Delta SARS-CoV-2 variant is entirely substituted by the omicron variant during the fifth COVID-19 wave in Attica region

https://doi.org/10.1016/j.scitotenv.2022.159062Get rights and content

Highlights

  • SARS-CoV-2 spike protein mutations of the delta and omicron variants were detected

  • Omicron variant completely prevailed within one month from its appearance

  • NGS and RT-PCR showed good concordance in calling mutation presence

  • Wastewater genomic surveillance has a lead time over clinical surveillanceSARS-CoV-2 RNA load was measured in wastewater over 10 consecutive months

Abstract

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.

Keywords

Wastewater
SARS-CoV-2
Omicron variant
delta variant
NGS
RT-qPCR

Data availability

All data generated or analyzed during this study are included in this published article (and its supplementary information files).

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