From 7a4e64c9b680a5b7d277fb845fa0bb38ded315ab Mon Sep 17 00:00:00 2001
From: Luis Aleixo <luis.aleixo@cern.ch>
Date: Fri, 24 Sep 2021 17:27:35 +0200
Subject: [PATCH] Added Beta VOC

---
 cara/apps/calculator/model_generator.py              |  2 +-
 .../templates/base/calculator.report.html.j2         |  2 ++
 .../calculator/templates/calculator.form.html.j2     |  2 ++
 cara/models.py                                       | 12 +++++++++---
 cara/monte_carlo/data.py                             |  6 ++++++
 5 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/cara/apps/calculator/model_generator.py b/cara/apps/calculator/model_generator.py
index 6e4a5527..885b4500 100644
--- a/cara/apps/calculator/model_generator.py
+++ b/cara/apps/calculator/model_generator.py
@@ -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'}
diff --git a/cara/apps/calculator/templates/base/calculator.report.html.j2 b/cara/apps/calculator/templates/base/calculator.report.html.j2
index 146478dc..963eea31 100644
--- a/cara/apps/calculator/templates/base/calculator.report.html.j2
+++ b/cara/apps/calculator/templates/base/calculator.report.html.j2
@@ -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" %}
diff --git a/cara/apps/calculator/templates/calculator.form.html.j2 b/cara/apps/calculator/templates/calculator.form.html.j2
index 65391454..b570d85d 100644
--- a/cara/apps/calculator/templates/calculator.form.html.j2
+++ b/cara/apps/calculator/templates/calculator.form.html.j2
@@ -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>
diff --git a/cara/models.py b/cara/models.py
index 67d4c62a..1f8fe188 100644
--- a/cara/models.py
+++ b/cara/models.py
@@ -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,
     ),
 }
 
diff --git a/cara/monte_carlo/data.py b/cara/monte_carlo/data.py
index 4cb5f388..1abddb91 100644
--- a/cara/monte_carlo/data.py
+++ b/cara/monte_carlo/data.py
@@ -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,