Updated user guide and interface support messages

For test use only.

cara/apps/calculator/model_generator.py

@@ -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_P1', 'SARS_CoV_2_B16172', 'SARS_CoV_2_Omicron'}
 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'}

cara/apps/calculator/templates/base/calculator.report.html.j2

@@ -206,6 +206,8 @@
 							<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_Omicron" %}
+							<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>

cara/apps/calculator/templates/calculator.form.html.j2

@@ -69,7 +69,8 @@
       <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_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_Omicron">SARS-CoV-2 (Omicron VOC)</option>
     </select>
     </div>
     </div>
@@ -517,6 +518,7 @@
     <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>
+    <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>

cara/apps/calculator/templates/userguide.html.j2

@@ -72,6 +72,7 @@ The choices are:</p>
 <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>
+<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>

cara/models.py

@@ -481,6 +481,10 @@ Virus.types = {
         viral_load_in_sputum=1e9,
         infectious_dose=30/1.6,
     ),
+    'SARS_CoV_2_Omicron': SARSCoV2(
+        viral_load_in_sputum=1e9,
+        infectious_dose=50/4.9841,
+    ),
 }
 
 

cara/monte_carlo/data.py

@@ -57,6 +57,10 @@ virus_distributions = {
                 viral_load_in_sputum=symptomatic_vl_frequencies,
                 infectious_dose=60/1.6,
                 ),
+    'SARS_CoV_2_Omicron': mc.SARSCoV2(
+                viral_load_in_sputum=symptomatic_vl_frequencies,
+                infectious_dose=50/4.334,
+                ),            
 }