Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina
The emergence of SARS-CoV-2 variants with concerning characteristics to public health has attracted the attention of the scientific community and governments both regionally and globally since the end of 2020. The most relevant variants described so far include: Alpha (lineage B.1.1.7), first detect...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Artículo |
| Lenguaje: | Inglés |
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Frontiers Media
2022
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| Acceso en línea: | http://hdl.handle.net/20.500.12123/11680 https://www.frontiersin.org/articles/10.3389/fmed.2021.755463/full https://doi.org/10.3389/fmed.2021.755463 |
| _version_ | 1855484821701132288 |
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| author | Torres, Carolina Mojsiejczuk, Laura Acuña, Dolores Alexay, Sofía Amadio, Ariel Aulicino, Paula Debat, Humberto Julio Fay, Fabián Fernandez, Franco Daniel Giri, Adriana A. Goya, Stephanie Konig, Guido Alberto Lucero, Horacio Nabaes Jodar, Mercedes Soledad Pianciola, Luis Sfalcin, Javier A. Acevedo, Raúl Maximiliano Bengoa Luoni, Sofía Ailin Bolatti, Elisa M. Brusés, Bettina Cacciabue, Marco Polo Domingo Casal, Pablo E. Cerri, Agustina Chouhy, Diego Dus Santos, Maria Jose Eberhardt, María Florencia Fernandez, Ailen Fernandez, Paula Del Carmen Fernández Do Porto, Darío Formichelli, Laura Gismondi, María Ines Irazoqui, Jose Matias Lorenzini Campos, Melina Lusso, Silvina Marquez, Nathalie Muñoz Hidalgo, Marianne Graziel Mussin, Javier Natale, Mónica Oria, Griselda Pisano, María Belén Posner, Victoria Puebla, Andrea Fabiana Viegas, Mariana |
| author_browse | Acevedo, Raúl Maximiliano Acuña, Dolores Alexay, Sofía Amadio, Ariel Aulicino, Paula Bengoa Luoni, Sofía Ailin Bolatti, Elisa M. Brusés, Bettina Cacciabue, Marco Polo Domingo Casal, Pablo E. Cerri, Agustina Chouhy, Diego Debat, Humberto Julio Dus Santos, Maria Jose Eberhardt, María Florencia Fay, Fabián Fernandez, Ailen Fernandez, Franco Daniel Fernandez, Paula Del Carmen Fernández Do Porto, Darío Formichelli, Laura Giri, Adriana A. Gismondi, María Ines Goya, Stephanie Irazoqui, Jose Matias Konig, Guido Alberto Lorenzini Campos, Melina Lucero, Horacio Lusso, Silvina Marquez, Nathalie Mojsiejczuk, Laura Mussin, Javier Muñoz Hidalgo, Marianne Graziel Nabaes Jodar, Mercedes Soledad Natale, Mónica Oria, Griselda Pianciola, Luis Pisano, María Belén Posner, Victoria Puebla, Andrea Fabiana Sfalcin, Javier A. Torres, Carolina Viegas, Mariana |
| author_facet | Torres, Carolina Mojsiejczuk, Laura Acuña, Dolores Alexay, Sofía Amadio, Ariel Aulicino, Paula Debat, Humberto Julio Fay, Fabián Fernandez, Franco Daniel Giri, Adriana A. Goya, Stephanie Konig, Guido Alberto Lucero, Horacio Nabaes Jodar, Mercedes Soledad Pianciola, Luis Sfalcin, Javier A. Acevedo, Raúl Maximiliano Bengoa Luoni, Sofía Ailin Bolatti, Elisa M. Brusés, Bettina Cacciabue, Marco Polo Domingo Casal, Pablo E. Cerri, Agustina Chouhy, Diego Dus Santos, Maria Jose Eberhardt, María Florencia Fernandez, Ailen Fernandez, Paula Del Carmen Fernández Do Porto, Darío Formichelli, Laura Gismondi, María Ines Irazoqui, Jose Matias Lorenzini Campos, Melina Lusso, Silvina Marquez, Nathalie Muñoz Hidalgo, Marianne Graziel Mussin, Javier Natale, Mónica Oria, Griselda Pisano, María Belén Posner, Victoria Puebla, Andrea Fabiana Viegas, Mariana |
| author_sort | Torres, Carolina |
| collection | INTA Digital |
| description | The emergence of SARS-CoV-2 variants with concerning characteristics to public health has attracted the attention of the scientific community and governments both regionally and globally since the end of 2020. The most relevant variants described so far include: Alpha (lineage B.1.1.7), first detected in the United Kingdom; Beta (lineage B.1.351), initially detected in South Africa; Gamma (lineage P.1), initially detected in Manaus, Brazil, and Japan; Delta (lineage B.1.627.2), initially detected in India; Lambda (lineage C.37), initially detected in Peru; Mu (lineage B.1.621), first detected in Colombia; Epsilon (lineages B.1.427 and B.1.429), initially detected in California, United States; and Zeta (lineage P.2), first detected in Rio de Janeiro, Brazil (1). Four of these variants (Alpha to Delta) have been defined as variants of concern (VOCs) given their increased transmissibility and other characteristics, while Lambda and Mu have been defined as variants of interest (VOIs). The VOCs have also been associated with an increased risk of hospitalization (2, 3) and, in the case of Beta, Gamma, and Delta, with a moderate to a substantial reduction in neutralizing activity of monoclonal antibodies, convalescent, and vaccine sera (4–6). Gamma and Lambda are particularly relevant for Argentina due to their major presence in the South American region during the time of this study.
Importantly, some of these variants share mutations in the Spike protein—several of them in the receptor-binding domain region—that potentially affect transmissibility, pathogenesis, and/or response to vaccination and immune-based therapies (7, 8).
PAIS is the interinstitutional federal consortium of SARS-CoV-2 genomics in Argentina. It was created by the Ministry of Science and Technology to monitor SARS-CoV-2 diversity and evolution in the country, including surveillance of SARS-CoV-2 variants of public health interest (http://pais.qb.fcen.uba.ar/).
The objective of this work was to implement a SARS-CoV-2 molecular surveillance strategy, in a context of limited resources, which allowed an assessment of the dynamic situation of circulation of viral variants, and at the same time, to perform genomic and evolutionary analyzes to study their origin and dispersion in our country. |
| format | Artículo |
| id | INTA11680 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | INTA116802025-03-07T14:32:56Z Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina Torres, Carolina Mojsiejczuk, Laura Acuña, Dolores Alexay, Sofía Amadio, Ariel Aulicino, Paula Debat, Humberto Julio Fay, Fabián Fernandez, Franco Daniel Giri, Adriana A. Goya, Stephanie Konig, Guido Alberto Lucero, Horacio Nabaes Jodar, Mercedes Soledad Pianciola, Luis Sfalcin, Javier A. Acevedo, Raúl Maximiliano Bengoa Luoni, Sofía Ailin Bolatti, Elisa M. Brusés, Bettina Cacciabue, Marco Polo Domingo Casal, Pablo E. Cerri, Agustina Chouhy, Diego Dus Santos, Maria Jose Eberhardt, María Florencia Fernandez, Ailen Fernandez, Paula Del Carmen Fernández Do Porto, Darío Formichelli, Laura Gismondi, María Ines Irazoqui, Jose Matias Lorenzini Campos, Melina Lusso, Silvina Marquez, Nathalie Muñoz Hidalgo, Marianne Graziel Mussin, Javier Natale, Mónica Oria, Griselda Pisano, María Belén Posner, Victoria Puebla, Andrea Fabiana Viegas, Mariana Severe Acute Respiratory Syndrome Coronavirus 2 Variants South America Surveillance Systems Argentina COVID-19 Coronavirus del Síndrome Respiratorio Agudo Grave 2 Variantes Sistemas de Vigilancia América del Sur SARS-CoV-2 Gamma Lambda Delta Surveillance Spike Sequences The emergence of SARS-CoV-2 variants with concerning characteristics to public health has attracted the attention of the scientific community and governments both regionally and globally since the end of 2020. The most relevant variants described so far include: Alpha (lineage B.1.1.7), first detected in the United Kingdom; Beta (lineage B.1.351), initially detected in South Africa; Gamma (lineage P.1), initially detected in Manaus, Brazil, and Japan; Delta (lineage B.1.627.2), initially detected in India; Lambda (lineage C.37), initially detected in Peru; Mu (lineage B.1.621), first detected in Colombia; Epsilon (lineages B.1.427 and B.1.429), initially detected in California, United States; and Zeta (lineage P.2), first detected in Rio de Janeiro, Brazil (1). Four of these variants (Alpha to Delta) have been defined as variants of concern (VOCs) given their increased transmissibility and other characteristics, while Lambda and Mu have been defined as variants of interest (VOIs). The VOCs have also been associated with an increased risk of hospitalization (2, 3) and, in the case of Beta, Gamma, and Delta, with a moderate to a substantial reduction in neutralizing activity of monoclonal antibodies, convalescent, and vaccine sera (4–6). Gamma and Lambda are particularly relevant for Argentina due to their major presence in the South American region during the time of this study. Importantly, some of these variants share mutations in the Spike protein—several of them in the receptor-binding domain region—that potentially affect transmissibility, pathogenesis, and/or response to vaccination and immune-based therapies (7, 8). PAIS is the interinstitutional federal consortium of SARS-CoV-2 genomics in Argentina. It was created by the Ministry of Science and Technology to monitor SARS-CoV-2 diversity and evolution in the country, including surveillance of SARS-CoV-2 variants of public health interest (http://pais.qb.fcen.uba.ar/). The objective of this work was to implement a SARS-CoV-2 molecular surveillance strategy, in a context of limited resources, which allowed an assessment of the dynamic situation of circulation of viral variants, and at the same time, to perform genomic and evolutionary analyzes to study their origin and dispersion in our country. Instituto de Patología Vegetal Fil: Torres, Carolina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular; Argentina Fil: Torres, Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Mojsiejczuk, Laura. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular; Argentina Fil: Mojsiejczuk, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Acuña, Dolores. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Acuña, Dolores. Hospital de Niños Dr. Ricardo Gutiérrez. Laboratorio de Virología; Argentina Fil: Alexay, Sofía. Hospital de Niños Dr. Ricardo Gutiérrez. Laboratorio de Virología; Argentina Fil: Amadio, Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Amadio, Ariel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela. Instituto de Investigación de la Cadena Láctea; Argentina Fil: Aulicino, Paula. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Aulicino, Paula. Hospital de Pediatría “Prof. Juan P. Garrahan". Laboratorio de Biología Celular y Retrovirus; Argentina Fil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina Fil: Fay, Fabián. CIBIC Laboratorio; Argentina Fil: Fernandez, Franco Daniel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina Fil: Giri, Adriana A. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Giri, Adriana A. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología Molecular y Celular de Rosario. Grupo Virología Humana; Argentina Fil: Goya, Stephanie. Hospital de Niños Dr. Ricardo Gutiérrez. Laboratorio de Virología; Argentina Fil: Konig, Guido Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Investigación Biotecnología; Argentina Fil: Konig, Guido Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Lucero, Horacio. Universidad Nacional del Nordeste. Instituto de Medicina Regional; Argentina Fil: Nabaes Jodar, Mercedes. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Nabaes Jodar, Mercedes. Hospital de Niños Dr. Ricardo Gutiérrez. Laboratorio de Virología; Argentina Fil: Pianciola, Luis. Ministerio de Salud. Laboratorio Central Ciudad de Neuquén; Argentina Fil: Sfalcin, Javier A. CIBIC Laboratorio; Argentina Fil: Acevedo, Raúl M. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Acevedo, Raúl M. Universidad Nacional del Nordeste-CONICET. Instituto de Botánica del Nordeste; Argentina Fil: Bengoa Luoni, Sofía Ailin. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Investigación Biotecnología; Argentina Fil: Bengoa Luoni, Sofia Ailin. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular; Argentina. Fil: Bolatti, Elisa M. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Bolatti, Elisa M. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología Molecular y Celular de Rosario. Grupo Virología Humana; Argentina Fil: Brusés, Bettina. Universidad Nacional del Nordeste. Instituto de Medicina Regional; Argentina Fil: Cacciabue, Marco Polo Domingo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Investigación Biotecnología; Argentina Fil: Cacciabue, Marco Polo Domingo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular; Argentina. Fil: Casal, Pablo E. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología Molecular y Celular de Rosario. Grupo Virología Humana; Argentina Fil: Cerri, Agustina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Cerri, Agustina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología Molecular y Celular de Rosario. Grupo Virología Humana; Argentina Fil: Chouhy, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Chouhy, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología Molecular y Celular de Rosario. Grupo Virología Humana; Argentina Fil: Dus Santos, Maria Jose. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Virología; Argentina Fil: Dus Santos, Maria Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Virología e Innovaciones Tecnológicas; Argentina Fil: Dus Santos, Maria Jose. Universidad Nacional de Hurlingham. Laboratorio de Diagnóstico-UNIDAD COVID; Argentina Fil: Eberhardt, María Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Eberhardt, María Florencia. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela. Instituto de Investigación de la Cadena Láctea; Argentina Fil: Fernandez, Ailen. Ministerio de Salud. Laboratorio Central Ciudad de Neuquén; Argentina Fil: Fernandez, Paula Del Carmen. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Investigación Biotecnología; Argentina Fil: Fernandez, Paula Del Carmen. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular; Argentina. Fil: Fernández Do Porto, Darío. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Fernández Do Porto, Darío. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Cálculo; Argentina Fil: Formichelli, Laura. Universidad Nacional del Nordeste. Instituto de Medicina Regional; Argentina Fil: Gismondi, María Inés. CIBIC Laboratorio; Argentina Fil: Gismondi, María Inés. Universidad Nacional de Luján. Departamento de Ciencias Básicas; Argentina Fil: Irazoqui, Jose Matias. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Irazoqui, Jose Matias. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela. Instituto de Investigación de la Cadena Láctea; Argentina Fil: Lorenzini Campos, Melina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Lorenzini Campos, Melina. Universidad Nacional del Nordeste. Instituto de Medicina Regional; Argentina Fil: Lusso, Silvina. Hospital de Niños Dr. Ricardo Gutiérrez. Laboratorio de Virología; Argentina Fil: Marquez, Nathalie. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina Fil: Muñoz Hidalgo, Marianne Graziel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Investigación Biotecnología. Unidad de Genómica; Argentina Fil: Muñoz Hidalgo, Marianne Graziel. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular; Argentina. Fil: Mussin, Javier. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Mussin, Javier. Universidad Nacional del Nordeste. Instituto de Medicina Regional; Argentina Fil: Natale, Mónica. Hospital de Niños Dr. Ricardo Gutiérrez. Laboratorio de Virología; Argentina Fil: Oria, Griselda. Universidad Nacional del Nordeste. Instituto de Medicina Regional; Argentina Fil: Pisano, María Belén. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Pisano, María Belén. Universidad Nacional de Córdoba(UNC). Facultad de Ciencias Médicas. Instituto de Virología “Dr. J. M. Vanella”; Argentina Fil: Posner, Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Posner, Victoria. Universidad Nacional de Rosario, Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Laboratorio Mixto de Biotecnología Acuática; Argentina Fil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Investigación Biotecnología. Unidad de Genómica; Argentina Fil: Puebla, Andrea Fabiana. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular; Argentina. Fil: Viegas, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Viegas, Mariana. Hospital de Niños Dr. Ricardo Gutiérrez. Laboratorio de Virología; Argentina 2022-04-20T10:58:48Z 2022-04-20T10:58:48Z 2021-12-10 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/11680 https://www.frontiersin.org/articles/10.3389/fmed.2021.755463/full 2296-858X (online) https://doi.org/10.3389/fmed.2021.755463 eng info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf Frontiers Media Frontiers in Medicine 8 : 755463. (Published: 10 December 2021) |
| spellingShingle | Severe Acute Respiratory Syndrome Coronavirus 2 Variants South America Surveillance Systems Argentina COVID-19 Coronavirus del Síndrome Respiratorio Agudo Grave 2 Variantes Sistemas de Vigilancia América del Sur SARS-CoV-2 Gamma Lambda Delta Surveillance Spike Sequences Torres, Carolina Mojsiejczuk, Laura Acuña, Dolores Alexay, Sofía Amadio, Ariel Aulicino, Paula Debat, Humberto Julio Fay, Fabián Fernandez, Franco Daniel Giri, Adriana A. Goya, Stephanie Konig, Guido Alberto Lucero, Horacio Nabaes Jodar, Mercedes Soledad Pianciola, Luis Sfalcin, Javier A. Acevedo, Raúl Maximiliano Bengoa Luoni, Sofía Ailin Bolatti, Elisa M. Brusés, Bettina Cacciabue, Marco Polo Domingo Casal, Pablo E. Cerri, Agustina Chouhy, Diego Dus Santos, Maria Jose Eberhardt, María Florencia Fernandez, Ailen Fernandez, Paula Del Carmen Fernández Do Porto, Darío Formichelli, Laura Gismondi, María Ines Irazoqui, Jose Matias Lorenzini Campos, Melina Lusso, Silvina Marquez, Nathalie Muñoz Hidalgo, Marianne Graziel Mussin, Javier Natale, Mónica Oria, Griselda Pisano, María Belén Posner, Victoria Puebla, Andrea Fabiana Viegas, Mariana Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina |
| title | Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina |
| title_full | Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina |
| title_fullStr | Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina |
| title_full_unstemmed | Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina |
| title_short | Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina |
| title_sort | cost effective method to perform sars cov 2 variant surveillance detection of alpha gamma lambda delta epsilon and zeta in argentina |
| topic | Severe Acute Respiratory Syndrome Coronavirus 2 Variants South America Surveillance Systems Argentina COVID-19 Coronavirus del Síndrome Respiratorio Agudo Grave 2 Variantes Sistemas de Vigilancia América del Sur SARS-CoV-2 Gamma Lambda Delta Surveillance Spike Sequences |
| url | http://hdl.handle.net/20.500.12123/11680 https://www.frontiersin.org/articles/10.3389/fmed.2021.755463/full https://doi.org/10.3389/fmed.2021.755463 |
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