Merge pull request #996 from ScilifelabDataCentre/develop

W24 updates

content/english/dashboards/npc-statistics.md

@@ -18,14 +18,14 @@ dashboards_topics: [COVID-19, Infectious diseases]
   <a href="https://nyheter.ki.se/covid-19-tester-ki-atergar-till-ordinarie-laboratorieverksamhet-men-har-fortsatt-beredskap">KI Press Release</a>
 </div>
 
-The dataset visualised in the graphs on this page is available [here](https://datagraphics.dckube.scilifelab.se/dataset/bbbaf64a25a1452287a8630503f07418).  The numbers reported here were compiled automatically and, as such, might not correspond to
+The dataset visualised in the graphs on this page is available [here](https://datagraphics.dc.scilifelab.se/dataset/bbbaf64a25a1452287a8630503f07418).  The numbers reported here were compiled automatically and, as such, might not correspond to
 the numbers reported through other sources for different reasons.
 
 #### Total NPC test numbers
 
 The total number of SARS-CoV-2 (COVID-19) tests conducted at the national Pandemic Centre (NPC) since the start of the pandemic, separated according to whether the results were positive, negative, or invalid/inconclusive.
 
-Source code for the below graph is available [here](https://datagraphics.dckube.scilifelab.se/graphic/ba0b27320fe74ad0aef59a26be6c37f1).
+Source code for the below graph is available [here](https://datagraphics.dc.scilifelab.se/graphic/ba0b27320fe74ad0aef59a26be6c37f1).
 
 <div class="d-lg-none alert alert-info">
   Scroll the plot sideways to view all data.
@@ -39,7 +39,7 @@ Source code for the below graph is available [here](https://datagraphics.dckube.
 
 The number of SARS-CoV-2 (COVID-19) tests ran daily or weekly, divided according to whether results were positive, negative, or invalid/inconclusive.
 
-Source code is available for both the [daily](https://datagraphics.dckube.scilifelab.se/graphic/ddb1119aefce47d58d0b3a49e98b4fcc) and [weekly](https://datagraphics.dckube.scilifelab.se/graphic/1f2322f4301c4773878c956c578e8caf) graphs below.
+Source code is available for both the [daily](https://datagraphics.dc.scilifelab.se/graphic/ddb1119aefce47d58d0b3a49e98b4fcc) and [weekly](https://datagraphics.dc.scilifelab.se/graphic/1f2322f4301c4773878c956c578e8caf) graphs below.
 
   <div id="dwbuttons"><button class="btn btn-secondary" type="button" data-toggle="collapse" data-target="#daily_stacked_bar_chart" aria-expanded="true" aria-controls="#daily_stacked_bar_chart">
     Daily
@@ -71,7 +71,7 @@ Source code is available for both the [daily](https://datagraphics.dckube.scilif
 The fraction of daily or weekly SARS-CoV-2 (COVID-19) tests that were positive,
 as percentage of all tests conducted (excluding invalid/inconclusive).
 
-Source code is available for both the [daily](https://datagraphics.dckube.scilifelab.se/graphic/b31c50be59c84c93986c25b052115a65) and [weekly](https://datagraphics.dckube.scilifelab.se/graphic/7f27ae237b8146a498ab4014aadc35db) graphs below.
+Source code is available for both the [daily](https://datagraphics.dc.scilifelab.se/graphic/b31c50be59c84c93986c25b052115a65) and [weekly](https://datagraphics.dc.scilifelab.se/graphic/7f27ae237b8146a498ab4014aadc35db) graphs below.
 
 <div id="dwbuttons"><button class="btn btn-secondary" type="button" data-toggle="collapse" data-target="#daily_positive_bar_chart" aria-expanded="true" aria-controls="#daily_positive_bar_chart">
   Daily
@@ -102,7 +102,7 @@ Source code is available for both the [daily](https://datagraphics.dckube.scilif
 The sum of all SARS-CoV-2 (COVID-19) virus tests conducted at NPC since the
 start of the pandemic, as a function of date, and divided according to whether results were positive, negative, or invalid/inconclusive.
 
-Source code for the below graph is available [here](https://datagraphics.dckube.scilifelab.se/graphic/9145856246004419983d39fcf56d9eb6).
+Source code for the below graph is available [here](https://datagraphics.dc.scilifelab.se/graphic/9145856246004419983d39fcf56d9eb6).
 
 <div class="d-lg-none alert alert-info">
   Scroll the plot sideways to view all data.
@@ -135,14 +135,14 @@ exclusively performed PCR-based analyses, not serological
 <script src="https://cdn.jsdelivr.net/npm/vega-lite@4.12.2"></script>
 <script src="https://cdn.jsdelivr.net/npm/vega-embed@6.8.0"></script>
 
-<script src="https://datagraphics.dckube.scilifelab.se/graphic/ba0b27320fe74ad0aef59a26be6c37f1.js?id=total-numbers-chart"></script>
+<script src="https://datagraphics.dc.scilifelab.se/graphic/ba0b27320fe74ad0aef59a26be6c37f1.js?id=total-numbers-chart"></script>
 
-<script src="https://datagraphics.dckube.scilifelab.se/graphic/ddb1119aefce47d58d0b3a49e98b4fcc.js?id=stacked-bar-chart"></script>
+<script src="https://datagraphics.dc.scilifelab.se/graphic/ddb1119aefce47d58d0b3a49e98b4fcc.js?id=stacked-bar-chart"></script>
 
-<script src="https://datagraphics.dckube.scilifelab.se/graphic/1f2322f4301c4773878c956c578e8caf.js?id=stacked-bar-chart-weekly"></script>
+<script src="https://datagraphics.dc.scilifelab.se/graphic/1f2322f4301c4773878c956c578e8caf.js?id=stacked-bar-chart-weekly"></script>
 
-<script src="https://datagraphics.dckube.scilifelab.se/graphic/b31c50be59c84c93986c25b052115a65.js?id=positive-bar-chart"></script>
+<script src="https://datagraphics.dc.scilifelab.se/graphic/b31c50be59c84c93986c25b052115a65.js?id=positive-bar-chart"></script>
 
-<script src="https://datagraphics.dckube.scilifelab.se/graphic/9145856246004419983d39fcf56d9eb6.js?id=cumulative-plot"></script>
+<script src="https://datagraphics.dc.scilifelab.se/graphic/9145856246004419983d39fcf56d9eb6.js?id=cumulative-plot"></script>
 
-<script src="https://datagraphics.dckube.scilifelab.se/graphic/7f27ae237b8146a498ab4014aadc35db.js?id=positive-bar-chart-weekly"></script>
+<script src="https://datagraphics.dc.scilifelab.se/graphic/7f27ae237b8146a498ab4014aadc35db.js?id=positive-bar-chart-weekly"></script>

content/english/dashboards/serology-statistics.md

@@ -180,6 +180,6 @@ Thålin. SARS-CoV-2 exposure, symptoms and seroprevalence in healthcare workers
 <script src="https://cdn.jsdelivr.net/npm/vega-lite@4.12.2"></script>
 <script src="https://cdn.jsdelivr.net/npm/vega-embed@6.8.0"></script>
 
-<script src="https://datagraphics.dckube.scilifelab.se/graphic/e5c031600d334d889f33080d3f0ac0dd.js?id=bar-chart"></script>
-<script src="https://datagraphics.dckube.scilifelab.se/graphic/4c635b2679e648e384d952dd3e506ff1.js?id=cumulative-plot"></script>
-<script src="https://datagraphics.dckube.scilifelab.se/graphic/63d9201aee8747c9b37c17ebb6b01c35.js?id=total-number"></script>
+<script src="https://datagraphics.dc.scilifelab.se/graphic/e5c031600d334d889f33080d3f0ac0dd.js?id=bar-chart"></script>
+<script src="https://datagraphics.dc.scilifelab.se/graphic/4c635b2679e648e384d952dd3e506ff1.js?id=cumulative-plot"></script>
+<script src="https://datagraphics.dc.scilifelab.se/graphic/63d9201aee8747c9b37c17ebb6b01c35.js?id=total-number"></script>

content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md

@@ -2,9 +2,11 @@
 title: Amount of SARS-CoV-2 in wastewater (SEEC-KTH)
 plotly: true
 aliases:
-    - /dashboards/wastewater/covid_quant_kth/
+  - /dashboards/wastewater/covid_quant_kth/
 ---
 
+<div class="alert alert-info">As of June 2023, the SARS-CoV-2 data will no longer be updated by SEEC-KTH. Data from after June 2023 is <a href="/dashboards/wastewater/covid_quantification/covid_quant_slu/">available from other research groups.</a></div>
+
 <div class="mt-3">
   <a href="/dashboards/wastewater/covid_quantification/"><i class="bi bi-arrow-left-circle-fill"></i> Go back to SARS-CoV-2 quantification within the wastewater epidemiology dashboard</a>
 </div>
@@ -99,9 +101,9 @@ Cetecioglu, Z. G., Williams, C., Khatami, K., Atasoy, M., Nandy, P., Jafferali,
 
 ## Methods
 
- To correct for variations in population size and wastewater flow, the group quantifies the pepper mild mottle virus (PMMoV) using a modified version of the assay of [Zhang *et al.* (2006)](https://doi.org/10.1371/journal.pbio.0040003). PMMoV is an abundant RNA virus in human faeces and serves as an estimator of human faecal content ([Symonds *et al.*, 2019](https://doi.org/10.1371/journal.ppat.1007639)). SARS-like virus specific N3-primers ([Lu *et al.*, 2020](https://doi.org/10.3201/eid2608.201246)) with SYBR Green chemistry ([Perez-Zabaleta *et al.*, 2023](https://doi.org/10.1016/j.scitotenv.2022.160023)) are used to quantify SARS-CoV-2.
+To correct for variations in population size and wastewater flow, the group quantifies the pepper mild mottle virus (PMMoV) using a modified version of the assay of [Zhang _et al._ (2006)](https://doi.org/10.1371/journal.pbio.0040003). PMMoV is an abundant RNA virus in human faeces and serves as an estimator of human faecal content ([Symonds _et al._, 2019](https://doi.org/10.1371/journal.ppat.1007639)). SARS-like virus specific N3-primers ([Lu _et al._, 2020](https://doi.org/10.3201/eid2608.201246)) with SYBR Green chemistry ([Perez-Zabaleta _et al._, 2023](https://doi.org/10.1016/j.scitotenv.2022.160023)) are used to quantify SARS-CoV-2.
 
-After concentration, filtering, and preparation, the samples are analysed using the qPCR technique for SARS CoV-2 RNA. Primers of the nucleocapsid (N) gene were used to detect the SARS-COV-2 gene (previously used and verified by [Medema *et al.* (2020)](https://doi.org/10.1021/acs.estlett.0c00357)). In some cases, raw wastewater samples were frozen at -20℃, and concentrated wastewater or purified RNA samples were sometimes stored at -80℃ before the next analysis step was carried out. The concentration method initially used by SEEC-KTH was based on one of their earlier studies ([Jafferali *et al.*, 2021](https://doi.org/10.1016/j.scitotenv.2020.142939)), which compared four different concentration methods. This method was used until week 35 of 2021. After this time, the group began to instead use [the Promega kit](https://se.promega.com/applications/virus-detection-assay-coronavirus-detection-covid-19-sars-cov-2/wastewater-based-epidemiology-covid19/) for the concentration step.
+After concentration, filtering, and preparation, the samples are analysed using the qPCR technique for SARS CoV-2 RNA. Primers of the nucleocapsid (N) gene were used to detect the SARS-COV-2 gene (previously used and verified by [Medema _et al._ (2020)](https://doi.org/10.1021/acs.estlett.0c00357)). In some cases, raw wastewater samples were frozen at -20℃, and concentrated wastewater or purified RNA samples were sometimes stored at -80℃ before the next analysis step was carried out. The concentration method initially used by SEEC-KTH was based on one of their earlier studies ([Jafferali _et al._, 2021](https://doi.org/10.1016/j.scitotenv.2020.142939)), which compared four different concentration methods. This method was used until week 35 of 2021. After this time, the group began to instead use [the Promega kit](https://se.promega.com/applications/virus-detection-assay-coronavirus-detection-covid-19-sars-cov-2/wastewater-based-epidemiology-covid19/) for the concentration step.
 
 ## Archived data
 

content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md

@@ -2,7 +2,7 @@
 title: Amount of SARS-CoV-2 in wastewater (SEEC-SLU)
 plotly: true
 aliases:
-    - /dashboards/wastewater/covid_quant_slu/
+  - /dashboards/wastewater/covid_quant_slu/
 ---
 
 <div class="mt-3">
@@ -18,7 +18,7 @@ The data and visualisation on this page are usually updated weekly, typically on
 
 ## Wastewater collection sites
 
-SLU-SEEC collect and analyse samples from multiple areas. The below table shows details about each of these sites. The table lists the towns/cities monitored, wastewater treatment plants (WWTP) that samples were collected from, the number of people in the catchment area (Number of people), and the dates that monitoring by SLU-SEEC started and ended monitoring (Start and End date, respectively). A value of 'null' for the end date indicates that collection is ongoing. An asterisk next to the number of people indicates that the figure is preliminary.  
+SLU-SEEC collect and analyse samples from multiple areas. The below table shows details about each of these sites. The table lists the towns/cities monitored, wastewater treatment plants (WWTP) that samples were collected from, the number of people in the catchment area (Number of people), and the dates that monitoring by SLU-SEEC started and ended monitoring (Start and End date, respectively). A value of 'null' for the end date indicates that collection is ongoing. An asterisk next to the number of people indicates that the figure is preliminary.
 
   <div class="plot_wrapper mb-3">
   <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_slusites.json" height="775px" >}}</div>
@@ -62,7 +62,7 @@ SLU-SEEC collect and analyse samples from multiple areas. The below table shows
 
 <div class="alert alert-info">Last updated: <span id="last_modified_uppsala"></span></div>
 
-<b>Important note:</b> Historical data for Knivsta, Vaxholm, and Österåker are available in the dataset (linked below). However, they are no longer included in the visualisation.
+<b>Important note:</b> Historical data for Ekerö, Enköping, Knivsta, Tierp, Vaxholm, Älvkarleby, and Österåker are available in the dataset (linked below). However, they are no longer included in the visualisation.
 
 Please note that although the same methods are used for all cities shown on this tab, differences in the wastewater collection systems and populations of different cities might bias direct comparisons between cities.
 
@@ -109,27 +109,27 @@ Please note that although the same methods are used for all cities shown on this
 
 ## Reports from the research group
 
-The group provide reports to summarise their latest findings. The latest report is available [here](https://blobserver.dc.scilifelab.se/blob/Latest_weekly_report_SEEC-SLU) (only available in Swedish).
+The group provide reports to summarise their latest findings. The latest report is available [here](https://blobserver.dc.scilifelab.se/blob/Latest_weekly_report_SEEC-SLU.pdf) (only available in Swedish).
 
 ## Dataset
 
 **Contact:** <anna.szekely@slu.se> and <maja.malmberg@slu.se>
 
-**Download the data:** [N1-gene copy number per PMMoV gene copy number, CSV file.](https://datagraphics.dckube.scilifelab.se/dataset/0ac8fa02871745048491de74e5689da9.csv). Data are available from week 38 of 2020; updated weekly.
+**Download the data:** [N1-gene copy number per PMMoV gene copy number, CSV file.](https://datagraphics.dc.scilifelab.se/dataset/0ac8fa02871745048491de74e5689da9.csv). Data are available from week 38 of 2020; updated weekly.
 
 **How to cite the dataset:**
 
 Székely, A. J., Vargas, J., Mohamed, N., Dafalla, I., Malmberg, M. (2021). Dataset of SARS-CoV-2 wastewater data from various towns in Sweden. [https://doi.org/10.17044/scilifelab.14256317](https://doi.org/10.17044/scilifelab.14256317).
 
 **How to cite the method:**
 
-Isaksson, F., Lundy, L., Hedström, A., Székely, A. J., Mohamed, N. (2022). Evaluating the Use of Alternative Normalization Approaches on SARS-CoV-2 Concentrations in Wastewater: Experiences from Two Catchments in Northern Sweden. *Environments*, *9*, 39. [https://doi.org/10.3390/environments9030039](https://doi.org/10.3390/environments9030039).
+Isaksson, F., Lundy, L., Hedström, A., Székely, A. J., Mohamed, N. (2022). Evaluating the Use of Alternative Normalization Approaches on SARS-CoV-2 Concentrations in Wastewater: Experiences from Two Catchments in Northern Sweden. _Environments_, _9_, 39. [https://doi.org/10.3390/environments9030039](https://doi.org/10.3390/environments9030039).
 
 ## Methods
 
 For most cities represented on this page, raw, untreated wastewater samples that are representative of a single day are collected by flow compensated samplers at the wastewater treatment plants (WWTP). Uppsala is the exception, with all measurements since week 16 of 2021 instead representing 1 week. In Uppsala, samples are collected daily, and then combined flow-proportionally into one composite weekly sample for the purpose of analyses.
 
-The freshly collected samples are processed according to standard methodologies. For samples collected up to and including week 18 of 2021, viral particles were concentrated using the electronegative filtration method ([Ahmed *et al.*, 2020](https://www.sciencedirect.com/science/article/pii/S004896972033480X)). Since week 19 of 2021, the viral genomic material has instead been concentrated and extracted by the direct capture method, using the Maxwell RSC Enviro TNA kit (Promega). Absolute quantification of the copy numbers of the SARS-CoV-2 genome is performed using the [SARS-CoV-2 specific N1 assay from the Centers for Disease Control and Prevention (CDC)](https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html). To correct for variations in population size and wastewater flow, the group quantifies the pepper mild mottle virus (PMMoV) using a modified version of the assay of [Zhang *et al.* (2006)](https://doi.org/10.1371/journal.pbio.0040003). PMMoV is an abundant RNA virus in human faeces and serves as an estimator of human faecal content ([Symonds *et al.*, 2019](https://doi.org/10.1371/journal.ppat.1007639)). For more details about the sample processing method, and the evaluation of the use of the PMMoV normalisation method for Swedish wastewater, please refer to the corresponding publication: [Isaksson *et al.* (2022)](https://www.mdpi.com/2076-3298/9/3/39).
+The freshly collected samples are processed according to standard methodologies. For samples collected up to and including week 18 of 2021, viral particles were concentrated using the electronegative filtration method ([Ahmed _et al._, 2020](https://www.sciencedirect.com/science/article/pii/S004896972033480X)). Since week 19 of 2021, the viral genomic material has instead been concentrated and extracted by the direct capture method, using the Maxwell RSC Enviro TNA kit (Promega). Absolute quantification of the copy numbers of the SARS-CoV-2 genome is performed using the [SARS-CoV-2 specific N1 assay from the Centers for Disease Control and Prevention (CDC)](https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html). To correct for variations in population size and wastewater flow, the group quantifies the pepper mild mottle virus (PMMoV) using a modified version of the assay of [Zhang _et al._ (2006)](https://doi.org/10.1371/journal.pbio.0040003). PMMoV is an abundant RNA virus in human faeces and serves as an estimator of human faecal content ([Symonds _et al._, 2019](https://doi.org/10.1371/journal.ppat.1007639)). For more details about the sample processing method, and the evaluation of the use of the PMMoV normalisation method for Swedish wastewater, please refer to the corresponding publication: [Isaksson _et al._ (2022)](https://www.mdpi.com/2076-3298/9/3/39).
 
 The data in the below graph and datafile represent the ratio of the copy numbers measured by the N1 and PMMoV-assays, multiplied by 10<sup>4</sup>. As N1 copy number is a proxy for SARS-CoV-2 virus content in the wastewater and PMMoV is a proxy of the faecal content (which is related to the contributing population), the ratio of the two can be considered to be a proxy for the prevalence of COVID-19 infections in the population of the wastewater catchment area.
 

content/english/dashboards/wastewater/covid_quantification/historic_orebro_umea.md

@@ -55,5 +55,5 @@ Malmberg, M., Myrmel, M. & Khatri, M. Dataset of SARS CoV-2 in wastewater in Ör
 <script src="https://cdn.jsdelivr.net/npm/vega-lite@5.1.0"></script>
 <script src="https://cdn.jsdelivr.net/npm/vega-embed@6.8.0"></script>
 
-<script src="https://datagraphics.dckube.scilifelab.se/graphic/030ac237d44248dda87e2c9277a49cc7.js?id=umea_combined"></script>
-<script src="https://datagraphics.dckube.scilifelab.se/graphic/fe03ef2220814eeeb3e99eb26a7c46e2.js?id=orebro_combined"></script>
+<script src="https://datagraphics.dc.scilifelab.se/graphic/030ac237d44248dda87e2c9277a49cc7.js?id=umea_combined"></script>
+<script src="https://datagraphics.dc.scilifelab.se/graphic/fe03ef2220814eeeb3e99eb26a7c46e2.js?id=orebro_combined"></script>

content/english/dashboards/wastewater/covid_quantification/historic_stockholm.md

@@ -34,4 +34,4 @@ Cetecioglu Z G, Williams, C, Khatami, K, Atasoy, M, Nandy, P, Jafferali, M H, Bi
 <script src="https://cdn.jsdelivr.net/npm/vega-lite@5.1.0"></script>
 <script src="https://cdn.jsdelivr.net/npm/vega-embed@6.8.0"></script>
 
-<script src="https://datagraphics.dckube.scilifelab.se/graphic/956f9390690043b8ae5f62b90d22f84f.js?id=stockholm_combined"></script>
+<script src="https://datagraphics.dc.scilifelab.se/graphic/956f9390690043b8ae5f62b90d22f84f.js?id=stockholm_combined"></script>