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Merge branch 'feature/omicron_voc' into 'master'

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Added omicron, based on 3 early studies.

See merge request cara/cara!310
This commit is contained in:
Andre Henriques 2022-01-06 17:51:18 +01:00
commit 789e60340f
7 changed files with 29 additions and 5 deletions
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2
cara/apps/calculator/__init__.py
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@ -33,7 +33,7 @@ from .user import AuthenticatedUser, AnonymousUser
# calculator version. If the calculator needs to make breaking changes (e.g. change
# form attributes) then it can also increase its MAJOR version without needing to
# increase the overall CARA version (found at ``cara.__version__``).
__version__ = "3.2.0"
__version__ = "3.3.0"
class BaseRequestHandler(RequestHandler):

2
cara/apps/calculator/model_generator.py
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@ -694,7 +694,7 @@ 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', 'SARS_CoV_2_B16172'}
VIRUS_TYPES = {'SARS_CoV_2', 'SARS_CoV_2_B117', 'SARS_CoV_2_B1351','SARS_CoV_2_P1', 'SARS_CoV_2_B16172', 'SARS_CoV_2_B11529'}
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'}

8
cara/apps/templates/base/calculator.form.html.j2
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@ -68,8 +68,10 @@
<select id="Variant" name="virus_type" class="form-control">
<option value="SARS_CoV_2">SARS-CoV-2 (nominal strain)</option>
<option value="SARS_CoV_2_B117">SARS-CoV-2 (Alpha VOC)</option>
<option value="SARS_CoV_2_B1351">SARS-CoV-2 (Beta VOC)</option>
<option value="SARS_CoV_2_P1">SARS-CoV-2 (Gamma VOC)</option>
<option selected value="SARS_CoV_2_B16172">SARS-CoV-2 (Delta VOC)</option>
<option value="SARS_CoV_2_B16172">SARS-CoV-2 (Delta VOC)</option>
<option selected value="SARS_CoV_2_B11529">SARS-CoV-2 (Omicron VOC)</option>
</select>
</div>
</div>
@ -516,9 +518,11 @@
<b>Virus data:</b> <br>
SARS-CoV-2 covers the original "wild type" strain of the virus and three variants of concern (VOC):<br>
<ul>
<li>Alpha (also known as B.1.1.7, first identified in UK, Dec 2020),</li>
<li>Alpha (also known as B.1.1.7, first identified in UK, Sept 2020),</li>
<li>Beta (also known as B.1.351, first identified in South Africa, May 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>
<li>Omicron (also known as B.1.1.529, first identified in South Africa, November 2021).</li>
</ul>
Modify the default as necessary, 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>

4
cara/apps/templates/base/calculator.report.html.j2
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@ -202,10 +202,14 @@
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 (Alpha VOC) </a>
{% elif form.virus_type == "SARS_CoV_2_B1351" %}
<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2021.26.24.2100509">SARS-CoV-2 (Beta VOC) </a>
{% elif form.virus_type == "SARS_CoV_2_P1" %}
<a href="https://doi.org/10.1126/science.abh2644">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>
{% elif form.virus_type == "SARS_CoV_2_B11529" %}
<a href="https://gitlab.cern.ch/cara/cara/-/issues/226">SARS-CoV-2 (Omicron VOC)</a>
{% endif %}
</p></li>
<li><p class="data_text">Room Volume: {{ model.concentration_model.room.volume }} m³</p></li>

2
cara/apps/templates/base/userguide.html.j2
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@ -70,8 +70,10 @@ The choices are:</p>
<ul>
<li><code>SARS-CoV-2 (nominal strain)</code>, covering typical strains and variants which are not of concern from an epidemiologic point of view of the virus;</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 (Beta VOC)</code>, first identified in South Africa in May 2020 which is found to be approximately 1.25x 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>
<li><code>SARS-CoV-2 (Omicron VOC)</code>, first identified in South Africa in November 2021 which is found to be at least 2.53x more transmissible compared to the DELTA VOC.</li>
</ul>
<p>The user can modify the selected variant from the default, according to the prevalence of the different variants in the local area. Access to this information can be found here:</p>
<ul>

4
cara/models.py
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@ -481,6 +481,10 @@ Virus.types = {
viral_load_in_sputum=1e9,
infectious_dose=30/1.6,
),
'SARS_CoV_2_B11529': SARSCoV2(
viral_load_in_sputum=1e9,
infectious_dose=50/4.9841,
),
}

12
cara/monte_carlo/data.py
View file

@ -40,6 +40,8 @@ symptomatic_vl_frequencies = LogCustomKernel(
# From CERN-OPEN-2021-04 and refererences therein
# NB the infectious dose is inversely proportional to infectiousness of the strain
# i.e. an infectious dose of 80 is 25% more infectious than a dose of 100, (1/(80/100))
virus_distributions = {
'SARS_CoV_2': mc.SARSCoV2(
viral_load_in_sputum=symptomatic_vl_frequencies,
@ -49,6 +51,10 @@ virus_distributions = {
viral_load_in_sputum=symptomatic_vl_frequencies,
infectious_dose=60,
),
'SARS_CoV_2_B1351': mc.SARSCoV2(
viral_load_in_sputum=symptomatic_vl_frequencies,
infectious_dose=80,
),
'SARS_CoV_2_P1': mc.SARSCoV2(
viral_load_in_sputum=symptomatic_vl_frequencies,
infectious_dose=100/2.25,
@ -56,7 +62,11 @@ virus_distributions = {
'SARS_CoV_2_B16172': mc.SARSCoV2(
viral_load_in_sputum=symptomatic_vl_frequencies,
infectious_dose=60/1.6,
),
),
'SARS_CoV_2_B11529': mc.SARSCoV2(
viral_load_in_sputum=symptomatic_vl_frequencies,
infectious_dose=(1/4.9841)*100,
),
}