Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing
SARS-CoV-2 surveillance of viral populations in wastewater samples is recognized as a useful tool for monitoring epidemic waves and boosting health preparedness. Next generation sequencing of viral RNA isolated from wastewater is a convenient and cost-effective strategy to understand the molecular e...
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| Médium: | article |
| Jazyk: | angličtina |
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2023
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| On-line přístup: | https://hdl.handle.net/20.500.12008/42513 |
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| _version_ | 1868890048282230784 |
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| author | Cancela, Florencia |
| author2 | Ramos, Natalia Smyth, Davida S Etchebehere, Claudia Berois, Mabel Rodríguez, Jesica Rufo, Caterina Alemán, Alicia Borzacconi, Liliana López, Julieta González, Elizabeth Botto, Germán Thornhill, Starla G Mirazo, Santiago Trujillo, Mónica |
| author2_role | author author author author author author author author author author author author author author |
| author_browse | Alemán, Alicia Berois, Mabel Borzacconi, Liliana Botto, Germán Cancela, Florencia Etchebehere, Claudia González, Elizabeth López, Julieta Mirazo, Santiago Ramos, Natalia Rodríguez, Jesica Rufo, Caterina Smyth, Davida S Thornhill, Starla G Trujillo, Mónica |
| author_facet | Cancela, Florencia Ramos, Natalia Smyth, Davida S Etchebehere, Claudia Berois, Mabel Rodríguez, Jesica Rufo, Caterina Alemán, Alicia Borzacconi, Liliana López, Julieta González, Elizabeth Botto, Germán Thornhill, Starla G Mirazo, Santiago Trujillo, Mónica |
| author_role | author |
| collection | COLIBRI |
| dc.contributor.none.fl_str_mv | Cancela Florencia, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Química Biológica Ramos Natalia, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Química Biológica Smyth Davida S, Texas A&M University-San Antonio (Estados Unidos). Department of Life Sciences Etchebehere Claudia, Ministerio de Educación y Cultura (Uruguay). Instituto de Investigaciones Biológicas Clemente Estable. Departamento de Bioquímica y Genómica Microbiana Berois Mabel, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Química Biológica Rodríguez Jesica, Universidad de la República (Uruguay). Facultad de Química. Polo Tecnológico de Pando. Laboratorio de Alimentos y Nutrición Rufo Caterina, Universidad de la República (Uruguay). Facultad de Química. Polo Tecnológico de Pando. Laboratorio de Alimentos y Nutrición Alemán Alicia, Universidad de la República (Uruguay). Facultad de Medicina. Instituto de Higiene. Unidad Académica de Medicina Preventiva Borzacconi Liliana, Universidad de la República (Uruguay). Facultad de Ingeniería. Instituto de Ingeniería Química López Julieta, Universidad de la República (Uruguay). Facultad de Ingeniería. Departamento de Ingeniería Ambiental González Elizabeth, Universidad de la República (Uruguay). Facultad de Ingeniería. Departamento de Ingeniería Ambiental Botto Germán, Universidad de la República (Uruguay). Facultad de Medicina. Departamento de Métodos Cuantitativos Thornhill Starla G, Texas A&M University-San Antonio (Estados Unidos). Department of Life Sciences Mirazo Santiago, Universidad de la República (Uruguay). Facultad de Medicina. Instituto de Higiene. Unidad Académica de Bacteriología y Virología Trujillo Mónica, Queensborough Community College of The City University of New York (Estados Unidos). Department of Biological Sciences and Geology |
| dc.creator.none.fl_str_mv | Cancela, Florencia Ramos, Natalia Smyth, Davida S Etchebehere, Claudia Berois, Mabel Rodríguez, Jesica Rufo, Caterina Alemán, Alicia Borzacconi, Liliana López, Julieta González, Elizabeth Botto, Germán Thornhill, Starla G Mirazo, Santiago Trujillo, Mónica |
| dc.date.none.fl_str_mv | 2023 2024-02-20T12:23:56Z 2024-02-20T12:23:56Z |
| dc.format.none.fl_str_mv | application/pdf |
| dc.identifier.none.fl_str_mv | CANCELA, F., RAMOS, N., SMYTH, DS., y otros. Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing. PLoS One [en línea] 18, 2023. DOI: 10.1371/journal.pone.0284483 https://hdl.handle.net/20.500.12008/42513 10.1371/journal.pone.0284483 |
| dc.language.none.fl_str_mv | en eng |
| dc.relation.none.fl_str_mv | PLoS One. 18, 2023 |
| dc.rights.none.fl_str_mv | info:eu-repo/semantics/openAccess Licencia Creative Commons Atribución (CC - By 4.0) |
| dc.source.none.fl_str_mv | reponame:COLIBRI instname:Universidad de la República instacron:Universidad de la República |
| dc.subject.none.fl_str_mv | Aguas Residuales SARS-CoV-2 |
| dc.title.none.fl_str_mv | Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing |
| dc.type.none.fl_str_mv | Artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
| description | SARS-CoV-2 surveillance of viral populations in wastewater samples is recognized as a useful tool for monitoring epidemic waves and boosting health preparedness. Next generation sequencing of viral RNA isolated from wastewater is a convenient and cost-effective strategy to understand the molecular epidemiology of SARS-CoV-2 and provide insights on the population dynamics of viral variants at the community level. However, in low- and middle-income countries, isolated groups have performed wastewater monitoring and data has not been extensively shared in the scientific community. Here we report the results of monitoring the co-circulation and abundance of variants of concern (VOCs) of SARS-CoV-2 in Uruguay, a small country in Latin America, between November 2020—July 2021 using wastewater surveillance. RNA isolated from wastewater was characterized by targeted sequencing of the Receptor Binding Domain region within the spike gene. Two computational approaches were used to track the viral variants. The results of the wastewater analysis showed the transition in the overall predominance of viral variants in wastewater from No-VOCs to successive VOCs, in agreement with clinical surveillance from sequencing of nasal swabs. The mutations K417T, E484K and N501Y, that characterize the Gamma VOC, were detected as early as December 2020, several weeks before the first clinical case was reported. Interestingly, a non-synonymous mutation described in the Delta VOC, L452R, was detected at a very low frequency since April 2021 when using a recently described sequence analysis tool (SAM Refiner). Wastewater NGS-based surveillance of SARS-CoV-2 is a reliable and complementary tool for monitoring the introduction and prevalence of VOCs at a community level allowing early public health decisions. This approach allows the tracking of symptomatic and asymptomatic individuals, who are generally under-reported in countries with limited clinical testing capacity. Our results suggests that wastewater-based epidemiology can contribute to improving public health responses in low- and middle-income countries. |
| eu_rights_str_mv | openAccess |
| format | article |
| id | anni_4feaebc8c8464b033abbd193402cb9e9 |
| identifier_str_mv | CANCELA, F., RAMOS, N., SMYTH, DS., y otros. Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing. PLoS One [en línea] 18, 2023. DOI: 10.1371/journal.pone.0284483 10.1371/journal.pone.0284483 |
| instacron_str | Universidad de la República |
| institution | Universidad de la República |
| instname_str | Universidad de la República |
| language | eng |
| language_invalid_str_mv | en |
| network_acronym_str | anni |
| network_name_str | oai-lr-anni |
| oai_identifier_str | oai:colibri.udelar.edu.uy:20.500.12008/42513 |
| publishDate | 2023 |
| publishDateSort | 2023 |
| reponame_str | COLIBRI |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | Licencia Creative Commons Atribución (CC - By 4.0) |
| spelling | Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencingCancela, FlorenciaRamos, NataliaSmyth, Davida SEtchebehere, ClaudiaBerois, MabelRodríguez, JesicaRufo, CaterinaAlemán, AliciaBorzacconi, LilianaLópez, JulietaGonzález, ElizabethBotto, GermánThornhill, Starla GMirazo, SantiagoTrujillo, MónicaAguas ResidualesSARS-CoV-2SARS-CoV-2 surveillance of viral populations in wastewater samples is recognized as a useful tool for monitoring epidemic waves and boosting health preparedness. Next generation sequencing of viral RNA isolated from wastewater is a convenient and cost-effective strategy to understand the molecular epidemiology of SARS-CoV-2 and provide insights on the population dynamics of viral variants at the community level. However, in low- and middle-income countries, isolated groups have performed wastewater monitoring and data has not been extensively shared in the scientific community. Here we report the results of monitoring the co-circulation and abundance of variants of concern (VOCs) of SARS-CoV-2 in Uruguay, a small country in Latin America, between November 2020—July 2021 using wastewater surveillance. RNA isolated from wastewater was characterized by targeted sequencing of the Receptor Binding Domain region within the spike gene. Two computational approaches were used to track the viral variants. The results of the wastewater analysis showed the transition in the overall predominance of viral variants in wastewater from No-VOCs to successive VOCs, in agreement with clinical surveillance from sequencing of nasal swabs. The mutations K417T, E484K and N501Y, that characterize the Gamma VOC, were detected as early as December 2020, several weeks before the first clinical case was reported. Interestingly, a non-synonymous mutation described in the Delta VOC, L452R, was detected at a very low frequency since April 2021 when using a recently described sequence analysis tool (SAM Refiner). Wastewater NGS-based surveillance of SARS-CoV-2 is a reliable and complementary tool for monitoring the introduction and prevalence of VOCs at a community level allowing early public health decisions. This approach allows the tracking of symptomatic and asymptomatic individuals, who are generally under-reported in countries with limited clinical testing capacity. Our results suggests that wastewater-based epidemiology can contribute to improving public health responses in low- and middle-income countries.Cancela Florencia, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Química BiológicaRamos Natalia, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Química BiológicaSmyth Davida S, Texas A&M University-San Antonio (Estados Unidos). Department of Life SciencesEtchebehere Claudia, Ministerio de Educación y Cultura (Uruguay). Instituto de Investigaciones Biológicas Clemente Estable. Departamento de Bioquímica y Genómica MicrobianaBerois Mabel, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Química BiológicaRodríguez Jesica, Universidad de la República (Uruguay). Facultad de Química. Polo Tecnológico de Pando. Laboratorio de Alimentos y NutriciónRufo Caterina, Universidad de la República (Uruguay). Facultad de Química. Polo Tecnológico de Pando. Laboratorio de Alimentos y NutriciónAlemán Alicia, Universidad de la República (Uruguay). Facultad de Medicina. Instituto de Higiene. Unidad Académica de Medicina PreventivaBorzacconi Liliana, Universidad de la República (Uruguay). Facultad de Ingeniería. Instituto de Ingeniería QuímicaLópez Julieta, Universidad de la República (Uruguay). Facultad de Ingeniería. Departamento de Ingeniería AmbientalGonzález Elizabeth, Universidad de la República (Uruguay). Facultad de Ingeniería. Departamento de Ingeniería AmbientalBotto Germán, Universidad de la República (Uruguay). Facultad de Medicina. Departamento de Métodos CuantitativosThornhill Starla G, Texas A&M University-San Antonio (Estados Unidos). Department of Life SciencesMirazo Santiago, Universidad de la República (Uruguay). Facultad de Medicina. Instituto de Higiene. Unidad Académica de Bacteriología y VirologíaTrujillo Mónica, Queensborough Community College of The City University of New York (Estados Unidos). Department of Biological Sciences and Geology2024-02-20T12:23:56Z2024-02-20T12:23:56Z2023Artículoinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfCANCELA, F., RAMOS, N., SMYTH, DS., y otros. Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing. PLoS One [en línea] 18, 2023. DOI: 10.1371/journal.pone.0284483https://hdl.handle.net/20.500.12008/4251310.1371/journal.pone.0284483reponame:COLIBRIinstname:Universidad de la Repúblicainstacron:Universidad de la RepúblicaenengPLoS One. 18, 2023Las obras depositadas en el Repositorio se rigen por la Ordenanza de los Derechos de la Propiedad Intelectual de la Universidad de la República.(Res. Nº 91 de C.D.C. de 8/III/1994 – D.O. 7/IV/1994) y por la Ordenanza del Repositorio Abierto de la Universidad de la República (Res. Nº 16 de C.D.C. de 07/10/2014)info:eu-repo/semantics/openAccessLicencia Creative Commons Atribución (CC - By 4.0)oai:colibri.udelar.edu.uy:20.500.12008/425132026-04-14T10:36:57Z |
| spellingShingle | Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing Cancela, Florencia Aguas Residuales SARS-CoV-2 |
| status_str | publishedVersion |
| title | Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing |
| title_full | Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing |
| title_fullStr | Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing |
| title_full_unstemmed | Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing |
| title_short | Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing |
| title_sort | Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing |
| topic | Aguas Residuales SARS-CoV-2 |
| url | https://hdl.handle.net/20.500.12008/42513 |