Timely Monitoring of SARS-CoV-2 RNA Fragments in Wastewater Shows the Emergence of JN.1 (BA.2.86.1.1, Clade 23I) in Berlin, Germany.

Timely Monitoring of SARS-CoV-2 RNA Fragments in Wastewater Shows the Emergence of JN.1 (BA.2.86.1.1, Clade 23I) in Berlin, Germany.

Publication date: Jan 10, 2024

The importance of COVID-19 surveillance from wastewater continues to grow since case-based surveillance in the general population has been scaled back world-wide. In Berlin, Germany, quantitative and genomic wastewater monitoring for SARS-CoV-2 is performed in three wastewater treatment plants (WWTP) covering 84% of the population since December 2021. The SARS-CoV-2 Omicron sublineage JN. 1 (B. 2.86. 1.1), was first identified from wastewater on 22 October 2023 and rapidly became the dominant sublineage. This change was accompanied by a parallel and still ongoing increase in the notification-based 7-day-hospitalization incidence of COVID-19 and COVID-19 ICU utilization, indicating increasing COVID-19 activity in the (hospital-prone) population and a higher strain on the healthcare system. In retrospect, unique mutations of JN. 1 could be identified in wastewater as early as September 2023 but were of unknown relevance at the time. The timely detection of new sublineages in wastewater therefore depends on the availability of new sequences from GISAID and updates to Pango lineage definitions and Nextclade. We show that genomic wastewater surveillance provides timely public health evidence on a regional level, complementing the existing indicators.

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Concepts Keywords
December Berlin
Germany COVID-19
Healthcare genomic surveillance
Increasing Germany
Viruses Germany
Humans
Omicron
RNA, Viral
RNA, Viral
SARS-CoV-2
SARS-CoV-2
Wastewater
Wastewater
wastewater sequencing
Wastewater-Based Epidemiological Monitoring

Semantics

Type Source Name
disease MESH COVID-19
disease VO population
disease VO time
disease MESH Infectious Diseases
drug DRUGBANK Coenzyme M
disease MESH severe acute respiratory syndrome
disease MESH infections
drug DRUGBANK Aspartame
disease VO volume
disease IDO assay
disease VO USA
disease IDO infection
disease VO frequency
disease VO effective
disease IDO quality
disease VO document
disease MESH Influenza
disease IDO pathogen
disease VO protocol

Original Article

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