From 61be4a57f56f2c2ec7dc42d62121d85886c9ea27 Mon Sep 17 00:00:00 2001
From: Luis Aleixo <luis.aleixo@cern.ch>
Date: Fri, 17 Sep 2021 14:46:45 +0200
Subject: [PATCH] Updated infected probability with f_inf that considers the
 host immunity and the viable-to-RNA distribution

---
 cara/models.py                                | 15 +++++++++++++--
 cara/monte_carlo/data.py                      |  6 ++++++
 cara/tests/models/test_concentration_model.py |  1 +
 cara/tests/models/test_exposure_model.py      |  1 +
 cara/tests/test_infected_population.py        |  1 +
 5 files changed, 22 insertions(+), 2 deletions(-)

diff --git a/cara/models.py b/cara/models.py
index 7b5d034d..410c48e3 100644
--- a/cara/models.py
+++ b/cara/models.py
@@ -429,6 +429,9 @@ class Virus:
     #: Dose to initiate infection, in RNA copies
     infectious_dose: _VectorisedFloat
 
+    #: viable-to-RNA virus ratio as a function of the viral load
+    viable_to_RNA: _VectorisedFloat
+
     #: Pre-populated examples of Viruses.
     types: typing.ClassVar[typing.Dict[str, "Virus"]]
 
@@ -465,19 +468,23 @@ Virus.types = {
         # as per https://www.dhs.gov/publication/st-master-question-list-covid-19
         # 50 comes from Buonanno et al.
         infectious_dose=50.,
+        viable_to_RNA = 0.5,
     ),
     'SARS_CoV_2_B117': SARSCoV2(
         # also called VOC-202012/01
         viral_load_in_sputum=1e9,
         infectious_dose=30.,
+        viable_to_RNA = 0.5,
     ),
     'SARS_CoV_2_P1': SARSCoV2(
         viral_load_in_sputum=1e9,
         infectious_dose=1/0.045,
+        viable_to_RNA = 0.5,
     ),
     'SARS_CoV_2_B16172': SARSCoV2(
         viral_load_in_sputum=1e9,
         infectious_dose=30/1.6,
+        viable_to_RNA = 0.5,
     ),
 }
 
@@ -706,6 +713,9 @@ class InfectedPopulation(_PopulationWithVirus):
     #: The type of expiration that is being emitted whilst doing the activity.
     expiration: _ExpirationBase
 
+    #: The percentage of host immunity
+    host_immunity: float = 0.
+
     @method_cache
     def emission_rate_when_present(self) -> _VectorisedFloat:
         """
@@ -962,9 +972,10 @@ class ExposureModel:
         inf_aero = (
             self.exposed.activity.inhalation_rate *
             (1 - self.exposed.mask.inhale_efficiency()) *
-            exposure * self.fraction_deposited
+            exposure * self.fraction_deposited * 
+            (self.concentration_model.infected.virus.viable_to_RNA * (1 - self.concentration_model.infected.host_immunity))
         )
-
+        
         # Probability of infection.
         return (1 - np.exp(-(inf_aero/self.concentration_model.virus.infectious_dose))) * 100
 
diff --git a/cara/monte_carlo/data.py b/cara/monte_carlo/data.py
index 71498ee0..1ecb25a1 100644
--- a/cara/monte_carlo/data.py
+++ b/cara/monte_carlo/data.py
@@ -99,24 +99,30 @@ symptomatic_vl_frequencies = LogCustomKernel(
     kernel_bandwidth=0.1
 )
 
+# From https://doi.org/10.1093/cid/ciaa1579
+infectious_virus_distribution = Uniform(0.15, 0.45)
 
 # From CERN-OPEN-2021-04 and refererences therein
 virus_distributions = {
     'SARS_CoV_2': mc.SARSCoV2(
                 viral_load_in_sputum=symptomatic_vl_frequencies,
                 infectious_dose=100,
+                viable_to_RNA=infectious_virus_distribution,
                 ),
     'SARS_CoV_2_B117': mc.SARSCoV2(
                 viral_load_in_sputum=symptomatic_vl_frequencies,
                 infectious_dose=60,
+                viable_to_RNA=infectious_virus_distribution,
                 ),
     'SARS_CoV_2_P1': mc.SARSCoV2(
                 viral_load_in_sputum=symptomatic_vl_frequencies,
                 infectious_dose=100/2.25,
+                viable_to_RNA=infectious_virus_distribution,
                 ),
     'SARS_CoV_2_B16172': mc.SARSCoV2(
                 viral_load_in_sputum=symptomatic_vl_frequencies,
                 infectious_dose=60/1.6,
+                viable_to_RNA=infectious_virus_distribution,
                 ),
 }
 
diff --git a/cara/tests/models/test_concentration_model.py b/cara/tests/models/test_concentration_model.py
index 7437f41d..117f00d5 100644
--- a/cara/tests/models/test_concentration_model.py
+++ b/cara/tests/models/test_concentration_model.py
@@ -42,6 +42,7 @@ def test_concentration_model_vectorisation(override_params):
             virus=models.SARSCoV2(
                 viral_load_in_sputum=defaults['viral_load_in_sputum'],
                 infectious_dose=50.,
+                viable_to_RNA = 0.5,
             ),
             expiration=models._ExpirationBase.types['Breathing'],
         )
diff --git a/cara/tests/models/test_exposure_model.py b/cara/tests/models/test_exposure_model.py
index ac82dae3..98d4e361 100644
--- a/cara/tests/models/test_exposure_model.py
+++ b/cara/tests/models/test_exposure_model.py
@@ -190,6 +190,7 @@ def test_infectious_dose_vectorisation():
         virus=models.SARSCoV2(
             viral_load_in_sputum=1e9,
             infectious_dose=np.array([50, 20, 30]),
+            viable_to_RNA = 0.5,
         ),
         expiration=models.Expiration.types['Talking']
     )
diff --git a/cara/tests/test_infected_population.py b/cara/tests/test_infected_population.py
index 13467f9f..9f7b06ab 100644
--- a/cara/tests/test_infected_population.py
+++ b/cara/tests/test_infected_population.py
@@ -32,6 +32,7 @@ def test_infected_population_vectorisation(override_params):
             virus=cara.models.Virus(
                 viral_load_in_sputum=defaults['viral_load_in_sputum'],
                 infectious_dose=50.,
+                viable_to_RNA = 0.5,
             ),
             expiration=cara.models._ExpirationBase.types['Breathing'],
     )