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Merge pull request #1138 from ScilifelabDataCentre/Paul/FREYA-723
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Paul/FREYA 723
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LianeHughes committed Jul 1, 2024
2 parents 256c172 + c79a407 commit 7b67226
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39 changes: 13 additions & 26 deletions content/english/dashboards/serology-statistics.md
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Expand Up @@ -14,6 +14,7 @@ menu:
aliases:
- /data_types/health_data/serology-statistics/
dashboards_topics: [COVID-19, Infectious diseases]
plotly: true
---

<div class="alert alert-info">
Expand All @@ -29,20 +30,6 @@ Serology tests involve testing bodily fluids for the presence of antibodies or o

<div class="alert alert-info">Data last updated: {{% serology_date_modified %}}.</div>

<!-- ## Number of serology tests completed
The below plot shows the total number (sum total) of serology tests related to SARS-CoV-2 completed by the SciLifeLab Autoimmunity and Serology Profiling unit since the beginning of the pandemic.
<br>
<div class="d-lg-none alert alert-info">
Scroll the plot sideways to view all of the data.
</div>
<div class="plot_wrapper">
<div class="w-100" id="total-number"></div>
</div> -->

## Weekly serology tests

The number of SARS-CoV-2 serology tests completed by the SciLifeLab Autoimmunity and Serology Profiling unit each week, divided according to whether tests were positive, negative, or research & development (R&D).
Expand All @@ -51,10 +38,14 @@ The number of SARS-CoV-2 serology tests completed by the SciLifeLab Autoimmunity
Scroll the plot sideways to view all of the data.
</div>

<div class="plot_wrapper">
<div class="w-100" id="bar-chart"></div>
<div class="plot_wrapper mb-3">
<div class="table-responsive" style="min-width: 800px">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/weekly_serology_tests.json" height="550px" >}}</div>
</div>

<!-- **Download the data:** [The number of R&D, negative, and positive tests done per week](https://blobserver.dc.scilifelab.se/blob/Serology-testing-statistics-dataset-20202021.csv) -->

**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/serology/weekly-serology-tests.py).

## Cumulative serology tests

The cumulative number of positive, negative, and research & development (R&D) SARS-CoV-2 serology tests completed over time at the SciLifeLab Autoimmunity and Serology Profiling unit.
Expand All @@ -63,22 +54,18 @@ The cumulative number of positive, negative, and research & development (R&D) SA
Scroll the plot sideways to view all of the data.
</div>

<div class="plot_wrapper">
<div class="w-100" id="cumulative-plot"></div>
<div class="plot_wrapper mb-3">
<div class="table-responsive" style="min-width: 800px">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/cumulative_serology_tests.json" height="550px" >}}</div>
</div>

<!-- **Download the data:** [The number of R&D, negative, and positive tests done per week](https://blobserver.dc.scilifelab.se/blob/Serology-testing-statistics-dataset-20202021.csv) -->

**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/serology/cumulative-serology-tests.py).

#### About serology testing at the Autoimmunity and Serology Profiling unit

Early in the COVID-19 pandemic, work was initiated to [develop a serological assay](https://www.scilifelab.se/capabilities/pandemic-laboratory-preparedness/pandemic-response/other-scilifelab-efforts/serology/) for large scale testing of plasma and serum samples for antibodies against SARS-CoV-2. The work was undertaken by three research groups at [the Department of Protein Science, KTH Royal Institute of Technology (KTH)](https://www.kth.se/pro) and the [Autoimmunity and Serology Profiling unit](https://www.scilifelab.se/facilities/autoimmunity-profiling/) at [SciLifeLab](https://www.scilifelab.se).

By comparing and combining a large number of variants of SARS-CoV-2 proteins as antigens, a [highly sensitive and specific multiplex bead-based assay](https://doi.org/10.1002/cti2.1312) was established. The high-throughput assay can be used to process up to 8000 samples per week. The vast majority of samples analysed to date originated from healthcare personnel, population-based studies, personnel in the pharmaceutical and biotechnology industry, and from within multiple research collaborations. Collaborators and sample providers include the community study at Danderyd University Hospital ([see news involving a follow-up study at Danderyd University Hospital](https://www.scilifelab.se/news/four-out-of-five-still-have-antibodies-against-sars-cov-2)), Karolinska University Hospital, Uppsala University Hospital, Skåne University Hospital, Örebro University Hospital, Sophiahemmet Hospital, Public Health Agency of Sweden, RISE (Research Institutes of Sweden), AstraZeneca, Cytiva, SVPH, Karolinska Institutet, KTH, Uppsala University, and Lund University.

Check out the [Autoimmunity and Serology Profiling unit page](https://www.scilifelab.se/units/autoimmunity-profiling/) on the SciLifeLab website to find out more about the unit itself. Publications produced by studies making use of the unit are available in the [SciLifeLab Infrastructure Publications database](https://publications.scilifelab.se/label/Autoimmunity%20and%20Serology%20Profiling).

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<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.dc.scilifelab.se/graphic/e5c031600d334d889f33080d3f0ac0dd.js?id=bar-chart"></script>
<script src="https://datagraphics.dc.scilifelab.se/graphic/4c635b2679e648e384d952dd3e506ff1.js?id=cumulative-plot"></script>
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39 changes: 13 additions & 26 deletions content/svenska/dashboards/serology-statistics.md
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Expand Up @@ -9,6 +9,7 @@ menu:
name: SARS-CoV-2 antikoppstester som utförts av SciLifeLab
aliases:
- /sv/data_types/health_data/serology-statistics/
plotly: true
---

<div class="alert alert-info">
Expand All @@ -24,20 +25,6 @@ Serologiska tester innebär att kroppsvätskor testas för förekomst av antikro

<div class="alert alert-info">Senaste uppdatering: {{% serology_date_modified %}}.</div>

<!-- ## Number of serology tests completed
The below plot shows the total number (sum total) of serology tests related to SARS-CoV-2 completed by the SciLifeLab Autoimmunity and Serology Profiling unit since the beginning of the pandemic.
<br>
<div class="d-lg-none alert alert-info">
Scroll the plot sideways to view all of the data.
</div>
<div class="plot_wrapper">
<div class="w-100" id="total-number"></div>
</div> -->

## Serologiska tester per vecka

Antalet SARS-CoV-2 serologitester som SciLifeLab Autoimmunity and Serology Profiling-enheten genomförde varje vecka, uppdelat efter om testerna var positiva, negativa eller inom forskning och utveckling (R&D).
Expand All @@ -46,10 +33,14 @@ Antalet SARS-CoV-2 serologitester som SciLifeLab Autoimmunity and Serology Profi
Att rotera mobiltelefonen kan förbättra grafens layout
</div>

<div class="plot_wrapper">
<div class="w-100" id="bar-chart"></div>
<div class="plot_wrapper mb-3">
<div class="table-responsive" style="min-width: 800px">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/weekly_serology_tests.json" height="550px" >}}</div>
</div>

<!-- **Ladda ner data:** [Serology-testing-statistics-dataset-20202021.csv](https://blobserver.dc.scilifelab.se/blob/Serology-testing-statistics-dataset-20202021.csv) -->

**Källkod som används för att skapa grafen:** [Källkod](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/serology/weekly-serology-tests.py).

## Kumulativa serologiska tester

Det kumulativa antalet positiva, negativa och forsknings- och utvecklingstester (R&D) av SARS-CoV-2-serologi som slutförts över tid vid SciLifeLab Autoimmunity and Serology Profiling-enheten.
Expand All @@ -58,22 +49,18 @@ Det kumulativa antalet positiva, negativa och forsknings- och utvecklingstester
Att rotera mobiltelefonen kan förbättra grafens layout
</div>

<div class="plot_wrapper">
<div class="w-100" id="cumulative-plot"></div>
<div class="plot_wrapper mb-3">
<div class="table-responsive" style="min-width: 800px">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/cumulative_serology_tests.json" height="550px" >}}</div>
</div>

<!-- **Ladda ner data:** [Serology-testing-statistics-dataset-20202021.csv](https://blobserver.dc.scilifelab.se/blob/Serology-testing-statistics-dataset-20202021.csv) -->

**Källkod som används för att skapa grafen:** [Källkod](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/serology/cumulative-serology-tests.py).

#### Om serologisk testning vid enheten för Autoimmunity and Serology Profiling

Tidigt under covid-19-pandemin inleddes arbetet med att [utveckla en serologisk analys](https://www.scilifelab.se/capabilities/pandemic-laboratory-preparedness/pandemic-response/other-scilifelab-efforts/serology/) för storskalig testning av plasma- och serumprover för antikroppar mot SARS-CoV-2. Arbetet utfördes av tre forskargrupper vid [institutionen för proteinvetenskap, Kungliga Tekniska Högskolan (KTH)](https://www.kth.se/sv/pro/protein-science-1.784558) och [enheten för autoimmunitet och serologisk profilering](https://www.scilifelab.se/facilities/autoimmunity-profiling/) vid [SciLifeLab](https://www.scilifelab.se).

Genom att jämföra och kombinera ett stort antal varianter av SARS-CoV-2-proteiner som antigener etablerades en [mycket känslig och specifik så kallad multiplex bead-based assay](https://doi.org/10.1002/cti2.1312). Assayen med hög kapacitet kan användas för att bearbeta upp till 8000 prover per vecka. De allra flesta prover som hittills har analyserats kommer från vårdpersonal, befolkningsbaserade studier, personal inom läkemedels- och bioteknikindustrin samt från flera olika forskningssamarbeten. Samarbetspartners och provleverantörer inkluderar samhällsstudien vid Danderyds universitetssjukhus ([se nyhet om uppföljningsstudie vid Danderyds universitetssjukhus](https://www.scilifelab.se/news/four-out-of-five-still-have-antibodies-against-sars-cov-2)), Karolinska universitetssjukhuset, Akademiska sjukhuset i Uppsala, Skånes universitetssjukhus, Universitetssjukhuset Örebro, Sophiahemmet, Folkhälsomyndigheten, RISE (Research Institutes of Sweden), AstraZeneca, Cytiva, SVPH, Karolinska Institutet, KTH, Uppsala universitet och Lunds universitet.

Kolla in [Autoimmunity and Serology Profiling unit page](https://www.scilifelab.se/units/autoimmunity-profiling/) på SciLifeLabs webbplats för att få reda på mer om själva enheten. Publikationer som producerats av studier som använder enheten finns tillgängliga i databasen [SciLifeLab Infrastructure Publications](https://publications.scilifelab.se/label/Autoimmunity%20and%20Serology%20Profiling).

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<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>
14 changes: 14 additions & 0 deletions devbox.json
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53 changes: 53 additions & 0 deletions devbox.lock
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