Vision Mission of JIIT

Network+ of Life and its Departments

Course Code: 16B1NBT531( Open Elective)

B Tech VII Semester

AY:2023-24
Programme
Educational
Core Course Objectives (PEOs)
of UG and PG
Programmes
Department of Biotechnology
JIIT NOIDA

Course Coordinator: Dr. Chakresh Jain

Spreading network/
epidemic model
Introduction
• The real-time prediction of an epidemic outbreak is a very recent
development.
• The ground was set by the development of the epidemic modeling
framework in the 1980s and by the 2003 SARS epidemic, which
resulted in worldwide reporting guidelines about ongoing outbreaks.
• The subsequent systematic availability of data pertaining to a
pandemic offered real-time input to modeling efforts
Some question
• The emergence of any new pathogen raises several key questions:
• • Where did the pathogen originate?
• • Where do we expect new cases?
• • When will the epidemic arrive at various densely populated areas?
• • How many infections are to be expected?
• • What can we do to slow its spread?
• • How can we eradicate it?
Introduction
• Most networks facilitate transfer
along their links: transfer of trust,
knowledge, habits or information
(social networks), electricity
(power grid), money (financial
networks), goods (trade
networks), Biological netwrok.
• To understand these phenomena,
we must understand how the
network topology affects these
dynamical processes
Modelling transmission/epidemic
• Modelling transmission within networks is a broad and challenging field
• Yellow fever, smallpox, measles, and polio are prime examples of epidemics.
• An epidemic disease doesn't necessarily have to be contagious
• Endemic: A disease outbreak is endemic when it is consistently present but
limited to a particular region. This makes the disease spread and rates
predictable. Malaria, for example, is considered endemic in certain countries and
regions.
• Pendamic: pandemic when a disease’s growth is exponential. This means the
growth rate skyrockets, and each day cases grow more than the day prior. In
being declared a pandemic, the virus has nothing to do with virology, population
immunity, or disease severity. It means a virus covers a wide area, affecting
several countries and populations.
• Epidemic as an unexpected increase in the number of disease cases in a specific
geographical area.
Network models
• Network models are widely used in epidemiology to simulate and
understand the spread of infectious diseases within populations.
• These models leverage the structure of contact networks, where
nodes represent individuals or locations, and edges represent
interactions or connections between them.
• The dynamics of disease transmission can be modeled by defining
how the infection spreads through the network over time
Epidemiological Models
• The SIR (Susceptible-Infectious-Recovered), SI (Susceptible-
Infectious), and SEIR (Susceptible-Exposed-Infectious-Recovered)
models are compartmental models commonly used in epidemiology
to study the spread of infectious diseases within a population.
• Each model represents individuals in different compartments based
on their disease status, and the transitions between these
compartments capture the dynamics of the epidemic
Epidemiological Models
SIR Model (Susceptible-Infectious-Recovered):
• The SIR model is a compartmental model that divides the population
into three compartments: susceptible (S), infectious (I), and recovered
(R).
• It assumes that individuals move from being susceptible to infectious
and then to recovered, gaining immunity.
• The connections in the network determine the probability of
transmission from infectious to susceptible individuals.
SIR Model (Susceptible-Infectious-Recovered):
• Compartments:
• Susceptible (S): Individuals who are not infected but are susceptible to the disease.
• Infectious (I): Individuals who are currently infected and can transmit the disease to
susceptible individuals.
• Recovered (R): Individuals who have recovered from the infection and gained immunity.
• Transitions:
• Susceptible individuals become infectious with a certain transmission rate.
• Infectious individuals recover and move to the recovered compartment.
• The model assumes that recovered individuals have lifelong immunity.
• Equations:

Key Features:
• Assumes a simple structure with no latency period (time between exposure and becoming
infectious).
• Assumes lifelong immunity after recovery.
SI Model (Susceptible-Infectious):

SI Model (Susceptible-Infectious):
• The SI model simplifies the SIR model by excluding the recovered
compartment.
• In this model, individuals move directly from being susceptible to
infectious, and there is no recovery or immunity.
SI Model (Susceptible-Infectious):

• Compartments:
• Susceptible (S): Individuals who are not infected but are susceptible to the disease.
• Infectious (I): Individuals who are currently infected and can transmit the disease.
• Transitions:
• Susceptible individuals become infectious with a certain transmission rate.
• Infectious individuals do not recover or gain immunity.
• Equations:

• Key Features:
• Does not include a recovered compartment.
• Assumes individuals remain infectious indefinitely.
Epidermiological Model
SEIR Model (Susceptible-Exposed-Infectious-Recovered):
• The SEIR model extends the SIR model by introducing an exposed (E)
compartment. Individuals in the exposed compartment have been
exposed to the infectious agent but are not yet infectious. This
addition accounts for the incubation period of certain diseases.
SEIR Model (Susceptible-Exposed-Infectious-
Recovered):
• Compartments:
• Susceptible (S): Individuals who are not infected but are susceptible to the disease.
• Exposed (E): Individuals who have been exposed to the infectious agent but are not yet infectious.
• Infectious (I): Individuals who are currently infected and can transmit the disease.
• Recovered (R): Individuals who have recovered from the infection and gained immunity.
• Transitions:
• Susceptible individuals become exposed, then infectious, and finally recover.
• Exposed individuals move to the infectious compartment after the incubation period.
• Infectious individuals recover and move to the recovered compartment.
• The model assumes recovered individuals have lifelong immunity.
• Equations:

• Key Features:
• Introduces an exposed compartment to account for the latent period before individuals become
infectious.
• Assumes recovered individuals have lifelong immunity.
Epidemiological Model
• Networks with Heterogeneous Mixing:
• In realistic scenarios, interactions between individuals are not uniform. Some
individuals may have more contacts than others.
• Models incorporating heterogeneous mixing capture this variation in contact
patterns, allowing for a more realistic representation of disease spread.
• Dynamic Networks:
• Dynamic network models account for changes in the network structure over
time.
• This is especially relevant in scenarios where connections between individuals
evolve, such as in the context of transportation networks or social dynamics.
Different model used in mapping spreading
Case study
• Epidemiological network models, which are conceived as a flexible way of
representing objects and their relationships.
• Many studies have used these models over the years, and they have also
been used to explain COVID-19. Based on the information provided by the
Web of Science database, exploratory, descriptive research based on the
techniques and tools of bibliometric analysis of scientific production on
epidemiological network models was carried out.
• The epidemiological models used in the papers are diverse, highlighting
those using the SIS (Susceptible-Infected-Susceptible), SIR (Susceptible-
Infected-Recovered) and SEIR (Susceptible-Exposed-Infected-Removed)
models. No model can perfectly predict the future, but they provide a
sufficiently accurate approximation for policy makers to determine the
actions needed to curb the pandemic
Case sudy
Differences among Various model
• The main differences between these models lie in the compartments
they include and the transitions between these compartments.
• The SIR model includes susceptible, infectious, and recovered
compartments, the SI model excludes the recovered compartment,
and the SEIR model introduces an exposed compartment to account
for the latent period before becoming infectious.
GLEaM model and role of network
• The role of network topology has a drastic impact on the dynamics of the
spreading process, offering distinct predictions for spreading on random
and on scale-free networks
• Modeling the spread of pathogens also represents an important practical
application of network science.
• The advances in this area were rather spectacular, giving birth to accurate
epidemic forecasts, something that was only a dream a decade earlier.
• Two advances made this possible.
• The first is the emergence of a robust theoretical framework to describe network-
based epidemics.
• The second is access to accurate real time data on human travel and demographics,
allowing us to reconstruct the mobility network that is responsible for the global
spread of a pathogen
Compartmental structure of the epidemic model within each
subpopulation of GLEaM
GLEaM: A compoutational model
• Epidemic forecast aims to foresee the real time spread of a pathogen,
predicting the number of infected individuals expected each week in
each major city .
• The first successful real time pandemic forecast based on network
science relied on the Global Epidemic and Mobility (GLEAM)
computational model
• GLEaM suitable for the computational modeling and anticipation of
the spatio-temporal patterns of global epidemic spreading, the
understanding of historical epidemics, the assessment of the role of
human mobility in shaping global epidemics
GLEAM
• GLEAM employs a network-based computational model:
• Global Epidemic and Mobility (GLEaM) model that integrates
sociodemographic and population mobility data in a spatially structured
stochastic disease approach to simulate the spread of epidemics at the
worldwide scale.
• • GLEAM maps each geographic location into the nodes of a network.
• • Transport between these nodes, representing the links, are provided by
global transportation data, like airline schedules
• • GLEAM estimates the epidemic parameters, like the transmission rate or
reproduction number, using a network-based approach: It relies on
chronological data that captures the worldwide spread of the disease
Main Features of GLEAM
• Mobility Data Integration: GLEAM incorporates data on human mobility, considering
factors such as travel patterns, transportation infrastructure, and migration trends. This
allows the model to simulate the movement of individuals across different regions.
• Demographic Information: The model takes into account demographic data to better
understand the distribution of population across various age groups and geographic
locations.
• Disease Parameters: considers the characteristics of the specific infectious disease under
investigation, such as its transmission rate, latent period, and other relevant parameters.
These factors influence how the disease spreads within the simulated population.
• Simulation and Visualization: it typically uses mathematical models and simulation
techniques to predict the spread of infectious diseases over time.
• Scenario Analysis: The model allows for scenario analysis, enabling researchers to
explore different intervention strategies and assess their potential effectiveness in
controlling the spread of an epidemic
GLEaM model
• GLEaM integrates three different data layers (population layer, . Mobility Layers, Disease
model)
• GLEaM simulates the mobility of individuals from one subpopulation to another by a
stochastic procedure in which the number of passengers of each compartment traveling
from a subpopulation j to a subpopulation ℓ is an integer random variable defined by a
stochastic process defined on the basis of real mobility data.
• Short range commuting between subpopulations is modeled with a time scale separation
approach that defines the effective force of infections in connected subpopulations.
• Superimposed on the worldwide population and mobility layers is the epidemic model
that defines the disease and population dynamics.
• The infection dynamics takes place within each subpopulation and assumes the classic
compartmentalization in which each individual is classified by one of the discrete states
such as susceptible, latent, infectious symptomatic, infectious non-symptomatic or
permanently recovered/removed
Ref
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3056392/