in public databases and a tracing procedure which is used to monitor the evolution of the pandemic and detect the spreading, within the infected population of emergent sub-clades with a potential positive selection. Analyses of a collection of monthly samples focused on Italy highlighted the appearance and evolution of all the main viral sub-trees emerging at the end of the first year of the pandemic. It also identified additional expanding subpopulations which spread during the second year (i.e., 2021). Three-dimensional (3D) modelling of the main amino acid changes in mutated viral proteins, including ORF1ab (nsp3, nsp4, 2'-o-ribose methyltransferase, nsp6, helicase, nsp12 [RdRp]), N, ORF3a, ORF8, and spike proteins, shows the potential of the analysed structural variations to result in epistatic modulation and positive/negative selection pressure. These analyzes will be of importance to the early identification of emerging clades, which can develop into new "variants of concern" (i.e., VOC). These analyses and settings will also help SARS-CoV-2 coronet genomic centers in other countries to trace emerging worldwide variants.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study Topics: Variants Limits: Humans Language: English Year: 2022 Document Type: Article Affiliation country: Ijms23084155

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study Topics: Variants Limits: Humans Language: English Year: 2022 Document Type: Article Affiliation country: Ijms23084155