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

Abstract

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.

Keywords: Germany; Omicron; SARS-CoV-2; genomic surveillance; wastewater sequencing.

Figure A1

Sublineages of SARS-CoV-2 during autumn 2023 in genomic wastewater monitoring for three wastewater treatment plants (Ruhleben, Schönerlinde and Wassmannsdorf), covering 84% of the Berlin population. XBB.1.9 is a sublineage of XBB and EG.5.1 is a sublineage of XBB.1.9. JN.1 is a sublineage of BA.2.86. The proportions of ancestors include the proportions of their all their descendants, e.g., BA.2.86 includes the proportion of JN.1. Wastewater data is shown until 26 November 2023 (last sampling date).

Figure 1

(A) 7-day notification rate for COVID-19 hospitalization during summer and autumn 2023 indicating an increase from October to December 2023. (B) COVID-19 intensive care unit utilization rate for the same time interval, also demonstrating an increase starting in October 2023. The 7-day COVID-19 hospitalization rate (A) and the intensive care unit utilization rate (B) are shown from 29 May to 8 December 2023. (C) Emergence of SARS-CoV-2 sublineage JN.1 (BA.2.86.1.1) during autumn 2023 in genomic wastewater monitoring for three wastewater treatment plants (Ruhleben, Schönerlinde and Wassmannsdorf), covering 84% of the Berlin population. Wastewater data is shown until 26 November 2023 (last sampling date).

Figure 2

Combined SARS-CoV-2 viral concentrations in Berlin from 29 May to 26 November 2023 (last sampling date), using data from three wastewater treatment plants (Ruhleben, Schönerlinde and Wassmannsdorf), covering 84% of the Berlin population. The blue line represents the total amount of target RNA copies per liter over time, the red curve indicates XBB attributed RNA copies per liter, and the violet line shows BA.2.86.x attributed RNA copies per liter.

Figure 3

Heatmap of unique mutations found in wastewater sequencing from the Ruhleben wastewater treatment plant from 7 August to 26 November 2023 showing fingerprint variants for clade 23I. WWTP Ruhleben is shown as an example since it is the largest WWTP in Berlin covering 1.6 Mio inhabitants, the other WWTPs are shown in the supplementary materials. Fingerprint mutations are exclusive for each lineage and can be used to determine the presence of a variant with a high degree of confidence. Although the fingerprint mutations for JN.1 (BA.2.86.1.1, clade 23I) were first detected in September, their significance was unknown as JN.1 would only be defined as a Pango-lineage on 29 September 2023 and was integrated in Nextstrain on 26 October 2023. Only as of the middle of October, the number and frequency of known fingerprint mutations allowed for the determination of JN.1.