Evaluation of low-cost SARS-CoV-2 RNA purification methods for viral quantification by RT-qPCR and next-generation sequencing analysis: Implications for wider wastewater-based epidemiology adoption
Wastewater: Based Epidemiology (WBE) consists of quantifying biomarkers in sewerage systems to derive real-time information on the health and/or lifestyle of the contributing population. WBE usefulness was vastly demonstrated in the context of the COVID-19 pandemic. Many methods for SARS-CoV-2 RNA d...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2023-06-01
|
| Series: | Heliyon |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405844023033376 |
| _version_ | 1797819923632750592 |
|---|---|
| author | Alonso Reyes-Calderón Elías Mindreau-Ganoza Braulio Pardo-Figueroa Katherine R. Garcia-Luquillas Sonia P. Yufra Pedro E. Romero Claudia Antonini Jose-Miguel Renom Cesar R. Mota Monica C. Santa-Maria |
| author_facet | Alonso Reyes-Calderón Elías Mindreau-Ganoza Braulio Pardo-Figueroa Katherine R. Garcia-Luquillas Sonia P. Yufra Pedro E. Romero Claudia Antonini Jose-Miguel Renom Cesar R. Mota Monica C. Santa-Maria |
| author_sort | Alonso Reyes-Calderón |
| collection | DOAJ |
| description | Wastewater: Based Epidemiology (WBE) consists of quantifying biomarkers in sewerage systems to derive real-time information on the health and/or lifestyle of the contributing population. WBE usefulness was vastly demonstrated in the context of the COVID-19 pandemic. Many methods for SARS-CoV-2 RNA determination in wastewater were devised, which vary in cost, infrastructure requirements and sensitivity. For most developing countries, implementing WBE for viral outbreaks, such as that of SARS-CoV-2, proved challenging due to budget, reagent availability and infrastructure constraints. In this study, we assessed low-cost methods for SARS-CoV-2 RNA quantification by RT-qPCR, and performed variant identification by NGS in wastewater samples. Results showed that the effect of adjusting pH to 4 and/or adding MgCl2 (25 mM) was negligible when using the adsorption-elution method, as well as basal physicochemical parameters in the sample. In addition, results supported the standardized use of linear rather than plasmid DNA for a more accurate viral RT-qPCR estimation. The modified TRIzol-based purification method in this study yielded comparable RT-qPCR estimation to a column-based approach, but provided better NGS results, suggesting that column-based purification for viral analysis should be revised. Overall, this work provides evaluation of a robust, sensitive and cost-effective method for SARS-CoV-2 RNA analysis that could be implemented for other viruses, for a wider WEB adoption. |
| first_indexed | 2024-03-13T09:29:45Z |
| format | Article |
| id | doaj.art-f5354d199d41490b8812013469e4ee7c |
| institution | Directory Open Access Journal |
| issn | 2405-8440 |
| language | English |
| last_indexed | 2024-03-13T09:29:45Z |
| publishDate | 2023-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Heliyon |
| spelling | doaj.art-f5354d199d41490b8812013469e4ee7c2023-05-26T04:21:45ZengElsevierHeliyon2405-84402023-06-0196e16130Evaluation of low-cost SARS-CoV-2 RNA purification methods for viral quantification by RT-qPCR and next-generation sequencing analysis: Implications for wider wastewater-based epidemiology adoptionAlonso Reyes-Calderón0Elías Mindreau-Ganoza1Braulio Pardo-Figueroa2Katherine R. Garcia-Luquillas3Sonia P. Yufra4Pedro E. Romero5Claudia Antonini6Jose-Miguel Renom7Cesar R. Mota8Monica C. Santa-Maria9Centro de Investigación y Tecnología del Agua - CITA, Universidad de Ingenieria y Tecnologia – UTEC, Jr. Medrano Silva 165, Lima, 15063, PeruFacultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Germán Amézaga s/n, Lima, 15081, PeruCentro de Investigación y Tecnología del Agua - CITA, Universidad de Ingenieria y Tecnologia – UTEC, Jr. Medrano Silva 165, Lima, 15063, PeruCentro de Investigación y Tecnología del Agua - CITA, Universidad de Ingenieria y Tecnologia – UTEC, Jr. Medrano Silva 165, Lima, 15063, PeruDepartamento de Ingeniería Metalúrgica e Ingeniería Ambiental, Universidad Nacional de San Agustín, Av. Independencia s/n, Arequipa, 04001, PeruFacultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Germán Amézaga s/n, Lima, 15081, PeruDepartamento de Ingeniería Industrial, Universidad de Ingenieria y Tecnologia - UTEC, Jr. Medrano Silva 165, Lima, 15063, PeruDepartamento de Ciencias, Universidad de Ingenieria y Tecnologia - UTEC, Jr. Medrano Silva 165, Lima, 15063, PeruDepartamento de Engenharia Sanitária e Ambiental, Escola de Engenharia, Universidade Federal de Minas Gerais (UFMG), Av. Antonio Carlos, Belo Horizonte, 6.627, 31270-901, BrazilCentro de Investigación y Tecnología del Agua - CITA, Universidad de Ingenieria y Tecnologia – UTEC, Jr. Medrano Silva 165, Lima, 15063, Peru; Corresponding author. Jr. Medrano Silva 165, Lima, 15063, Peru.Wastewater: Based Epidemiology (WBE) consists of quantifying biomarkers in sewerage systems to derive real-time information on the health and/or lifestyle of the contributing population. WBE usefulness was vastly demonstrated in the context of the COVID-19 pandemic. Many methods for SARS-CoV-2 RNA determination in wastewater were devised, which vary in cost, infrastructure requirements and sensitivity. For most developing countries, implementing WBE for viral outbreaks, such as that of SARS-CoV-2, proved challenging due to budget, reagent availability and infrastructure constraints. In this study, we assessed low-cost methods for SARS-CoV-2 RNA quantification by RT-qPCR, and performed variant identification by NGS in wastewater samples. Results showed that the effect of adjusting pH to 4 and/or adding MgCl2 (25 mM) was negligible when using the adsorption-elution method, as well as basal physicochemical parameters in the sample. In addition, results supported the standardized use of linear rather than plasmid DNA for a more accurate viral RT-qPCR estimation. The modified TRIzol-based purification method in this study yielded comparable RT-qPCR estimation to a column-based approach, but provided better NGS results, suggesting that column-based purification for viral analysis should be revised. Overall, this work provides evaluation of a robust, sensitive and cost-effective method for SARS-CoV-2 RNA analysis that could be implemented for other viruses, for a wider WEB adoption.http://www.sciencedirect.com/science/article/pii/S2405844023033376Wastewater-based epidemiologySARS-CoV-2COVID-19Virus quantificationViral genomic surveillanceRNA purification |
| spellingShingle | Alonso Reyes-Calderón Elías Mindreau-Ganoza Braulio Pardo-Figueroa Katherine R. Garcia-Luquillas Sonia P. Yufra Pedro E. Romero Claudia Antonini Jose-Miguel Renom Cesar R. Mota Monica C. Santa-Maria Evaluation of low-cost SARS-CoV-2 RNA purification methods for viral quantification by RT-qPCR and next-generation sequencing analysis: Implications for wider wastewater-based epidemiology adoption Heliyon Wastewater-based epidemiology SARS-CoV-2 COVID-19 Virus quantification Viral genomic surveillance RNA purification |
| title | Evaluation of low-cost SARS-CoV-2 RNA purification methods for viral quantification by RT-qPCR and next-generation sequencing analysis: Implications for wider wastewater-based epidemiology adoption |
| title_full | Evaluation of low-cost SARS-CoV-2 RNA purification methods for viral quantification by RT-qPCR and next-generation sequencing analysis: Implications for wider wastewater-based epidemiology adoption |
| title_fullStr | Evaluation of low-cost SARS-CoV-2 RNA purification methods for viral quantification by RT-qPCR and next-generation sequencing analysis: Implications for wider wastewater-based epidemiology adoption |
| title_full_unstemmed | Evaluation of low-cost SARS-CoV-2 RNA purification methods for viral quantification by RT-qPCR and next-generation sequencing analysis: Implications for wider wastewater-based epidemiology adoption |
| title_short | Evaluation of low-cost SARS-CoV-2 RNA purification methods for viral quantification by RT-qPCR and next-generation sequencing analysis: Implications for wider wastewater-based epidemiology adoption |
| title_sort | evaluation of low cost sars cov 2 rna purification methods for viral quantification by rt qpcr and next generation sequencing analysis implications for wider wastewater based epidemiology adoption |
| topic | Wastewater-based epidemiology SARS-CoV-2 COVID-19 Virus quantification Viral genomic surveillance RNA purification |
| url | http://www.sciencedirect.com/science/article/pii/S2405844023033376 |
| work_keys_str_mv | AT alonsoreyescalderon evaluationoflowcostsarscov2rnapurificationmethodsforviralquantificationbyrtqpcrandnextgenerationsequencinganalysisimplicationsforwiderwastewaterbasedepidemiologyadoption AT eliasmindreauganoza evaluationoflowcostsarscov2rnapurificationmethodsforviralquantificationbyrtqpcrandnextgenerationsequencinganalysisimplicationsforwiderwastewaterbasedepidemiologyadoption AT brauliopardofigueroa evaluationoflowcostsarscov2rnapurificationmethodsforviralquantificationbyrtqpcrandnextgenerationsequencinganalysisimplicationsforwiderwastewaterbasedepidemiologyadoption AT katherinergarcialuquillas evaluationoflowcostsarscov2rnapurificationmethodsforviralquantificationbyrtqpcrandnextgenerationsequencinganalysisimplicationsforwiderwastewaterbasedepidemiologyadoption AT soniapyufra evaluationoflowcostsarscov2rnapurificationmethodsforviralquantificationbyrtqpcrandnextgenerationsequencinganalysisimplicationsforwiderwastewaterbasedepidemiologyadoption AT pedroeromero evaluationoflowcostsarscov2rnapurificationmethodsforviralquantificationbyrtqpcrandnextgenerationsequencinganalysisimplicationsforwiderwastewaterbasedepidemiologyadoption AT claudiaantonini evaluationoflowcostsarscov2rnapurificationmethodsforviralquantificationbyrtqpcrandnextgenerationsequencinganalysisimplicationsforwiderwastewaterbasedepidemiologyadoption AT josemiguelrenom evaluationoflowcostsarscov2rnapurificationmethodsforviralquantificationbyrtqpcrandnextgenerationsequencinganalysisimplicationsforwiderwastewaterbasedepidemiologyadoption AT cesarrmota evaluationoflowcostsarscov2rnapurificationmethodsforviralquantificationbyrtqpcrandnextgenerationsequencinganalysisimplicationsforwiderwastewaterbasedepidemiologyadoption AT monicacsantamaria evaluationoflowcostsarscov2rnapurificationmethodsforviralquantificationbyrtqpcrandnextgenerationsequencinganalysisimplicationsforwiderwastewaterbasedepidemiologyadoption |