<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Avgeris, M.</style></author><author><style face="normal" font="default" size="100%">Adamopoulos, P.G.</style></author><author><style face="normal" font="default" size="100%">Galani, A.</style></author><author><style face="normal" font="default" size="100%">Xagorari, M.</style></author><author><style face="normal" font="default" size="100%">Gourgiotis, D.</style></author><author><style face="normal" font="default" size="100%">Trougakos, I.P.</style></author><author><style face="normal" font="default" size="100%">Voulgaris, N.</style></author><author><style face="normal" font="default" size="100%">Dimopoulos, M.A.</style></author><author><style face="normal" font="default" size="100%">Thomaidis, N.S.</style></author><author><style face="normal" font="default" size="100%">Scorilas, A.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater</style></title><secondary-title><style face="normal" font="default" size="100%">Int J Mol Sci</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">*COVID-19/epidemiology/virology</style></keyword><keyword><style  face="normal" font="default" size="100%">*Pandemics</style></keyword><keyword><style  face="normal" font="default" size="100%">2019-nCov</style></keyword><keyword><style  face="normal" font="default" size="100%">231-0004089064) and on 22 March 2021 to the Patent Cooperation Treaty (PCT</style></keyword><keyword><style  face="normal" font="default" size="100%">application number PCT/EP2021/057316). All other authors declare no competing</style></keyword><keyword><style  face="normal" font="default" size="100%">Covid-19</style></keyword><keyword><style  face="normal" font="default" size="100%">D614g</style></keyword><keyword><style  face="normal" font="default" size="100%">Environmental Monitoring/methods</style></keyword><keyword><style  face="normal" font="default" size="100%">February 2021 to the Hellenic Industrial Property Organisation (case number</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">interests.</style></keyword><keyword><style  face="normal" font="default" size="100%">nested PCR</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA virus in an environmental sample</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Viral/*isolation &amp; purification</style></keyword><keyword><style  face="normal" font="default" size="100%">SARS-CoV-2 mutations</style></keyword><keyword><style  face="normal" font="default" size="100%">SARS-CoV-2 NGS</style></keyword><keyword><style  face="normal" font="default" size="100%">SARS-CoV-2 sequencing</style></keyword><keyword><style  face="normal" font="default" size="100%">SARS-CoV-2/*isolation &amp; purification</style></keyword><keyword><style  face="normal" font="default" size="100%">Sewage</style></keyword><keyword><style  face="normal" font="default" size="100%">spike protein</style></keyword><keyword><style  face="normal" font="default" size="100%">University of Athens, and the authors M.A., P.G.A., N.V., N.S.T. and A.S. on 11</style></keyword><keyword><style  face="normal" font="default" size="100%">wastewater-based epidemiology</style></keyword><keyword><style  face="normal" font="default" size="100%">Wastewater/*virology</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">Aug 7</style></date></pub-dates></dates><number><style face="normal" font="default" size="100%">16</style></number><volume><style face="normal" font="default" size="100%">22</style></volume><isbn><style face="normal" font="default" size="100%">1422-0067 (Electronic)1422-0067 (Linking)</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Considering the lack of effective treatments against COVID-19, wastewater-based epidemiology (WBE) is emerging as a cost-effective approach for real-time population-wide SARS-CoV-2 monitoring. Here, we report novel molecular assays for sensitive detection and mutational/variant analysis of SARS-CoV-2 in wastewater. Highly stable regions of SARS-CoV-2 RNA were identified by RNA stability analysis and targeted for the development of novel nested PCR assays. Targeted DNA sequencing (DNA-seq) was applied for the analysis and quantification of SARS-CoV-2 mutations/variants, following hexamers-based reverse transcription and nested PCR-based amplification of targeted regions. Three-dimensional (3D) structure models were generated to examine the predicted structural modification caused by genomic variants. WBE of SARS-CoV-2 revealed to be assay dependent, and significantly improved sensitivity achieved by assay combination (94%) vs. single-assay screening (30%-60%). Targeted DNA-seq allowed the quantification of SARS-CoV-2 mutations/variants in wastewater, which agreed with COVID-19 patients' sequencing data. A mutational analysis indicated the prevalence of D614G (S) and P323L (RdRP) variants, as well as of the Beta.1.1.7/alpha variant of concern, in agreement with the frequency of Beta.1.1.7/alpha variant in clinical samples of the same period of the third pandemic wave at the national level. Our assays provide an innovative cost-effective platform for real-time monitoring and early-identification of SARS-CoV-2 variants at community/population levels.</style></abstract><accession-num><style face="normal" font="default" size="100%">34445204</style></accession-num><notes><style face="normal" font="default" size="100%">Avgeris, MargaritisAdamopoulos, Panagiotis GGalani, AikateriniXagorari, MarietaGourgiotis, DimitriosTrougakos, Ioannis PVoulgaris, NikolaosDimopoulos, Meletios-AthanasiosThomaidis, Nikolaos SScorilas, Andreaseng16689/Special Account for Research Grants of the National and Kapodistrian University of Athens/Switzerland2021/08/28 06:00Int J Mol Sci. 2021 Aug 7;22(16):8498. doi: 10.3390/ijms22168498.</style></notes><custom2><style face="normal" font="default" size="100%">PMC8395163</style></custom2><auth-address><style face="normal" font="default" size="100%">Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15771 Athens, Greece.Laboratory of Clinical Biochemistry and Molecular Diagnostics, Second Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, &quot;P. &amp; A. Kyriakou&quot; Children's Hospital, 11527 Athens, Greece.Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece.Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, 15771 Athens, Greece.Division of Geophysics &amp; Geothermics, Department of Geology &amp; Geoenvironment, National and Kapodistrian University of Athens, 15771 Athens, Greece.Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, 11528 Athens, Greece.</style></auth-address></record></records></xml>