RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2023 |
| Outros Autores: | , , , , , , , , , , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Institucional da FIOCRUZ (ARCA) |
| Texto Completo: | https://www.arca.fiocruz.br/handle/icict/56508 |
Resumo: | Behalf of The Brazilian COVID-19 Research Group: Aline Pedroso Lorenz (Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil); Crhistinne Cavalheiro Maymone Gonçalves (Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil); Wellington Santos Fava (Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil); James Venturini (Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil); Luiz Demarchi (Central Public Health Laboratory of the State of Mato Grosso do Sul (LACEN-MS), Campo Grande, Mato Grosso do Sul, Brazil). |
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Costa, Vanessa Duarte daSantos, Alanna CalheirosSilva, Lucas Lima daWiggers, Wilian JeanIvantes, Claudia Alexandra PontesLima, Danielle MaltaColares, Jeová Keny BaimaDallacqua, Deusilene Souza VieiraCastro, Ana Rita Coimbra MottaDávila, Alberto Martín RiveraTeles, Sheila AraujoCarneiro, Megmar Aparecida dos SantosCaetano, Karlla Antonieta AmorimAnunciação, Fernando Antonio CostaPaula, Vanessa Salete deVillar, Livia Melo2023-01-19T11:18:32Z2023-01-19T11:18:32Z2023COSTA, Vanessa Duarte da et al. RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples. Diagnostics, v. 13, 210, p. 1-13, Jan. 2023.2075-4418https://www.arca.fiocruz.br/handle/icict/5650810.3390/diagnostics13020210Behalf of The Brazilian COVID-19 Research Group: Aline Pedroso Lorenz (Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil); Crhistinne Cavalheiro Maymone Gonçalves (Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil); Wellington Santos Fava (Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil); James Venturini (Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil); Luiz Demarchi (Central Public Health Laboratory of the State of Mato Grosso do Sul (LACEN-MS), Campo Grande, Mato Grosso do Sul, Brazil).This research was funded by the Oswaldo Cruz Foundation (FIOCRUZ) via INOVA FIOCRUZ VPPCB-005-FIO-20-2-52 program grant number 484015522386498, the Carlos Chagas Filho Foundation for Research Support of the State of Rio de Janeiro (FAPERJ) grant numbers E26/204.196, E-26/204.197/2021, and E-26/200.821/202, the Higher Education Personnel Improvement Coordination (CAPES) grant numbers 88887.661289/2022-00 and 88887.661288/2022-00, and the National Council for Scientific and Technological Development (CNPq) grant number 315967/2021-8.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório Brasileiro de Referência em Hepatites Virais. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório Brasileiro de Referência em Hepatites Virais. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório Brasileiro de Referência em Hepatites Virais. Rio de Janeiro, RJ, Brasil.Hospital Nossa Senhora das Graças. Serviço de Gastroenterologia, Hepatologia e Transplante Hepático. Curitiba, PR, Brasil.Hospital Nossa Senhora das Graças. Serviço de Gastroenterologia, Hepatologia e Transplante Hepático. Curitiba, PR, Brasil.Universidade de Fortaleza. Programa de Pós-Graduação em Ciências Médicas. Fortaleza, CE, Brasil.Universidade de Fortaleza. Programa de Pós-Graduação em Ciências Médicas. Fortaleza, CE, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Virologia Molecular. Rio de Janeiro, RJ, Brasil.Universidade Federal de Mato Grosso do Sul. Campo Grande, MS, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Programa de Pós-Graduação em Biodiversidade e Saúde. Laboratório de Biologia Computacional e de Sistemas. Rio de Janeiro, RJ, Brasil.Universidade Federal de Goiás. Faculdade Federal. Goiânia, GO, Brasil.Universidade Federal de Goiás. Faculdade Federal. Goiânia, GO, Brasil.Universidade Federal de Goiás. Faculdade Federal. Goiânia, GO, Brasil.Hospital Getúlio Vargas. Teresina, PI, Brasil / Instituto Natan Portela de Doenças Tropicais. Teresina, PI, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Virologia Molecular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório Brasileiro de Referência em Hepatites Virais. Rio de Janeiro, RJ, Brasil.Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a rapid method that can replace RT-qPCR. A simple molecular assay for SARS-CoV-2 RNA detection in gold-standard diagnosis through swabs and alternative specimens such as saliva could be helpful in promoting genomic surveillance. A multicenter study was conducted to evaluate the RT-LAMP assay method as an alternative for the molecular detection of SARS-CoV-2 lineages in swab and saliva samples. A total of 350 swabs from individuals with (n = 276) or without (n = 74) COVID-19 tested by RT-qPCR were collected. Paired saliva was also collected from 90 individuals who had SARS-CoV-2 RNA that was detectable (n = 30) or undetectable (n = 60) via RT-qPCR. For the RT-LAMP methodology, six primers were used for ORF1 gene amplification. As for SARS-CoV-2 genotyping, 39 swabs had the whole genome sequenced by MinION. The sensitivity of RT-LAMP to the swab was 90.2%. For the swab samples with Ct 30, the sensitivity improved by 96%. Considering saliva with Ct 30 in RT-qPCR testing, the RT-LAMP sensitivity was 100%. The RT-LAMP specificity was 100% for both the swab and saliva samples. This RT-LAMP assay was capable of detecting all the SARS-CoV-2 lineages circulating in the Brazilian swab samples. The RT-LAMP method has significant potential for use in clinical routines since it was capable of detecting SARS-CoV-2 RNA in swab and saliva samples.engMDPILAMPSARS-CoV-2COVID-19DiagnósticoLAMPSARS-CoV-2COVID-19DiagnosisRT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samplesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/56508/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALVanessada Costa_Livia M.Vilar_etal_IOC_2022.pdfVanessada Costa_Livia M.Vilar_etal_IOC_2022.pdfapplication/pdf721040https://www.arca.fiocruz.br/bitstream/icict/56508/2/Vanessada%20Costa_Livia%20M.Vilar_etal_IOC_2022.pdffd68a1583ed980fee5ee176f25c2883fMD52icict/565082023-09-04 11:03:05.333oai:www.arca.fiocruz.br:icict/56508Q0VTU8ODTyBOw4NPIEVYQ0xVU0lWQSBERSBESVJFSVRPUyBBVVRPUkFJUwoKQW8gYWNlaXRhciBvcyBURVJNT1MgZSBDT05EScOHw5VFUyBkZXN0YSBDRVNTw4NPLCBvIEFVVE9SIGUvb3UgVElUVUxBUiBkZSBkaXJlaXRvcwphdXRvcmFpcyBzb2JyZSBhIE9CUkEgZGUgcXVlIHRyYXRhIGVzdGUgZG9jdW1lbnRvOgoKKDEpIENFREUgZSBUUkFOU0ZFUkUsIHRvdGFsIGUgZ3JhdHVpdGFtZW50ZSwgw6AgRklPQ1JVWiAtIEZVTkRBw4fDg08gT1NXQUxETyBDUlVaLCBlbQpjYXLDoXRlciBwZXJtYW5lbnRlLCBpcnJldm9nw6F2ZWwgZSBOw4NPIEVYQ0xVU0lWTywgdG9kb3Mgb3MgZGlyZWl0b3MgcGF0cmltb25pYWlzIE7Dg08KQ09NRVJDSUFJUyBkZSB1dGlsaXphw6fDo28gZGEgT0JSQSBhcnTDrXN0aWNhIGUvb3UgY2llbnTDrWZpY2EgaW5kaWNhZGEgYWNpbWEsIGluY2x1c2l2ZSBvcyBkaXJlaXRvcwpkZSB2b3ogZSBpbWFnZW0gdmluY3VsYWRvcyDDoCBPQlJBLCBkdXJhbnRlIHRvZG8gbyBwcmF6byBkZSBkdXJhw6fDo28gZG9zIGRpcmVpdG9zIGF1dG9yYWlzLCBlbQpxdWFscXVlciBpZGlvbWEgZSBlbSB0b2RvcyBvcyBwYcOtc2VzOwoKKDIpIEFDRUlUQSBxdWUgYSBjZXNzw6NvIHRvdGFsIG7Do28gZXhjbHVzaXZhLCBwZXJtYW5lbnRlIGUgaXJyZXZvZ8OhdmVsIGRvcyBkaXJlaXRvcyBhdXRvcmFpcwpwYXRyaW1vbmlhaXMgbsOjbyBjb21lcmNpYWlzIGRlIHV0aWxpemHDp8OjbyBkZSBxdWUgdHJhdGEgZXN0ZSBkb2N1bWVudG8gaW5jbHVpLCBleGVtcGxpZmljYXRpdmFtZW50ZSwKb3MgZGlyZWl0b3MgZGUgZGlzcG9uaWJpbGl6YcOnw6NvIGUgY29tdW5pY2HDp8OjbyBww7pibGljYSBkYSBPQlJBLCBlbSBxdWFscXVlciBtZWlvIG91IHZlw61jdWxvLAppbmNsdXNpdmUgZW0gUmVwb3NpdMOzcmlvcyBEaWdpdGFpcywgYmVtIGNvbW8gb3MgZGlyZWl0b3MgZGUgcmVwcm9kdcOnw6NvLCBleGliacOnw6NvLCBleGVjdcOnw6NvLApkZWNsYW1hw6fDo28sIHJlY2l0YcOnw6NvLCBleHBvc2nDp8OjbywgYXJxdWl2YW1lbnRvLCBpbmNsdXPDo28gZW0gYmFuY28gZGUgZGFkb3MsIHByZXNlcnZhw6fDo28sIGRpZnVzw6NvLApkaXN0cmlidWnDp8OjbywgZGl2dWxnYcOnw6NvLCBlbXByw6lzdGltbywgdHJhZHXDp8OjbywgZHVibGFnZW0sIGxlZ2VuZGFnZW0sIGluY2x1c8OjbyBlbSBub3ZhcyBvYnJhcyBvdQpjb2xldMOibmVhcywgcmV1dGlsaXphw6fDo28sIGVkacOnw6NvLCBwcm9kdcOnw6NvIGRlIG1hdGVyaWFsIGRpZMOhdGljbyBlIGN1cnNvcyBvdSBxdWFscXVlciBmb3JtYSBkZQp1dGlsaXphw6fDo28gbsOjbyBjb21lcmNpYWw7CgooMykgUkVDT05IRUNFIHF1ZSBhIGNlc3PDo28gYXF1aSBlc3BlY2lmaWNhZGEgY29uY2VkZSDDoCBGSU9DUlVaIC0gRlVOREHDh8ODTyBPU1dBTERPCkNSVVogbyBkaXJlaXRvIGRlIGF1dG9yaXphciBxdWFscXVlciBwZXNzb2Eg4oCTIGbDrXNpY2Egb3UganVyw61kaWNhLCBww7pibGljYSBvdSBwcml2YWRhLCBuYWNpb25hbCBvdQplc3RyYW5nZWlyYSDigJMgYSBhY2Vzc2FyIGUgdXRpbGl6YXIgYW1wbGFtZW50ZSBhIE9CUkEsIHNlbSBleGNsdXNpdmlkYWRlLCBwYXJhIHF1YWlzcXVlcgpmaW5hbGlkYWRlcyBuw6NvIGNvbWVyY2lhaXM7CgooNCkgREVDTEFSQSBxdWUgYSBvYnJhIMOpIGNyaWHDp8OjbyBvcmlnaW5hbCBlIHF1ZSDDqSBvIHRpdHVsYXIgZG9zIGRpcmVpdG9zIGFxdWkgY2VkaWRvcyBlIGF1dG9yaXphZG9zLApyZXNwb25zYWJpbGl6YW5kby1zZSBpbnRlZ3JhbG1lbnRlIHBlbG8gY29udGXDumRvIGUgb3V0cm9zIGVsZW1lbnRvcyBxdWUgZmF6ZW0gcGFydGUgZGEgT0JSQSwKaW5jbHVzaXZlIG9zIGRpcmVpdG9zIGRlIHZveiBlIGltYWdlbSB2aW5jdWxhZG9zIMOgIE9CUkEsIG9icmlnYW5kby1zZSBhIGluZGVuaXphciB0ZXJjZWlyb3MgcG9yCmRhbm9zLCBiZW0gY29tbyBpbmRlbml6YXIgZSByZXNzYXJjaXIgYSBGSU9DUlVaIC0gRlVOREHDh8ODTyBPU1dBTERPIENSVVogZGUKZXZlbnR1YWlzIGRlc3Blc2FzIHF1ZSB2aWVyZW0gYSBzdXBvcnRhciwgZW0gcmF6w6NvIGRlIHF1YWxxdWVyIG9mZW5zYSBhIGRpcmVpdG9zIGF1dG9yYWlzIG91CmRpcmVpdG9zIGRlIHZveiBvdSBpbWFnZW0sIHByaW5jaXBhbG1lbnRlIG5vIHF1ZSBkaXogcmVzcGVpdG8gYSBwbMOhZ2lvIGUgdmlvbGHDp8O1ZXMgZGUgZGlyZWl0b3M7CgooNSkgQUZJUk1BIHF1ZSBjb25oZWNlIGEgUG9sw610aWNhIEluc3RpdHVjaW9uYWwgZGUgQWNlc3NvIEFiZXJ0byBkYSBGSU9DUlVaIC0gRlVOREHDh8ODTwpPU1dBTERPIENSVVogZSBhcyBkaXJldHJpemVzIHBhcmEgbyBmdW5jaW9uYW1lbnRvIGRvIHJlcG9zaXTDs3JpbyBpbnN0aXR1Y2lvbmFsIEFSQ0EuCgpBIFBvbMOtdGljYSBJbnN0aXR1Y2lvbmFsIGRlIEFjZXNzbyBBYmVydG8gZGEgRklPQ1JVWiAtIEZVTkRBw4fDg08gT1NXQUxETyBDUlVaIHJlc2VydmEKZXhjbHVzaXZhbWVudGUgYW8gQVVUT1Igb3MgZGlyZWl0b3MgbW9yYWlzIGUgb3MgdXNvcyBjb21lcmNpYWlzIHNvYnJlIGFzIG9icmFzIGRlIHN1YSBhdXRvcmlhCmUvb3UgdGl0dWxhcmlkYWRlLCBzZW5kbyBvcyB0ZXJjZWlyb3MgdXN1w6FyaW9zIHJlc3BvbnPDoXZlaXMgcGVsYSBhdHJpYnVpw6fDo28gZGUgYXV0b3JpYSBlIG1hbnV0ZW7Dp8OjbwpkYSBpbnRlZ3JpZGFkZSBkYSBPQlJBIGVtIHF1YWxxdWVyIHV0aWxpemHDp8Ojby4KCkEgUG9sw610aWNhIEluc3RpdHVjaW9uYWwgZGUgQWNlc3NvIEFiZXJ0byBkYSBGSU9DUlVaIC0gRlVOREHDh8ODTyBPU1dBTERPIENSVVoKcmVzcGVpdGEgb3MgY29udHJhdG9zIGUgYWNvcmRvcyBwcmVleGlzdGVudGVzIGRvcyBBdXRvcmVzIGNvbSB0ZXJjZWlyb3MsIGNhYmVuZG8gYW9zIEF1dG9yZXMKaW5mb3JtYXIgw6AgSW5zdGl0dWnDp8OjbyBhcyBjb25kacOnw7VlcyBlIG91dHJhcyByZXN0cmnDp8O1ZXMgaW1wb3N0YXMgcG9yIGVzdGVzIGluc3RydW1lbnRvcy4KRepositório 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| dc.title.en_US.fl_str_mv |
RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples |
| title |
RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples |
| spellingShingle |
RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples Costa, Vanessa Duarte da LAMP SARS-CoV-2 COVID-19 Diagnóstico LAMP SARS-CoV-2 COVID-19 Diagnosis |
| title_short |
RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples |
| title_full |
RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples |
| title_fullStr |
RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples |
| title_full_unstemmed |
RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples |
| title_sort |
RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples |
| author |
Costa, Vanessa Duarte da |
| author_facet |
Costa, Vanessa Duarte da Santos, Alanna Calheiros Silva, Lucas Lima da Wiggers, Wilian Jean Ivantes, Claudia Alexandra Pontes Lima, Danielle Malta Colares, Jeová Keny Baima Dallacqua, Deusilene Souza Vieira Castro, Ana Rita Coimbra Motta Dávila, Alberto Martín Rivera Teles, Sheila Araujo Carneiro, Megmar Aparecida dos Santos Caetano, Karlla Antonieta Amorim Anunciação, Fernando Antonio Costa Paula, Vanessa Salete de Villar, Livia Melo |
| author_role |
author |
| author2 |
Santos, Alanna Calheiros Silva, Lucas Lima da Wiggers, Wilian Jean Ivantes, Claudia Alexandra Pontes Lima, Danielle Malta Colares, Jeová Keny Baima Dallacqua, Deusilene Souza Vieira Castro, Ana Rita Coimbra Motta Dávila, Alberto Martín Rivera Teles, Sheila Araujo Carneiro, Megmar Aparecida dos Santos Caetano, Karlla Antonieta Amorim Anunciação, Fernando Antonio Costa Paula, Vanessa Salete de Villar, Livia Melo |
| author2_role |
author author author author author author author author author author author author author author author |
| dc.contributor.author.fl_str_mv |
Costa, Vanessa Duarte da Santos, Alanna Calheiros Silva, Lucas Lima da Wiggers, Wilian Jean Ivantes, Claudia Alexandra Pontes Lima, Danielle Malta Colares, Jeová Keny Baima Dallacqua, Deusilene Souza Vieira Castro, Ana Rita Coimbra Motta Dávila, Alberto Martín Rivera Teles, Sheila Araujo Carneiro, Megmar Aparecida dos Santos Caetano, Karlla Antonieta Amorim Anunciação, Fernando Antonio Costa Paula, Vanessa Salete de Villar, Livia Melo |
| dc.subject.other.en_US.fl_str_mv |
LAMP SARS-CoV-2 COVID-19 Diagnóstico |
| topic |
LAMP SARS-CoV-2 COVID-19 Diagnóstico LAMP SARS-CoV-2 COVID-19 Diagnosis |
| dc.subject.en.en_US.fl_str_mv |
LAMP SARS-CoV-2 COVID-19 Diagnosis |
| description |
Behalf of The Brazilian COVID-19 Research Group: Aline Pedroso Lorenz (Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil); Crhistinne Cavalheiro Maymone Gonçalves (Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil); Wellington Santos Fava (Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil); James Venturini (Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil); Luiz Demarchi (Central Public Health Laboratory of the State of Mato Grosso do Sul (LACEN-MS), Campo Grande, Mato Grosso do Sul, Brazil). |
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2023 |
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2023-01-19T11:18:32Z |
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2023-01-19T11:18:32Z |
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2023 |
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info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/article |
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article |
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COSTA, Vanessa Duarte da et al. RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples. Diagnostics, v. 13, 210, p. 1-13, Jan. 2023. |
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https://www.arca.fiocruz.br/handle/icict/56508 |
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2075-4418 |
| dc.identifier.doi.none.fl_str_mv |
10.3390/diagnostics13020210 |
| identifier_str_mv |
COSTA, Vanessa Duarte da et al. RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples. Diagnostics, v. 13, 210, p. 1-13, Jan. 2023. 2075-4418 10.3390/diagnostics13020210 |
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https://www.arca.fiocruz.br/handle/icict/56508 |
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eng |
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eng |
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MDPI |
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MDPI |
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