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Add new virus type (indian variant)

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This commit is contained in:
Andre Henriques 2021-06-25 09:10:04 +00:00
parent d36203f703
commit 3f89657355
6 changed files with 25 additions and 12 deletions
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2
cara/apps/calculator/model_generator.py
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@ -631,7 +631,7 @@ MECHANICAL_VENTILATION_TYPES = {'mech_type_air_changes', 'mech_type_air_supply',
MASK_TYPES = {'Type I', 'FFP2'}
MASK_WEARING_OPTIONS = {'mask_on', 'mask_off'}
VENTILATION_TYPES = {'natural_ventilation', 'mechanical_ventilation', 'no_ventilation'}
VIRUS_TYPES = {'SARS_CoV_2', 'SARS_CoV_2_B117', 'SARS_CoV_2_P1'}
VIRUS_TYPES = {'SARS_CoV_2', 'SARS_CoV_2_B117', 'SARS_CoV_2_P1', 'SARS_CoV_2_B16172'}
VOLUME_TYPES = {'room_volume_explicit', 'room_volume_from_dimensions'}
WINDOWS_OPENING_REGIMES = {'windows_open_permanently', 'windows_open_periodically', 'not-applicable'}
WINDOWS_TYPES = {'window_sliding', 'window_hinged', 'not-applicable'}

6
cara/apps/calculator/templates/base/calculator.report.html.j2
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@ -40,9 +40,11 @@
{% if form.virus_type == "SARS_CoV_2" %}
SARS-CoV-2 (nominal strain)
{% elif form.virus_type == "SARS_CoV_2_B117" %}
<a href="https://www.ecdc.europa.eu/en/publications-data/covid-19-risk-assessment-spread-new-sars-cov-2-variants-eueea">SARS-CoV-2 (B.1.1.7)</a>
<a href="https://www.ecdc.europa.eu/en/publications-data/covid-19-risk-assessment-spread-new-sars-cov-2-variants-eueea">SARS-CoV-2 (Alpha VOC) </a>
{% elif form.virus_type == "SARS_CoV_2_P1" %}
<a href="https://github.com/CADDE-CENTRE/Novel-SARS-CoV-2-P1-Lineage-in-Brazil/blob/main/manuscript/FINAL_P1_MANUSCRIPT_25-02-2021_combined.pdf">SARS-CoV-2 (P.1)</a>
<a href="https://github.com/CADDE-CENTRE/Novel-SARS-CoV-2-P1-Lineage-in-Brazil/blob/main/manuscript/FINAL_P1_MANUSCRIPT_25-02-2021_combined.pdf">SARS-CoV-2 (Gamma VOC)</a>
{% elif form.virus_type == "SARS_CoV_2_B16172" %}
<a href="https://www.bmj.com/content/373/bmj.n1513">SARS-CoV-2 (Delta VOC)</a>
{% endif %}
</p></li>
<li><p class="data_text">Room Volume: {{ model.concentration_model.room.volume }} m³</p></li>

12
cara/apps/calculator/templates/calculator.form.html.j2
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@ -61,8 +61,9 @@ v{{ calculator_version }} <span style="float:right; font-weight:bold">Please sen
<label class="col-xl-3 col-lg-4 col-sm-3 col-form-label">Variant:</label>
<select id="Variant" name="virus_type" class="col-xl-5 col-lg-7 col-sm-7 col-7">
<option value="SARS_CoV_2">SARS-CoV-2 (nominal strain)</option>
<option value="SARS_CoV_2_B117">SARS-CoV-2 (B.1.1.7)</option>
<option value="SARS_CoV_2_P1">SARS-CoV-2 (P.1)</option>
<option value="SARS_CoV_2_B117">SARS-CoV-2 (Alpha VOC)</option>
<option value="SARS_CoV_2_P1">SARS-CoV-2 (Gamma VOC)</option>
<option value="SARS_CoV_2_B16172">SARS-CoV-2 (Delta VOC)</option>
</select>
</div>
@ -324,10 +325,11 @@ v{{ calculator_version }} <span style="float:right; font-weight:bold">Please sen
<b>Quick Guide:</b><br>
This tool simulates the long range airborne spread SARS-CoV-2 virus in a finite volume and estimates the risk of COVID-19 infection. It is based on current scientific data and can be used to compare the effectiveness of different mitigation measures.<br>
<b>Virus data:</b> <br>
SARS-CoV-2 covers typical strains of the virus and two variants of concern (VOC):<br>
SARS-CoV-2 covers typical strains of the virus and three variants of concern (VOC):<br>
<ul>
<li>B.1.1.7 (first identified in UK, Dec 2020),</li>
<li>P.1 (first identified in Brazil/Japan, Jan 2021).</li>
<li>Alpha (also known as B.1.1.7, first identified in UK, Dec 2020),</li>
<li>Gamma (also known as P.1, first identified in Brazil/Japan, Jan 2021).</li>
<li>Delta (also known as B.1.617.2, first identified in India, Oct 2020).</li>
</ul>
Choose variant according to local area prevalence, e.g. for <a href="https://www.covid19.admin.ch/fr/epidemiologic/virus-variants?detGeo=GE">Geneva</a>
or <a href="https://www.santepubliquefrance.fr/dossiers/coronavirus-covid-19/covid-19-cartographie-des-variants-en-france-donnees-par-region-et-par-departement">Ain (France)</a>.<br>

9
cara/apps/calculator/templates/userguide.html.j2
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@ -57,18 +57,19 @@ This has a significant effect on the probability of infection.
The choices are:</p>
<ul>
<li><code>SARS-CoV-2 (nominal strain)</code>, covering typical strains and varaints which are not of concern from an epidemiologic point of view of the virus;</li>
<li><code>SARS-CoV-2 (B.1.1.7)</code>, the VOC first identified in the UK at the end of 2020 which is found to be approximately 1.5x more transmissible compared to the non-VOCs; </li>
<li><code>SARS-CoV-2 (P.1)</code>, the VOC first identified in Brazil in January 2021 which is found to be approximately 2.2x more transmissible compared to the non-VOCs.</li>
<li><code>SARS-CoV-2 (Alpha VOC)</code>, first identified in the UK at the end of 2020 which is found to be approximately 1.5x more transmissible compared to the non-VOCs; </li>
<li><code>SARS-CoV-2 (Gamma VOC)</code>, first identified in Brazil in January 2021 which is found to be approximately 2.2x more transmissible compared to the non-VOCs.</li>
<li><code>SARS-CoV-2 (Delta VOC)</code>, first identified in India towards the end of 2020 which is found to be approximately 60% more transmissible compared to the ALPHA VOC.</li>
</ul>
<p>The user can base their choice according to the prevalence of the different variants in the local area. Access to this information can be found here:</p>
<ul>
<li>Geneva: <a href="https://www.covid19.admin.ch/fr/epidemiologic/virus-variants?detGeo=GE">https://www.covid19.admin.ch/fr/epidemiologic/virus-variants?detGeo=GE</a></li>
<li>Ain (France): <a href="https://www.santepubliquefrance.fr/dossiers/coronavirus-covid-19/covid-19-cartographie-des-variants-en-france-donnees-par-region-et-par-departement">https://www.santepubliquefrance.fr/dossiers/coronavirus-covid-19/covid-19-cartographie-des-variants-en-france-donnees-par-region-et-par-departement</a></li>
</ul>
<p>N.B. The transmission data for the P.1 variant has been taken from a study data gathered in Manaus, Brazil where the variant was first observed.
<p>N.B. The transmission data for the Gamma variant has been taken from a study data gathered in Manaus, Brazil where the variant was first observed.
The local population in Manaus had very high levels of Covid-19 antibodies (&gt;67%) in recent months.
This factor has been taken into account by the authors of the study, via statistical adjustments to the transmission value (i.e. it has been increased, to account for spread in a population with significant acquired Covid-19 immunity).
However, this value may be revised in the future as more studies of P.1 transmission in different geographical locations become available.</p>
However, this value may be revised in the future as more studies of the Gamma VOC transmission in different geographical locations become available.</p>
<h3>Room Data</h3>
<p>Please enter either the room volume (in m³) or both the floor area (m²) and the room height (m).
This information is available via GIS Portal (<a href="https://gis.cern.ch/gisportal/">https://gis.cern.ch/gisportal/</a>).</p>

4
cara/models.py
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@ -469,6 +469,10 @@ Virus.types = {
viral_load_in_sputum=1e9,
quantum_infectious_dose=1/0.045,
),
'SARS_CoV_2_B16172': SARSCoV2(
viral_load_in_sputum=1e9,
quantum_infectious_dose=30/1.6,
),
}

4
cara/monte_carlo/data.py
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@ -53,4 +53,8 @@ virus_distributions = {
viral_load_in_sputum=symptomatic_vl_frequencies,
quantum_infectious_dose=100/2.25,
),
'SARS_CoV_2_B16172': mc.SARSCoV2(
viral_load_in_sputum=symptomatic_vl_frequencies,
quantum_infectious_dose=60/1.6,
),
}