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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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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10121012/
https://www.ncbi.nlm.nih.gov/pubmed/37083889
http://dx.doi.org/10.1371/journal.pone.0284483
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author 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_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_sort Cancela, Florencia
collection PubMed
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.
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spelling pubmed-101210122023-04-22 Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing 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 PLoS One Research Article 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. Public Library of Science 2023-04-21 /pmc/articles/PMC10121012/ /pubmed/37083889 http://dx.doi.org/10.1371/journal.pone.0284483 Text en © 2023 Cancela et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
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
Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing
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 Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10121012/
https://www.ncbi.nlm.nih.gov/pubmed/37083889
http://dx.doi.org/10.1371/journal.pone.0284483
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