The Role of Molecular Epidemiology

in Tracing the Source of Infection

11th National Public Health Conference & 1st Global

Public Health Conference 25th-27th July 2023
Langkawi Malaysia

Dr Ravindran Thayan
Molecular Virologist and Head of Infectious Disease Research Centre,
Institute for Medical Research
National Institutes of Health, Setia Alam
 Outline of presentation
➢ Molecular Epidemiology and updates that has transformed
infectious diseases investigations

➢ Genome epidemiology

➢ Examples of successful usage of WGS in molecular

epidemiology

➢ Conclusions
 Molecular Epidemiology: Focus on Infectious Diseases
➢ Molecular tools are increasingly integrated into the practice of
Infectious diseases epidemiology

➢ Characterization of nucleic acid or amino-acid based content able :

➢ provide evidence of diseases occurrence in community
➢ Association between host, agent and environment/exposures
(enhance understanding of association)
➢ Assist in disease surveillance/
outbreak investigations

➢ Transmission pattern, risk group

➢ Detection on fastidious/uncultivable organism
➢ Better understanding of diseases pathogenesis at molecular level

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➢ Genomic Epidemiology has transformed precision in
Infectious Diseases Investigation

➢ Genomic information of infecting pathogens assist in

elucidating the source, timing, transmission and
spread of the diseases

➢ Previously – dependent on case incidence data, interview-

based contact tracing to estimate key epidemic parameters
(eg reproduction numbers, incubation period, serial
intervals- to re-construct transmission chain

➢ But these can be limited by – incomplete case reporting

due to labour intensive contact tracing or uncertain
reporting due to dependence on clinical symptoms to
identify cases. 4
 Molecular Epidemiology for
Tracing Infection

➢ Can be defined as using molecular tools to characterize

nucleic acid in combination with epidemiology to study
distribution and determinants of disease occurrence in human
population

➢ Includes tracing the source of infection which is crucial

for control measures.

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Examples of Local Incidence where Molecular
epidemiology was used for tracing infection (Eg 1)

➢ First case of Avian

Influenza H7N9 in
Malaysia (2014)

➢ Identified in a tourist
from China

➢ Able to trace source of

infection to strains
circulating in Guangzhou,
China

➢ Control measures carried

out accordingly
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Examples of Local Incidence where Molecular
epidemiology was used for tracing infection (Eg 2)

➢ First case of MERS-CoV (2014)

➢ Identified in a local man

returning from pilgrimage

➢ Able to trace source of infection

to strains circulating in Saudi
Arabia

➢ Control measures carried out

accordingly
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Examples of Local Incidence where Molecular
epidemiology was used for tracing infection (Eg 3)

➢ First case of Rabies in

Sarawak (2017)

➢ Able to trace source of

infection to strains
circulating in Kalimantan,
Indonesia

➢ Control measures carried

out accordingly (vaccine +
immunoglobulins)

➢ Implementation of immune
belt along the borders
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Examples of Genomic Epidemiology (Elsewhere)
Pathogens Location Findings
MRSA Cambridge, WGS of bacteria was used to re-construct transmission chains
UK and identify likely source of MRSA within a hospital ward- led
to targeted decolonization
Ebola West Africa WGS of virus was used to re-construct transmission chain and
confirm first case of sexual transmission. Led to immediate
changes to guidelines for male survivors including semen
testing for presence of viral RNA
HIV USA NGS was used to identify low frequency drug resistance
variants (>1-3%) within individual patients. Baseline presence
of a resistance variant, even at low frequency, increased
probability of virologic failure
Candida Oxford, UK WGS of fungus from patient and environment isolates was
auris used to identify contaminated equipment as the source of
infection within the hospital ICUs.
Lujo Virus Zambia and Metagenomics sequencing of human samples able to discover
South Africa novel virus responsible for cluster of fatal haemorrhagic fever
E. Coli Germany and WGS of E. coli isolates was used to dissect European outbreak
0104:H4 France of bloody diarrhea and haemolytic uremic syndrome by Shiga-
toxin producing E. coli
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 Examples of Tools in Molecular Epidemiology

➢ Tools include real time PCR, Sequencing (targeted or whole

genome), bioinformatics, interpretation for molecular
epidemiology
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 WGS in Molecular Epidemiology

➢ Whole-genome sequencing (WGS) provides higher

resolution and accuracy than classical molecular typing
methods, contributing to a better understanding of
infectious disease and drug resistance transmission
patterns

➢ As a result, enable effective

interventions for their control.

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 ONT, Illumina,
Sanger etc

48 hours-6 days

➢ Registration of genome data in a common sharing database, eg

GISAID, NCBI
 Locations of Facilities that have Genome
Sequencing Facilities in Malaysia

Consortium members include IMR, Universities (8), MGI ( Total= 10)

Non- Consortium members include Public Health Laboratories (4)
Sites where samples for genome surveillance collected and send
to Institute for Medical Research for re-distribution

In addition, there are also some services provided by other players (esp
universities not part of Consortium)
Global Initiative on Sharing All Influenza Data (GISAID)
➢ Important
database for
registration of
genomic data

➢ Expanded to
include COVID-
19, Mpox,
Arbovirus

➢ Able to access
circulating
viruses in each
region

➢ Similar database
for other
pathogens
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➢ Registration
of COVID-19
genomic data
from Malaysia

➢ At least
40,815
COVID-19
isolates

➢ Information
on all variants
of the viruses
and location

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 What’s the implication for getting access to
genome data worldwide?

➢ Access to information of what types of pathogen circulating in

geographical region (based on surveillance)

➢ Compare that information with local circulation.

Possible in-coming or out-going strains?

➢ Monitor circulation of pathogens of public

health implications (such as those with
drug-resistance, higher transmission,
higher virulence

➢ Useful to design vaccine or therapeutics

or diagnostics based on genome information

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Inferring Phylogenetic Tree

➢ Source
➢ Divergence
➢ Duration
➢ Selection pressure
Examples of a Phylogenetic tree

➢ Single source

➢ Divergence
according to area
and time

➢ Multiple
introduction,
selection
pressure,
mutations,
causing resulting
in more divergent

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Examples of a Phylogenetic tree

➢ Divergence
according to area
and time

➢ Multiple
introduction,
selection
pressure,
mutations,
causing resulting
in more divergent

➢ Dominant strain
branching further

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Pathogen sequencing during infectious disease
outbreaks can inform precise interventions

➢ Whole-genome sequencing of
pathogens can now be done directly
from clinical samples in near real
time during an outbreak (ONT)

➢ By analyzing these genomes and

their metadata in the context of
other sequences generated from the
same outbreak, as well as
previously characterized variants,
researchers can inform individual-
and population level intervention
strategies to minimize the burden of
infectious diseases.

➢ This collective approach—

sequencing, analysis, and
response—as precision epidemiology

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 Inferring Source of SARS-CoV-2

Showcases :
➢ The emergence of SARS-CoV-2 and the outbreak of COVID-19.
➢ Depicts a hypothesized origin of the virus
➢ Generalised route of transmission of the epidemic zoonotic
coronavirus.
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Possible cyclic risk pathway (based on various
surveillance)

➢ Cyclic risk pathways

➢ Infected patients Hospital

Man sewage Faecal Route

➢ Possibility of pathogen being

“maintained” in the community

➢ Continuous replication of the

pathogen in the community-
may result in a pathogen with
mutations providing advantages
– immune escape or causing
severe symptoms

➢ Thus- surveillance is crucial in

community and the
environment during “downtime”

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 Examples how molecular epidemiology assisted in
identification and control

(1) Identification of Infectious Diseases Reservoirs

➢ Tools were used to detect trace amounts of genetic materials in the

environment, water, soil and human (which failed using traditional
methods)
➢ Able to successfully detect new reservoir and design effective preventive
strategies

➢ Association of pathogen from infected individual were closely related to

strains from suspected sources – by phylogenetic analysis
➢ Identification of chicken as new reservoir for Extra-intestinal Pathogenic
Escherichia coli (ExPEC), which causes UTI in human

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 Examples how molecular
epidemiology assisted in
identification and control

(2) Circulation of Variants of Concern/ Variants of Interest during

pandemic COVID-19

➢ WGS was widely used to identify circulation of COVID-19 variants of

concern (VOC) or variants of interest (VOI).
➢ Continuous circulation of these variants in the community resulted in the
appearance of VOC and VOI.
➢ Some characteristics associated with these VOC/VOI include immune
escape, increased in transmissibility, diagnostic failure (if S gene were
used as target in real time RT-PCR) and increase in severity.
➢ With such information, efforts include recommendation of booster doses,
close monitoring of those with co-morbidities and use on anti-virals
(Paxlovid) 24
 Examples how molecular epidemiology assisted in
identification and control
(3) Identification of inter-community transmission

➢ Phylogenetic methods combined with socio-demographic and

behavioural data were analysed to conclude common source of
pathogen in Afghanistan and Iran
➢ HIV-1 subtype CRF3S-AD was found circulating both in Afghanistan and
Iran based on phylogenetic tree analysis

➢ Behavioural and socio-demographic data shows that that HIV-subtype

was found primarily among IVDUs.
➢ Possible migration of refugees from Afghanistan to Iran.
➢ Enhanced screening as well as steps to control prevent IVDU
transmission

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 Conclusions

➢ Whole Genome Sequencing (WGS) coupled with epidemiological and

environmental investigations delivers ultimate resolution for detecting and
analyzing transmission routes

➢ WGS also assist tracing sources of epidemic infections as well as

assessing microbial virulence and antimicrobial drug resistance
determinants.

➢ Post COVID-19, access to WGS is better and costs have come done
tremendously. Bioinformatics is key for interpretation of genome data.

➢ Advances in the speed and granularity of pathogen genome generation

have improved the capability to track and understand pathogen
transmission, leading to potential improvements in the design and
implementation of population-level public health interventions.
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Contact: rthayan@gmail.com or ravin@moh.gov.my