This is a summary of the course molecular epidemiology of infectious diseases from the master infectious and tropical diseases. It contains class notes and exercises.
Summary Molecular Epidemiology
1. Introduction
A. What is Molecular Epidemiology?
Epidemiology = Study of the relationships existing between diseases and factors (environmental,
behavioral, social…) prone to influence their frequency, distribution, and evolution.
Molecular epidemiology is an integration between molecular biology and traditional epidemiologic
research. Molecular biologists look close at the reality, they look at the DNA of a given pathogen in a
test tube, while the epidemiologist look at it from a higher distance to the reality. Epidemiology looks
at the bigger picture, molecular epidemiology only focuses on the details. The richness and major
challenges in molecular epidemiology are that molecular biologists and epidemiologists often have a
different vision of the reality, ‘myopia’ and ‘presbyopia’ respectively. Waiting for sufficient hybrids
between these two scientists, communication needs to be optimal among them.
Epidemiology is the basic science of public health. It answers several questions like:
• What causes disease?
• How does disease spread?
• What prevents disease?
• What works in controlling disease?
Molecular epidemiology will use molecular tools to answer these questions. You have to distinguish
infection from disease. An infection is caused by a pathogen, but this is not necessarily a disease.
Only when the individual is experiencing symptoms, we call it a disease.
Why molecular epidemiology? What for?
1) Provide the scientific basis to prevent disease & injury and promote health.
This is the rapid evolution of HIV in a SINGLE patient. A phylogenetic analysis is made on the
sequence of HIV on different timepoints. You see that over 13 years the HIV strain has already
evolved very quickly and that it drifted away from the initial transmitted virus.
,2) Determine relative importance to establish priorities for research & action.
Here you see a risk mapping
of Cutaneous Leishmania in
Iran from 2009 and 2013. You
see an evolution in the places
where you have a high risk of
Leishmania infection. When
you know this, you can for
example just target a region
instead of the whole country.
3) Identify sections of the population at greatest risk to target interventions.
In molecular epidemiology they are often using molecular tools to identify transmission chain. In the
picture you see a patient that is infected. With sequencing you identify it as a green pathogen. In
molecular epidemiology you would like to know where this person got infected with the pathogen.
This can be done by trying to find some possible sources: bore, river, swamp, infected neighbour. You
see here that the swamp is the source and caused the transmission to the patient. Transmission
chain studies are often used for nosocomial infection in hospitals to try to identify the source of the
infection: nurse, doctor, airco, water, …. Once you know the source you can have a targeted
intervention to cut the transmission chain/spread.
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,4) Evaluate effectiveness of programs in improving the health of the population.
Safety and effectiveness of mass drug administration (MDA) to accelerate elimination of artemisinin-
resistant falciparum malaria: A pilot trial in four villages of Eastern Myanmar. Wellcome Open Res.
2017 Sep 6;2:81. doi: 10.12688/wellcomeopenres.12240.1. eCollection 2017.
This MDA was safe and feasible,
and could accelerate elimination
of P. falciparum in addition to EDT
and LLINs when community
participation was sufficient
5) Study natural history of disease from precursor states through clinical course
This is a study that was done in 2010 in a village in Nepal. They wanted to know what the natural
history was of Leishmania infection in that region. All the dots are houses and there they took
samples of humans and animals. They wanted to know if animals could play a role in the natural
history of leishmania. They found that a lot of animals were positive (PCR) which mean that they
were infected with leishmania. These animals were living in close proximity to the positive humans (=
close contact). The boxes are places where we found positive humans and animals. This really
suggested that there was really a transmission between animals and humans, but they did not know
if the animals were the reservoir.
Conclusion: with molecular tools they really found an epidemiological link between the animals and
humans.
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, 6) Conduct surveillance of disease and injury occurrence in populations (humans or animals or …)
Surveillance is obviously
one of the most important
applications of molecular
epidemiology. In the figure
you see the spread of the
different variances of HIV
throughout the world.
7) Investigate disease outbreaks
Here you see the spread of HIV around
the world and the origin is the Congo
River Basin. This picture could be
replaced with Coronavirus. The origin
would than not be the same (China).
Molecular epidemiology has the tools to
investigate this.
Epidemiology is highly dynamic!
Epidemiology of an infectious disease is dynamic. Here you see all the flights around the world during
the day. Imagine that in each of this flight is a person that is infected with a dangerous disease, you
can see how easy it is nowadays to have a propagation of a pathogen. This picture shows how weak
we are in front of the pathogen.
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