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...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2023-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0284483 |
| _version_ | 1797829894873284608 |
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| author | Florencia Cancela Natalia Ramos Davida S Smyth Claudia Etchebehere Mabel Berois Jesica Rodríguez Caterina Rufo Alicia Alemán Liliana Borzacconi Julieta López Elizabeth González Germán Botto Starla G Thornhill Santiago Mirazo Mónica Trujillo |
| author_facet | Florencia Cancela Natalia Ramos Davida S Smyth Claudia Etchebehere Mabel Berois Jesica Rodríguez Caterina Rufo Alicia Alemán Liliana Borzacconi Julieta López Elizabeth González Germán Botto Starla G Thornhill Santiago Mirazo Mónica Trujillo |
| author_sort | Florencia Cancela |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-09T13:28:37Z |
| format | Article |
| id | doaj.art-7573a597287f436281519d1ce511afa1 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-09T13:28:37Z |
| publishDate | 2023-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-7573a597287f436281519d1ce511afa12023-05-10T05:31:43ZengPublic Library of Science (PLoS)PLoS ONE1932-62032023-01-01184e028448310.1371/journal.pone.0284483Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing.Florencia CancelaNatalia RamosDavida S SmythClaudia EtchebehereMabel BeroisJesica RodríguezCaterina RufoAlicia AlemánLiliana BorzacconiJulieta LópezElizabeth GonzálezGermán BottoStarla G ThornhillSantiago MirazoMónica TrujilloSARS-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.https://doi.org/10.1371/journal.pone.0284483 |
| spellingShingle | Florencia Cancela Natalia Ramos Davida S Smyth Claudia Etchebehere Mabel Berois Jesica Rodríguez Caterina Rufo Alicia Alemán Liliana Borzacconi Julieta López Elizabeth González Germán Botto Starla G Thornhill Santiago Mirazo Mónica Trujillo Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing. PLoS ONE |
| 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 |
| url | https://doi.org/10.1371/journal.pone.0284483 |
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