@@ -24,7 +27,7 @@ In 2017, and since 2020, the Norder group at the University of Gothenburg (GU) c
This page details the [latest method used in monitoring](#methods), as well as [a brief summary information about the viruses](#basic-virus-information), and [information about the data collected](#dataset).
-The enteric virus monitoring by the Norder group was done alongside their ongoing monitoring of SARS-CoV-2 in wastewater, the data for which are [also shared on this portal](/dashboards/wastewater/covid_quantification/covid_quant_gu/).
+The enteric virus monitoring by the Norder group was done alongside their ongoing monitoring of SARS-CoV-2 in wastewater, the data for which are [also shared on this portal](/dashboards/covid_quantification/covid_quant_gu/).
The data and visualisations on this page is **no longer being updated**.
@@ -85,7 +88,7 @@ Nucleic acids are extracted from 1ml of the concentrated sample using the QIAamp
## Archived data
-[Historic enteric virus data from Gothenburg collected between week 2 and week 43 of 2023](/dashboards/wastewater/enteric_quantification/historic_enteric_gu/).
+[Historic enteric virus data from Gothenburg collected between week 2 and week 43 of 2023](/dashboards/enteric_quantification/historic_enteric_gu/).
### Basic virus information
diff --git a/content/english/dashboards/wastewater/enteric_quantification/historic_enteric_gu.md b/content/english/dashboards/enteric_quantification/historic_enteric_gu.md
similarity index 97%
rename from content/english/dashboards/wastewater/enteric_quantification/historic_enteric_gu.md
rename to content/english/dashboards/enteric_quantification/historic_enteric_gu.md
index ee2dadde2..b7a1c1356 100644
--- a/content/english/dashboards/wastewater/enteric_quantification/historic_enteric_gu.md
+++ b/content/english/dashboards/enteric_quantification/historic_enteric_gu.md
@@ -3,13 +3,14 @@ title: Historic enteric virus data from Gothenburg
plotly: true
aliases:
- /dashboards/wastewater/historic_enteric_GU/
+ - /dashboards/wastewater/enteric_quantification/historic_enteric_gu/
---
The data presented here is no longer updated but is kept for historical reference.
-This page shows historic wastewater epidemiology data for enteric viruses. The data was collected in Gothenburg, Sweden by the group led by Professor Helene Norder (University of Gothenburg, GU). The work was supported by co-workers from the University of Gothenburg and Sahlgrenska University Hospital (Hao Wang, Marianela Patzi Churqui, Timur Tunovic, Fredy Saguti, and Kristina Nyström), and Lucica Enache at Ryaverket, Gryaab AB, Gothenburg. The data shown on this page was collected between week 2 and week 43 of 2023 (i.e. between 9th January and 23rd October 2023). The group started to use a new method from week 20 of 2023 (15th May). Data produced using this new method continues to be updated approximately weekly, and is available on the ['Amount of enteric virus in wastewater (GU)' page](../).
+This page shows historic wastewater epidemiology data for enteric viruses. The data was collected in Gothenburg, Sweden by the group led by Professor Helene Norder (University of Gothenburg, GU). The work was supported by co-workers from the University of Gothenburg and Sahlgrenska University Hospital (Hao Wang, Marianela Patzi Churqui, Timur Tunovic, Fredy Saguti, and Kristina Nyström), and Lucica Enache at Ryaverket, Gryaab AB, Gothenburg. The data shown on this page was collected between week 2 and week 43 of 2023 (i.e. between 9th January and 23rd October 2023). The group started to use a new method from week 20 of 2023 (15th May). Data produced using this new method continues to be updated approximately weekly, and is available on the ['Amount of enteric virus in wastewater (GU)' page](/dashboards/enteric_quantification/).
## Introduction
@@ -17,9 +18,9 @@ Enteric viruses are a large group of viruses including, for example, calicivirus
Wastewater contains many different types of viruses that infect humans because viruses are shed in the faeces and urine of infected individuals. The Norder group at the University of Gothenburg showed that the relative levels of some enteric viruses in wastewater could be used to predict upcoming outbreaks ([Hellmér _et al._, 2014](https://pubmed.ncbi.nlm.nih.gov/25172863/)). Indeed, previous studies by the Norder group have shown that the levels of noroviruses in wastewater increase 1-2 weeks before larger outbreaks in nursing homes and hospital wards.
-In 2017, and since 2020, the Norder group at the University of Gothenburg (GU) conducted weekly monitoring of the levels of some enteric viruses in wastewater. They quantify the levels of enteroviruses (including poliovirus), adenoviruses, GG2 (a norovirus causing winter vomiting disease), astroviruses, sapoviruses and also pepper molt mild virus (PMMoV). This page details the [historic methods used in monitoring](#methods), as well as [a brief summary information about the viruses](#basic-virus-information), and [information about citing the historic data](#dataset). Data collected using the updated method is available on the page ['Amount of enteric virus in wastewater (GU)'](../).
+In 2017, and since 2020, the Norder group at the University of Gothenburg (GU) conducted weekly monitoring of the levels of some enteric viruses in wastewater. They quantify the levels of enteroviruses (including poliovirus), adenoviruses, GG2 (a norovirus causing winter vomiting disease), astroviruses, sapoviruses and also pepper molt mild virus (PMMoV). This page details the [historic methods used in monitoring](#methods), as well as [a brief summary information about the viruses](#basic-virus-information), and [information about citing the historic data](#dataset). Data collected using the updated method is available on the page ['Amount of enteric virus in wastewater (GU)'](/dashboards/enteric_quantification/).
-The enteric virus monitoring by the Norder group was done alongside their ongoing monitoring of SARS-CoV-2 in wastewater, the data for which is [also shared on this portal](/dashboards/wastewater/covid_quantification/covid_quant_gu/).
+The enteric virus monitoring by the Norder group was done alongside their ongoing monitoring of SARS-CoV-2 in wastewater, the data for which is [also shared on this portal](/dashboards/covid_quantification/covid_quant_gu/).
## Wastewater collection sites
diff --git a/content/english/dashboards/influenza_quantification/_index.md b/content/english/dashboards/influenza_quantification/_index.md
new file mode 100644
index 000000000..f5e44902f
--- /dev/null
+++ b/content/english/dashboards/influenza_quantification/_index.md
@@ -0,0 +1,94 @@
+---
+title: Amount of influenza virus in wastewater (SLU)
+plotly: true
+banner: /dashboard_thumbs/wastewater_influenza.png
+description: Explore Influenza A and B virus levels in wastewater across Sweden. Weekly data from SLU-SEEC tracks Influenza trends, covering 43% of the Swedish population, and aids in predicting potential outbreaks.
+menu:
+ dashboard_menu:
+ identifier: wastewater_influenza_quantification
+ name: "Wastewater: Influenza Quantification (SLU)"
+aliases:
+ - /dashboards/wastewater/influenza_quantification/
+dashboards_topics: [Wastewater Surveillance, Influenza, Epidemiology]
+data_status: "updating"
+---
+
+## Introduction
+
+Influenza viruses are negative-sense, single-stranded, segmented RNA viruses within the family Orthomyxoviridae. Influenza A and influenza B viruses cause seasonal epidemics of influenza, commonly known as “the flu”, a highly contagious respiratory disease characterized by symptoms such as fever, cough, sore throat, body aches, and fatigue but diarrhea and vomiting can also occur. Influenza A virus is widespread in water birds but also infects other birds and various mammals, including humans and pigs, while influenza B virus primarily infects humans. Influenza viruses mutate rapidly, leading to different strains and seasonal outbreaks. Both influenza A and influenza B viruses can cause seasonal outbreaks, but only influenza A is known to cause pandemics due to its broad host range and resulting potential for interspecies genetic reassortment. For more information about symptoms, risks and vaccination against influenza viruses, visit the corresponding site of the [Swedish Public Health Agency](https://www.folkhalsomyndigheten.se/smittskydd-beredskap/smittsamma-sjukdomar/influensa-/).
+
+The data presented on this page is generated in the SLU (Swedish University of Agricultural Sciences) laboratories of SEEC (Swedish Environmental Epidemiology Center). The data and visualisation on this page are usually updated weekly, typically on Mondays. Please refer to the [Methods](#methods) for details on measurements and calculations. All related dashboards can be found on the [Wastewater Surveillance](/dashboards/topics/wastewater-surveillance/) page, and sampling sites and project details are available in the [Wastewater Monitoring Background](/dashboards/wastewater_background/).
+
+
+Important Note:
+The scores provided in the dataset and depicted in the plot below are preliminary, so corrections and changes may occur. Data and information about the group on this dashboard are updated frequently, so please check back regularly to stay up to date. 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.
+
+
+## Visualisations
+
+
Last updated:
+
+### Influenza A
+
+
+ Rotating your phone may improve graph layout
+
+
+
+
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_slu_infA.json" height="800px" >}}
+
+
+**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/combined_slu_influenza_a.py).
+
+### Influenza B
+
+
+ Rotating your phone may improve graph layout
+
+
+
+
{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_slu_infB.json" height="800px" >}}
+
+
+**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/combined_slu_influenza_b.py).
+
+## Commentary from the research group
+
+
Date:
Commentary:
+
+{{< ww_dynamic_content >}}
+
+## 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.pdf) (only available in Swedish).
+
+## Dataset
+
+**Contact:**
and
+
+**Download the data:** [Respiratory virus gene copy numbers normalised per PMMoV gene copy number.CSV file](https://blobserver.dc.scilifelab.se/blob/SLU_wastewater_data.csv). Data are available for Influenza A from week 42 of 2022 and for Influenza B from week 12 of 2023; updated weekly.
+
+**How to cite the dataset:**
+
+Székely, A. J., Malmberg, M., Vargas, J., Mohamed, N., Dafalla, I., Petrini, F., Davies, L. (2023). Dataset of SARS-CoV-2, influenza A and influenza B virus content in wastewater samples from wastewater treatment plants in Sweden. .
+
+## Methods
+
+Wastewater is collected from several different treatment plants around the country. For more information about the treatment plants, visit the page about [the background of wastewater surveillance](/dashboards/wastewater_background/). 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, where samples are collected daily, and then combined flow-proportionally into one composite weekly sample for the purpose of analyses.
+
+The viral genomic material from the freshly collected samples is extracted by the direct capture method, using the Maxwell RSC Enviro TNA kit (Promega).
+
+Absolute quantification of the copy numbers of the genome of influenza A and B viruses is performed by One-Step RT-qPCR using the Flu SC2 Multiplex Assay from the Centers for Disease Control and Prevention (CDC). To correct for variations in population size and wastewater flow, pepper mild mottle virus (PMMoV) is quantified 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)).
+
+The data in the graphs and datafile is presented in three different formats:
+- **PMMoV normalised Influenza content** represents the ratio of the copy numbers of influenza and PMMoV measured by the influenza assay and PMMoV-assays, respectively, multiplied by 1000. As the influenza assay provides proxies for influenza 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 influenza infections in the population of the wastewater catchment area.
+- **Influenza genome copies concentration** presents the influenza copy number concentration measured in the wastewater. These data is influenced by the setup of the different wastewater collection nsystems and is therefore not suitable for comparison betwwen sites. The virus concentrations in the wastewater are also influenced by the weather events that impact wastewater flow (e.g., heavy rain or snow melt).
+- **Influenza genome copies/day/inhabitant** represents the daily virus amount estimated in the wastewater normalized for the number of inhabitants connected to the system. These data allows for comparison of different sites but some delays in the presentation of these data may occur compared to the other.
+
+**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. .
+
+## Archived data from SLU
+
+- [Historic Influenza data in wastewater from SEEC-SLU](/dashboards/influenza_quantification/historic_influenza_SLU)
\ No newline at end of file
diff --git a/content/english/dashboards/wastewater/influenza_quantification/_index.md b/content/english/dashboards/influenza_quantification/historic_influenza_SLU.md
similarity index 62%
rename from content/english/dashboards/wastewater/influenza_quantification/_index.md
rename to content/english/dashboards/influenza_quantification/historic_influenza_SLU.md
index 9dfbf4054..d7619cb0f 100644
--- a/content/english/dashboards/wastewater/influenza_quantification/_index.md
+++ b/content/english/dashboards/influenza_quantification/historic_influenza_SLU.md
@@ -1,20 +1,13 @@
---
-title: Amount of influenza virus in wastewater (SLU)
+title: Historic data of influenza virus in wastewater (SLU)
plotly: true
-type: wastewater
-menu:
- wastewater:
- name: Influenza quantification (SLU)
- weight: 40
---
## Introduction
-Influenza viruses are negative-sense, single-stranded, segmented RNA viruses within the family Orthomyxoviridae. Influenza A and influenza B viruses cause seasonal epidemics of influenza, commonly known as "the flu", a highly contagious respiratory disease characterized by symptoms such as fever, cough, sore throat, body aches, and fatigue but diarrhea and vomiting can also occur. Influenza A virus is widespread in water birds but also infects other birds and various mammals, including humans and pigs, while influenza B virus primarily infects humans. Influenza viruses mutate rapidly, leading to different strains and seasonal outbreaks. Both influenza A and influenza B viruses can cause seasonal outbreaks, but only influenza A is known to cause pandemics due to its broad host range and resulting potential for interspecies genetic reassortment. Globally the "seasonal flu” is estimated to be responsible for 290,000–645,000 deaths/year.
+The data presented on this page was generated in the SLU (Swedish University of Agricultural Sciences) laboratories of SEEC (Swedish Environmental Epidemiology Center). The project was part of SciLifeLab’s Pandemic Laboratory Preparedness (PLP) Program, led by Anna J. Székely (Dep. of Aquatic Sciences and Assessment, SLU). Wastewater analyses were overseen by Anna J. Székely, Javier Vargas, and Maja Malmberg (Virology unit of Department of Biomedical Science and Veterinary Public Health, SLU). This page pertains to the historic quantification of the levels of influenza A and B viruses in multiple cities across Sweden. The project had the broadest geographic coverage across Sweden, generating data for 43% of the Swedish population.
-The data presented on this page is generated in the SLU (Swedish University of Agricultural Sciences) laboratories of SEEC (Swedish Environmental Epidemiology Center). The project is part of SciLifeLab’s Pandemic Laboratory Preparedness (PLP) Program, and is led by Anna J. Székely (Dep. of Aquatic Sciences and Assessment, SLU). Wastewater analyses are overseen by Anna J. Székely, Javier Vargas and Maja Malmberg (Virology unit of Department of Biomedical Science and Veterinary Public Health, SLU). This page pertains to the quantification of the levels of influenza A and B viruses in multiple cities across Sweden. This project currently has the broadest geographic coverage across Sweden; generating data for 43% of the Swedish population.
-
-The data and visualisation on this page are usually updated weekly, typically on Fridays. Please note that the scores provided in the dataset and depicted in plot below are preliminary, so corrections and changes may occur. Data and information about the group on this dashboard are updated frequently, so please check back regularly to stay up to date.
+Please note that the data and visualizations on this page are no longer updated. The scores in the dataset and depicted in the plots are final, though minor corrections may have been applied retrospectively. This dashboard serves as a record of the project's results during the active monitoring period.
## Wastewater collection sites
@@ -26,7 +19,8 @@ SLU-SEEC collects and analyses samples for influenza A and B viruses from multip
## Visualisations
-Last updated:
+Last updated: 2024-09-30
+
Important note: 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.
@@ -37,10 +31,10 @@ SLU-SEEC collects and analyses samples for influenza A and B viruses from multip