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SARS-CoV-2 Transmission. at <https:\/\/www.cdc.gov\/coronavirus\/2019-ncov\/science\/science-briefs\/sars-cov-2-transmission.html#print> (2021)."},{"key":"ref31","article-title":"Coronavirus Disease (COVID-19): How is it Transmitted","volume-title":"World Health Organization","year":"2021","unstructured":"World Health Organization. Coronavirus Disease (COVID-19): How is it Transmitted? at <https:\/\/www.who.int\/news-room\/q-a-detail\/coronavirus-disease-covid-19-how-is-it-transmitted>. (2021)."},{"key":"ref32","doi-asserted-by":"crossref","first-page":"151137","DOI":"10.1016\/j.scitotenv.2021.151137","type":"journal-article","article-title":"A review on measurements of SARS-CoV-2 genetic material in air in outdoor and indoor environments: Implication for airborne transmission","volume":"809","author":"Dinoi","year":"2022","unstructured":"Dinoi, A. et al. A review on measurements of SARS-CoV-2 genetic material in air in outdoor and indoor environments: Implication for airborne transmission. The Science of the Total Environment. 809, 151137 (2022).","journal-title":"The Science of the Total Environment"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1007\/s12161-010-9161-5","type":"journal-article","article-title":"Analytical methods for virus detection in water and food","volume":"4","author":"Bosch","year":"2011","unstructured":"Bosch, A. et al. Analytical methods for virus detection in water and food. 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(2022)."},{"issue":"16","key":"ref42","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","type":"journal-article","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","unstructured":"Li, H. et al. The sequence alignment\/map format and SAMtools. Bioinformatics. 25 (16), 2078-2079 (2009).","journal-title":"Bioinformatics"},{"key":"ref43","volume-title":"Freyja","year":"2022","unstructured":"Freyja. at <https:\/\/github.com\/andersen-lab\/Freyja>. (2022)."},{"issue":"21","key":"ref44","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","type":"journal-article","article-title":"A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data","volume":"27","author":"Li","year":"2011","unstructured":"Li, H. 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Journal of Virological Methods. 284, 113926 (2020).","journal-title":"Journal of Virological Methods"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"138764","DOI":"10.1016\/j.scitotenv.2020.138764","type":"journal-article","article-title":"First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community","volume":"728","author":"Ahmed","year":"2020","unstructured":"Ahmed, W. et al. First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community. 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SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases. mSystems. 5 (4), e00614-20 (2020).","journal-title":"mSystems"},{"issue":"50","key":"ref59","first-page":"2000776","type":"journal-article","article-title":"Evaluation of lockdown effect on SARS-CoV-2 dynamics through viral genome quantification in waste water, Greater Paris, France, 5 March to 23 April 2020","volume":"25","author":"Wurtzer","year":"2020","unstructured":"Wurtzer, S. et al. Evaluation of lockdown effect on SARS-CoV-2 dynamics through viral genome quantification in waste water, Greater Paris, France, 5 March to 23 April 2020. European Communicable Disease Bulletin. 25 (50), 2000776 (2020).","journal-title":"European Communicable Disease Bulletin"},{"key":"ref60","volume-title":"VATar COVID-19 | Caso de Exito - Ministerio para la Transici\u00f3n Ecologica y el Reto Demografico","year":"2022","unstructured":"VATar COVID-19 | Caso de \u00c9xito - Ministerio para la Transici\u00f3n Ecol\u00f3gica y el Reto Demogr\u00e1fico. at <https:\/\/www.esri.es\/es-es\/descubre-los-gis\/casos-de-exito\/administracion-\/vatar-covod19-miteco-cs>. (2023)."},{"issue":"6","key":"ref61","doi-asserted-by":"crossref","first-page":"100098","DOI":"10.1016\/j.xcrm.2020.100098","type":"journal-article","article-title":"Temporal detection and phylogenetic assessment of SARS-CoV-2 in municipal wastewater","volume":"1","author":"Nemudryi","year":"2020","unstructured":"Nemudryi, A. et al. Temporal detection and phylogenetic assessment of SARS-CoV-2 in municipal wastewater. Cell Reports. Medicine. 1 (6), 100098 (2020).","journal-title":"Cell Reports. Medicine"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"100202","DOI":"10.1016\/j.lanepe.2021.100202","type":"journal-article","article-title":"Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing","volume":"10","author":"Rios","year":"2021","unstructured":"Rios, G. et al. Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing. The Lancet Regional Health. Europe. 10, 100202 (2021).","journal-title":"The Lancet Regional Health. Europe"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"1574","DOI":"10.3390\/ijerph20021574","type":"journal-article","article-title":"Environmental dissemination of SARS-CoV-2 in a University Hospital during the COVID-19 5th wave Delta variant peak in Castile-Le\u00f3n, Spain","volume":"20","author":"Gomes da Silva","year":"2023","unstructured":"Gomes da Silva, P. et al. Environmental dissemination of SARS-CoV-2 in a University Hospital during the COVID-19 5th wave Delta variant peak in Castile-Le\u00f3n, Spain. International Journal of Environmental Research and Public Health. 20 (2), 1574 (2023).","journal-title":"International Journal of Environmental Research and Public Health"},{"key":"ref64","type":"book","volume-title":"Exposure assessment of SARS-CoV-2 and Nov GII\/GII in aerosols generated by a municipal wastewater treatment plant","author":"Gon\u00e7alves","year":"2022","unstructured":"Gon\u00e7alves, J. et al. Exposure assessment of SARS-CoV-2 and Nov GII\/GII in aerosols generated by a municipal wastewater treatment plant. (2022)."},{"key":"ref65","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1016\/j.ijid.2021.04.063","type":"journal-article","article-title":"Isolation of SARS-CoV-2 from the air in a car driven by a COVID patient with mild illness","volume":"108","author":"Lednicky","year":"2021","unstructured":"Lednicky, J. 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