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da-Costa-Rodrigues B, Cheohen C, Sciammarella F, Pierre-Bonetti-Pozzobon A, Ribeiro L, Nepomuceno-Silva JL, Medeiros M, Mury F, Monteiro-de-Barros C, Lazoski C, Leal-da-Silva M, Tanuri A, Nunes-da-Fonseca R. SARS-CoV-2 Spatiotemporal Genomic and Molecular Analysis of the First Wave of the COVID-19 Pandemic in Macaé, the Brazilian Capital of Oil. Int J Mol Sci 2022; 23:ijms231911497. [PMID: 36232806 PMCID: PMC9569756 DOI: 10.3390/ijms231911497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/23/2022] [Accepted: 09/25/2022] [Indexed: 11/25/2022] Open
Abstract
The SARS-CoV-2 virus infection led to millions of deaths during the COVID-19 pandemic. Hundreds of workers from several other Brazilian cities, as well as from other countries, arrive daily in Macaé to work in the oil supply chain, making this city a putative hotspot for the introduction of new viral lineages. In this study, we performed a genomic survey of SARS-CoV-2 samples from Macaé during the first outbreak of COVID-19, combined with clinical data and a molecular integrative analysis. First, phylogenomic analyses showed a high occurrence of viral introduction events and the establishment of local transmissions in Macaé, including the ingression and spread of the B.1.1.28 lineage in the municipality from June to August 2020. Second, SARS-CoV-2 mutations were identified in patients with distinct levels of COVID-19 severity. Third, molecular interactions of the mutated spike protein from three B.1.1.33 local samples and human ACE2 showed higher interactions than that of the wild-type spike protein from the ancestral virus. Altogether, these results elucidate the SARS-CoV-2 genomic profile in a strategic Brazilian city and further explore the functional aspects of SARS-CoV-2 with a characterization of emerging viral mutations associated with clinical data and the potential targets for drug development against SARS-CoV-2.
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Affiliation(s)
- Bruno da-Costa-Rodrigues
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
- Programa de Ciências Morfológicas, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-170, Brazil
- Correspondence: (B.d.-C.-R.); (R.N.-d.-F.)
| | - Caio Cheohen
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Felipe Sciammarella
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | - Allan Pierre-Bonetti-Pozzobon
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Lupis Ribeiro
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - José Luciano Nepomuceno-Silva
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Marcio Medeiros
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Flávia Mury
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Cintia Monteiro-de-Barros
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Cristiano Lazoski
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | - Manuela Leal-da-Silva
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Amilcar Tanuri
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | - Rodrigo Nunes-da-Fonseca
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
- Programa de Ciências Morfológicas, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-170, Brazil
- Correspondence: (B.d.-C.-R.); (R.N.-d.-F.)
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Boccia A, Tufano R, Ferrucci V, Sepe L, Bianchi M, Pascarella S, Zollo M, Paolella G. SARS-CoV-2 Pandemic Tracing in Italy Highlights Lineages with Mutational Burden in Growing Subsets. Int J Mol Sci 2022; 23:4155. [PMID: 35456974 PMCID: PMC9029933 DOI: 10.3390/ijms23084155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/31/2022] [Accepted: 04/06/2022] [Indexed: 02/07/2023] Open
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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Affiliation(s)
- Angelo Boccia
- Ceinge Biotecnologie Avanzate, 80145 Naples, Italy; (A.B.); (R.T.); (V.F.); (L.S.)
| | - Rossella Tufano
- Ceinge Biotecnologie Avanzate, 80145 Naples, Italy; (A.B.); (R.T.); (V.F.); (L.S.)
| | - Veronica Ferrucci
- Ceinge Biotecnologie Avanzate, 80145 Naples, Italy; (A.B.); (R.T.); (V.F.); (L.S.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Università degli Studi di Napoli Federico II, 80131 Naples, Italy
| | - Leandra Sepe
- Ceinge Biotecnologie Avanzate, 80145 Naples, Italy; (A.B.); (R.T.); (V.F.); (L.S.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Università degli Studi di Napoli Federico II, 80131 Naples, Italy
| | - Martina Bianchi
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy; (M.B.); (S.P.)
| | - Stefano Pascarella
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy; (M.B.); (S.P.)
| | - Massimo Zollo
- Ceinge Biotecnologie Avanzate, 80145 Naples, Italy; (A.B.); (R.T.); (V.F.); (L.S.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Università degli Studi di Napoli Federico II, 80131 Naples, Italy
- DAI Medicina di Laboratorio e Trasfusionale, AOU Azienda Ospedaliera ‘Federico II’, 80131 Naples, Italy
| | - Giovanni Paolella
- Ceinge Biotecnologie Avanzate, 80145 Naples, Italy; (A.B.); (R.T.); (V.F.); (L.S.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), Università degli Studi di Napoli Federico II, 80131 Naples, Italy
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Lo Presti A, Di Martino A, Faggioni G, Giordani F, Fillo S, Anselmo A, Fain VV, Fortunato A, Petralito G, Molinari F, Palomba S, De Santis R, Fiore S, Fabiani C, Di Mario G, Facchini M, Calzoletti L, Lista F, Rezza G, Stefanelli P. Analysis of Genomic Characteristics of SARS-CoV-2 in Italy, 29 January to 27 March 2020. Viruses 2022; 14:472. [PMID: 35336879 PMCID: PMC8951147 DOI: 10.3390/v14030472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 02/01/2022] [Accepted: 02/09/2022] [Indexed: 12/14/2022] Open
Abstract
We performed next-generation sequencing (NGS), phylogenetic analysis, gene flows, and N- and O-glycosylation prediction on SARS-CoV-2 genomes collected from lab-confirmed cases from different Italian regions. To this end, a total of 111 SARS-CoV-2 genomes collected in Italy between 29 January and 27 March 2020 were investigated. The majority of the genomes belonged to lineage B.1, with some descendant lineages. The gene flow analysis showed that the spread occurred mainly from the north to the center and to the south of Italy, as confirmed by epidemiological data. The mean evolutionary rate estimated here was 8.731 × 10-4 (95% highest posterior density, HPD intervals 5.809 × 10-4 to 1.19 × 10-3), in line with values reported by other authors. The dated phylogeny suggested that SARS-CoV-2 lineage B.1 probably entered Italy between the end of January and early February 2020. Continuous molecular surveillance is needed to trace virus circulation and evolution.
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Affiliation(s)
- Alessandra Lo Presti
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (S.F.); (C.F.); (G.D.M.); (M.F.); (L.C.); (P.S.)
| | - Angela Di Martino
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (S.F.); (C.F.); (G.D.M.); (M.F.); (L.C.); (P.S.)
| | - Giovanni Faggioni
- Scientific Department, Army Medical Center, 00184 Rome, Italy; (G.F.); (F.G.); (S.F.); (A.A.); (V.V.F.); (A.F.); (G.P.); (F.M.); (R.D.S.); (F.L.)
| | - Francesco Giordani
- Scientific Department, Army Medical Center, 00184 Rome, Italy; (G.F.); (F.G.); (S.F.); (A.A.); (V.V.F.); (A.F.); (G.P.); (F.M.); (R.D.S.); (F.L.)
| | - Silvia Fillo
- Scientific Department, Army Medical Center, 00184 Rome, Italy; (G.F.); (F.G.); (S.F.); (A.A.); (V.V.F.); (A.F.); (G.P.); (F.M.); (R.D.S.); (F.L.)
| | - Anna Anselmo
- Scientific Department, Army Medical Center, 00184 Rome, Italy; (G.F.); (F.G.); (S.F.); (A.A.); (V.V.F.); (A.F.); (G.P.); (F.M.); (R.D.S.); (F.L.)
| | - Vanessa Vera Fain
- Scientific Department, Army Medical Center, 00184 Rome, Italy; (G.F.); (F.G.); (S.F.); (A.A.); (V.V.F.); (A.F.); (G.P.); (F.M.); (R.D.S.); (F.L.)
- Department of Science, University of Rome “Roma Tre”, 00146 Rome, Italy
| | - Antonella Fortunato
- Scientific Department, Army Medical Center, 00184 Rome, Italy; (G.F.); (F.G.); (S.F.); (A.A.); (V.V.F.); (A.F.); (G.P.); (F.M.); (R.D.S.); (F.L.)
| | - Giancarlo Petralito
- Scientific Department, Army Medical Center, 00184 Rome, Italy; (G.F.); (F.G.); (S.F.); (A.A.); (V.V.F.); (A.F.); (G.P.); (F.M.); (R.D.S.); (F.L.)
| | - Filippo Molinari
- Scientific Department, Army Medical Center, 00184 Rome, Italy; (G.F.); (F.G.); (S.F.); (A.A.); (V.V.F.); (A.F.); (G.P.); (F.M.); (R.D.S.); (F.L.)
| | - Stefano Palomba
- General Directorate of Military Medical Services-Medical Situation Awareness Branch, 00184 Rome, Italy;
| | - Riccardo De Santis
- Scientific Department, Army Medical Center, 00184 Rome, Italy; (G.F.); (F.G.); (S.F.); (A.A.); (V.V.F.); (A.F.); (G.P.); (F.M.); (R.D.S.); (F.L.)
| | - Stefano Fiore
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (S.F.); (C.F.); (G.D.M.); (M.F.); (L.C.); (P.S.)
| | - Concetta Fabiani
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (S.F.); (C.F.); (G.D.M.); (M.F.); (L.C.); (P.S.)
| | - Giuseppina Di Mario
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (S.F.); (C.F.); (G.D.M.); (M.F.); (L.C.); (P.S.)
| | - Marzia Facchini
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (S.F.); (C.F.); (G.D.M.); (M.F.); (L.C.); (P.S.)
| | - Laura Calzoletti
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (S.F.); (C.F.); (G.D.M.); (M.F.); (L.C.); (P.S.)
| | - Florigio Lista
- Scientific Department, Army Medical Center, 00184 Rome, Italy; (G.F.); (F.G.); (S.F.); (A.A.); (V.V.F.); (A.F.); (G.P.); (F.M.); (R.D.S.); (F.L.)
| | - Giovanni Rezza
- Health Prevention Directorate, Ministry of Health, 00144 Rome, Italy;
| | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (S.F.); (C.F.); (G.D.M.); (M.F.); (L.C.); (P.S.)
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