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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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Parker E, Anderson C, Zeller M, Tibi A, Havens JL, Laroche G, Benlarbi M, Ariana A, Robles-Sikisaka R, Latif AA, Watts A, Awidi A, Jaradat SA, Gangavarapu K, Ramesh K, Kurzban E, Matteson NL, Han AX, Hughes LD, McGraw M, Spencer E, Nicholson L, Khan K, Suchard MA, Wertheim JO, Wohl S, Côté M, Abdelnour A, Andersen KG, Abu-Dayyeh I. Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions. Nat Commun 2022; 13:4784. [PMID: 35970983 PMCID: PMC9376901 DOI: 10.1038/s41467-022-32536-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/04/2022] [Indexed: 01/02/2023] Open
Abstract
Regional connectivity and land travel have been identified as important drivers of SARS-CoV-2 transmission. However, the generalizability of this finding is understudied outside of well-sampled, highly connected regions. In this study, we investigated the relative contributions of regional and intercontinental connectivity to the source-sink dynamics of SARS-CoV-2 for Jordan and the Middle East. By integrating genomic, epidemiological and travel data we show that the source of introductions into Jordan was dynamic across 2020, shifting from intercontinental seeding in the early pandemic to more regional seeding for the travel restrictions period. We show that land travel, particularly freight transport, drove introduction risk during the travel restrictions period. High regional connectivity and land travel also drove Jordan's export risk. Our findings emphasize regional connectedness and land travel as drivers of transmission in the Middle East.
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Affiliation(s)
- Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ahmad Tibi
- Biolab Diagnostic Laboratories, Amman, Jordan
| | - Jennifer L Havens
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Geneviève Laroche
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | - Mehdi Benlarbi
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | - Ardeshir Ariana
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alaa Abdel Latif
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Abdalla Awidi
- Cell Therapy Center, The University of Jordan, Amman, Jordan
- Thrombosis, haemostasis laboratory, School of Medicine, The University of Jordan, Amman, Jordan
| | - Saied A Jaradat
- Princess Haya Biotechnology Center, Jordan University of Science and Technology, Irbid, Jordan
| | - Karthik Gangavarapu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Karthik Ramesh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alvin X Han
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Laura D Hughes
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Michelle McGraw
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Scripps Research Translational Institute, La Jolla, CA, USA
| | | | | | - Marc A Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | | | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Issa Abu-Dayyeh
- Biolab Diagnostic Laboratories, Amman, Jordan.
- Cell Therapy Center, The University of Jordan, Amman, Jordan.
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Choi Y, Ladoy A, De Ridder D, Jacot D, Vuilleumier S, Bertelli C, Guessous I, Pillonel T, Joost S, Greub G. Detection of SARS-CoV-2 infection clusters: The useful combination of spatiotemporal clustering and genomic analyses. Front Public Health 2022; 10:1016169. [PMID: 36568782 PMCID: PMC9771593 DOI: 10.3389/fpubh.2022.1016169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/15/2022] [Indexed: 12/04/2022] Open
Abstract
Background The need for effective public health surveillance systems to track virus spread for targeted interventions was highlighted during the COVID-19 pandemic. It spurred an interest in the use of spatiotemporal clustering and genomic analyses to identify high-risk areas and track the spread of the SARS-CoV-2 virus. However, these two approaches are rarely combined in surveillance systems to complement each one's limitations; spatiotemporal clustering approaches usually consider only one source of virus transmission (i.e., the residential setting) to detect case clusters, while genomic studies require significant resources and processing time that can delay decision-making. Here, we clarify the differences and possible synergies of these two approaches in the context of infectious disease surveillance systems by investigating to what extent geographically-defined clusters are confirmed as transmission clusters based on genome sequences, and how genomic-based analyses can improve the epidemiological investigations associated with spatiotemporal cluster detection. Methods For this purpose, we sequenced the SARS-CoV-2 genomes of 172 cases that were part of a collection of spatiotemporal clusters found in a Swiss state (Vaud) during the first epidemic wave. We subsequently examined intra-cluster genetic similarities and spatiotemporal distributions across virus genotypes. Results Our results suggest that the congruence between the two approaches might depend on geographic features of the area (rural/urban) and epidemic context (e.g., lockdown). We also identified two potential superspreading events that started from cases in the main urban area of the state, leading to smaller spreading events in neighboring regions, as well as a large spreading in a geographically-isolated area. These superspreading events were characterized by specific mutations assumed to originate from Mulhouse and Milan, respectively. Our analyses propose synergistic benefits of using two complementary approaches in public health surveillance, saving resources and improving surveillance efficiency.
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Affiliation(s)
- Yangji Choi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Anaïs Ladoy
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Group of Geographic Information Research and Analysis in Population Health (GIRAPH), Geneva, Switzerland
| | - David De Ridder
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Group of Geographic Information Research and Analysis in Population Health (GIRAPH), Geneva, Switzerland.,Faculty of Medicine, University of Geneva (UNIGE), Geneva, Switzerland.,Division and Department of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Damien Jacot
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Séverine Vuilleumier
- La Source School of Nursing, University of Applied Sciences and Arts Western Switzerland (HES-SO), Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Idris Guessous
- Group of Geographic Information Research and Analysis in Population Health (GIRAPH), Geneva, Switzerland.,Faculty of Medicine, University of Geneva (UNIGE), Geneva, Switzerland.,Division and Department of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Group of Geographic Information Research and Analysis in Population Health (GIRAPH), Geneva, Switzerland.,La Source School of Nursing, University of Applied Sciences and Arts Western Switzerland (HES-SO), Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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