Τίτλος:
Novel nested-seq approach for SARS-CoV-2 real-time epidemiology and in-depth mutational profiling in wastewater
Γλώσσες Τεκμηρίου:
Αγγλικά
Περίληψη:
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 B.1.1.7/alpha variant of concern, in agreement with the frequency of B.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. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.
Συγγραφείς:
Avgeris, M.
Adamopoulos, P.G.
Galani, A.
Xagorari, M.
Gourgiotis, D.
Trougakos, I.P.
Voulgaris, N.
Dimopoulos, M.-A.
Thomaidis, N.S.
Scorilas, A.
Περιοδικό:
International Journal of Molecular Sciences
Λέξεις-κλειδιά:
virus RNA, environmental monitoring; epidemiology; human; isolation and purification; pandemic; procedures; virology; wastewater, COVID-19; Environmental Monitoring; Humans; Pandemics; RNA, Viral; SARS-CoV-2; Waste Water
DOI:
10.3390/ijms22168498
