Delta SARS-CoV-2 variant is entirely substituted by the omicron variant during the fifth COVID-19 wave in Attica region.
NGS
Omicron variant
RT-qPCR
SARS-CoV-2
Wastewater
delta variant
Journal
The Science of the total environment
ISSN: 1879-1026
Titre abrégé: Sci Total Environ
Pays: Netherlands
ID NLM: 0330500
Informations de publication
Date de publication:
15 Jan 2023
15 Jan 2023
Historique:
received:
18
07
2022
revised:
21
09
2022
accepted:
23
09
2022
pubmed:
2
10
2022
medline:
24
11
2022
entrez:
1
10
2022
Statut:
ppublish
Résumé
Wastewater analysis is the most attractive alternative way for the quantification and variant profiling of SARS-CoV-2. Infection dynamics can be monitored by RT-qPCR assays while NGS can provide evidence for the presence of existing or new emerging SARS-CoV-2 variants. Herein, apart from the infection dynamic in Attica since June 1st, 2021, the monitoring of 9 mutations of the omicron and 4 mutations of the delta SARS-CoV-2 variants, utilizing both novel Nested-Seq and RT-PCR, is reported and the substitution of the delta variant (B.1.617.2) by the omicron variant (B.1.1.529) in Attica, Greece within approximately one month is highlighted. The key difference between the two methodologies is discovery power. RT-PCR can only detect known sequences cost-effectively, while NGS is a hypothesis-free approach that does not require prior knowledge to detect novel genes. Overall, the potential of wastewater genomic surveillance for the early discovery and monitoring of variants important for disease management at the community level is underlined. This is the first study, reporting the SARS-CoV-2 infection dynamic for an extended time period and the first attempt to monitor two of the most severe variants with two different methodologies in Greece.
Identifiants
pubmed: 36181801
pii: S0048-9697(22)06161-7
doi: 10.1016/j.scitotenv.2022.159062
pmc: PMC9519360
pii:
doi:
Substances chimiques
Waste Water
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
159062Commentaires et corrections
Type : ErratumIn
Informations de copyright
Copyright © 2022 Elsevier B.V. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
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