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Added Beta VOC

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This commit is contained in:
Luis Aleixo 2021-09-24 17:27:35 +02:00
parent 1eb9d85b24
commit 7a4e64c9b6
5 changed files with 20 additions and 4 deletions
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2
cara/apps/calculator/model_generator.py
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@ -699,7 +699,7 @@ 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_P1', 'SARS_CoV_2_B16172', 'SARS_CoV_2_B1351'}
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'}

2
cara/apps/calculator/templates/base/calculator.report.html.j2
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@ -195,6 +195,8 @@
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_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" %}

2
cara/apps/calculator/templates/calculator.form.html.j2
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@ -64,6 +64,7 @@ v{{ calculator_version }} <span style="float:right; font-weight:bold">Please sen
<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 (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>
</select>
@ -347,6 +348,7 @@ v{{ calculator_version }} <span style="float:right; font-weight:bold">Please sen
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>Beta (also known as B.1.351, first identified in South Africa, Oct 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>

12
cara/models.py
View file

@ -480,19 +480,25 @@ Virus.types = {
viral_load_in_sputum=1e9,
infectious_dose=50.,
viable_to_RNA_ratio = 0.5,
transmissibility_factor=0.6,
transmissibility_factor=0.78,
),
'SARS_CoV_2_B1351': SARSCoV2(
viral_load_in_sputum=1e9,
infectious_dose=50.,
viable_to_RNA_ratio=0.5,
transmissibility_factor=0.8,
),
'SARS_CoV_2_P1': SARSCoV2(
viral_load_in_sputum=1e9,
infectious_dose=50.,
viable_to_RNA_ratio = 0.5,
transmissibility_factor=0.45,
transmissibility_factor=0.72,
),
'SARS_CoV_2_B16172': SARSCoV2(
viral_load_in_sputum=1e9,
infectious_dose=50.,
viable_to_RNA_ratio = 0.5,
transmissibility_factor=0.38,
transmissibility_factor=0.51,
),
}

6
cara/monte_carlo/data.py
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@ -119,6 +119,12 @@ virus_distributions = {
viable_to_RNA_ratio=viable_to_RNA_ratio_distribution,
transmissibility_factor=0.78,
),
'SARS_CoV_2_B1351': mc.SARSCoV2(
viral_load_in_sputum=symptomatic_vl_frequencies,
infectious_dose=infectious_dose_distribution,
viable_to_RNA_ratio=viable_to_RNA_ratio_distribution,
transmissibility_factor=0.8,
),
'SARS_CoV_2_P1': mc.SARSCoV2(
viral_load_in_sputum=symptomatic_vl_frequencies,
infectious_dose=infectious_dose_distribution,