From 70cde42c4114509d1a1de3869176eac5872393b7 Mon Sep 17 00:00:00 2001 From: Fabian Engelniederhammer Date: Wed, 4 Sep 2024 14:53:02 +0200 Subject: [PATCH] feat: adapt wastewater story text resolves #1014 --- src/models/wasteWater/constants.ts | 2 +- .../wasteWater/story/WasteWaterStoryPage.tsx | 45 ++++++++++--------- 2 files changed, 26 insertions(+), 21 deletions(-) diff --git a/src/models/wasteWater/constants.ts b/src/models/wasteWater/constants.ts index eb972ca7..574e8302 100644 --- a/src/models/wasteWater/constants.ts +++ b/src/models/wasteWater/constants.ts @@ -39,4 +39,4 @@ export const discontinuedLocations = new Set([ 'test_legacylocation', // for tests ]); -export const discontinuedDate = ' since Jan 1, 2024'; +export const discontinuedDate = ' since March 26th, 2024'; diff --git a/src/models/wasteWater/story/WasteWaterStoryPage.tsx b/src/models/wasteWater/story/WasteWaterStoryPage.tsx index b62a2217..26b32e72 100644 --- a/src/models/wasteWater/story/WasteWaterStoryPage.tsx +++ b/src/models/wasteWater/story/WasteWaterStoryPage.tsx @@ -13,18 +13,17 @@ export const WasteWaterStoryPage = () => {

Wastewater in Switzerland

by{' '} - Computational Biology Group, ETH Zurich + Computational Biology Group, ETH Zürich

- We analyze wastewater samples collected at different Swiss wastewater treatment plants ( see data + We analyze wastewater samples collected at different Swiss wastewater treatment plants (see data sources below) using next-generation sequencing (done by{' '} FGCZ), process the resulting short-read data with{' '} V-pipe, and search for mutations - characteristic of several variants of concern. The relative frequency of each signature mutation is - determined, and all frequencies are combined per day, which provides an estimate of the relative - prevalence of the variant in the population. Some variants have specific signature mutations that - co-occur on the same fragment. Amplicons with such co-occurrences are included in the heatmaps of the - wastewater data displayed on covSpectrum (see{' '} + characteristic of variants of concern. The relative frequency of each signature mutation is + determined, and all mutation frequencies are combined within a selected time window and translated + into estimates of the relative prevalence of the variant in the population for each day. Some variants + have specific signature mutations that co-occur on the same fragment. (see{' '} doi:10.1101/2021.01.08.21249379 @@ -36,8 +35,9 @@ export const WasteWaterStoryPage = () => {

Detecting variants in wastewater is challenging if the RNA concentration is low, for example, due to - low infection numbers in the catchment area of the wastewater treatment plant. Estimates of the - proportions of variants are less reliable in this situation. + low infection numbers in the catchment area of the wastewater treatment plant. Variants with very + similar mutation profiles can also be harder to distinguish. Estimates of the proportions of variants + are less reliable in these situations.

!isDiscontinuedSite(location)} /> @@ -68,14 +68,18 @@ const DataSources = () => { Eawag {' '} - collects samples daily at multiple locations around Switzerland. Over the course of the project - different locations have been covered. Since January 1st of 2024 the following eight wastewater - treatment plants are monitored: Altenrhein (SG), Chur (GR), Genève (GE), Laupen (BE), Lugano (TI), - Zürich (ZH), Luzern (LU) and Bern (BE). + collects samples at multiple locations around Switzerland. Over the course of the project, different + locations have been covered. Since March 26th of 2024 the following eight wastewater treatment plants + are sampled three times per week: Altenrhein (SG), Chur (GR), Genève (GE), Laupen (BE), Lugano (TI), + Zürich (ZH), Luzern (LU) and Basel (BS).

- Until end of December 2023 the project covered six additional wastewater treatment plants: Lausanne - (VD), Basel (BS), Porrentruy (JU), Neuchâtel (NE), Solothurn (SO) and Schwyz (SZ). + Previously, the project covered six additional wastewater treatment plants: Lausanne (VD), Bern (BE), + Porrentruy (JU), Neuchâtel (NE), Solothurn (SO), and Schwyz (SZ). +

+

+ Monitoring of Bern (BE) ended on March 25th, 2024. Monitoring of Lausanne ended February 24th, 2024. + The monitoring of all other discontinued treatment plants ended on December 31st, 2023.

Previously, Microsynth AG provided samples from the wastewater treatment plants of Lausanne (Vidy), @@ -86,7 +90,7 @@ const DataSources = () => { three times per week (once per week until the end of 2022).

- Until end of May 2022 three times a week the Cantonal Laboratory Zurich (KLZH) provided samples that + Until end of May 2022, three times a week the Cantonal Laboratory Zurich (KLZH) provided samples that assess the Canton of Zurich by pooling samples from 12 plants across the canton, namely Zürich-Werdhölzli (also used by Eawag), Winterthur-Hard, Dietikon-Limmattal, Dübendorf-Neugut, Niederglatt-Fischbach, Uster, Bülach-Furt, Wetzikon-Flos, Horgen-Oberrieden, Meilen, Affoltern @@ -118,7 +122,7 @@ const VideoPresentation = () => { "Detecting COVID-19 Variants in Wastewater" by the International Water Association (IWA) - , Prof. Tamar Kohn and Prof. Niko Beerenwinkel have presented this surveillance project. The + , Prof. Tamar Kohn, and Prof. Niko Beerenwinkel have presented this surveillance project. The presentation is the second session of this webinar, "Detection and surveillance of SARS-CoV-2 genomic variants in Swiss wastewater" (timecode 22:17). @@ -144,7 +148,7 @@ const Acknowledgements = () => {

@@ -200,8 +204,9 @@ const Contact = () => { return (

Contact

- Computational Biology, D-BSSE, ETHZ. Niko - Beerenwinkel, +

+ Prof. Niko Beerenwinkel, ETH Zürich. +

); };