Covid-19 and

Genomic Surveillance
Covid-19 Facts and Overview
The COVID-19 pandemic is a global
outbreak of coronavirus, an
infectious disease caused by the
severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) virus.
The first case was detected in China in
December 2019, with the virus Leading cause of death by
spreading rapidly to other countries
an infectious disease
across the world.
This led WHO to declare a Public
Health Emergency of International
Concern (PHEIC) on 30 January 2020,
and to characterize the outbreak as a
pandemic on 11 March 2020.
Covid-19 Facts and Overview
COVID-19 current situation
Origin and evolution of SARS‐CoV, MERS‐CoV, and SARS‐CoV‐2
in different hosts

Ashour et al, Pathogens, 2020

Timeline of coronavirus emergence
Morphology and Molecular
Characterization of SARS-
CoV2
SARS-CoV2 structure

Coronaviruses are the largest known RNA viruses, with genomes

up to 32 kb.
These viruses possess an envelope and a single-stranded,
positive-sense RNA genome.
Encoded 27 proteins including RdRP RNA dependent RNA
polymerase and 4 structural protein
4 structural protein : Spike surface glycoprotein (S); Small
envelope protein (E) ; Matrix Protein (M) ; Nucleocapsid protein
(N)
S gene is divergent with <75% nucleotides similarity
Virus maybe found in aerosols (<5 um) for at least up to 3h
SARS-CoV-2 Genome

Gordon et al, bioRxiv, 2020

The SARS-CoV-2 interactome reveals novel aspects of SARS-CoV-2
biology

Interactions between SARS-CoV-2 proteins and human proteins

with a range of functions including:
DNA replication (Nsp1)
Epigenetic and gene expression regulators (Nsp5, Nsp8, Nsp13, E)
Vesicle trafficking (Nsp6, Nsp7, Nsp10, Nsp13, Nsp15, Orf3a, E, Orf8)
Lipid modification (Spike)
RNA processing and regulation (Nsp8, N)
Ubiquitin ligases (Orf10)
Signaling (Nsp8, Nsp13, N, Orf9b)
Nuclear transport machinery (Nsp9, Nsp15, Orf6)
Cytoskeleton (Nsp1, Nsp13)
Mitochondria (Nsp4, Nsp8, Orf9c)
Extracellular matrix (Nsp9)
Gordon et al, bioRxiv, 2020
 The RdRp gene is the one most commonly used for PCR
amplification in CoV surveillance, since it contains the most regions
that are conserved in all CoVs

Anindita PD,
Detection of coronavirus
genomes in moluccan naked-
backed fruit bats in Indonesia
, Springer, 2015
Genomic
surveillance of
COVID-19
Importance of Genomic
Surveillance in Controlling the
Pandemic
Understanding the virus
Genomic surveillance provides researchers and public health
officials with valuable information about the virus’s mutations
and how it spreads, helping them to more effectively manage
the pandemic.

2 Tracking outbreaks
By tracking the spread of the virus in real time, genomic
surveillance can help public health officials create more
targeted interventions, such as contact tracing and quarantine
measures.
How to Perform Genomic Surveillance

Sequence samples
Use next-generation sequencing
technologies, such as Oxford Nanopore, to
analyze the genetic makeup of the virus in
the collected samples.

2 3

Collect samples Analyze data

Collect samples from infected patients or Analyze the sequence data to identify any
individuals at high risk of infection, such as changes to the virus’s genome and track
healthcare workers. its spread over time.
Overview of Next Generation Sequencing
Technologies

Illumina Ion Torrent Oxford Nanopore

sequencing sequencing sequencing
Illumina sequencing is Ion Torrent sequencing is Oxford Nanopore
one of the most a relatively new sequencing offers real-
commonly used next- technology that can be time genomic
generation sequencing used for rapid genomic surveillance capabilities,
technologies for genomic surveillance of the virus. enabling researchers to
surveillance, particularly track the virus’s spread in
in high-income countries. near real-time.
Introduction to Oxford Nanopore's
Sequencing Technology

About the Technology Sequencing Workflow

Oxford Nanopore’s sequencing technology The Oxford Nanopore sequencing process
uses electrical signals to analyze individual involves several steps, including sample
strands of DNA, providing researchers with preparation, library construction, and data
real-time data on the virus’s genomic makeup. analysis.
Application of Oxford Nanopore Technology in
Covid Genomic Surveillance
Rapid results
The real-time capabilities of Oxford Nanopore sequencing enable public health
officials to quickly detect the virus and track its spread in real time.

Precision tracking
Oxford Nanopore’s sequencing technology allows researchers to track the virus’s
genetic changes with a high degree of precision, providing valuable insights into
how the virus is evolving over time.

3 Regional monitoring
By monitoring the virus’s genomic makeup in different regions, public health
officials can more effectively manage localized outbreaks and prevent the virus
from spreading more widely.
Benefits and Challenges of Using Oxford
Nanopore Technology
Benefits
Oxford Nanopore technology provides real-
time data about the virus’s genomic
makeup, enabling public health officials to
act quickly and prevent further spread of
the virus.
The technology is highly portable and easy
to use, making it ideal for use in remote or
low-resource settings.
Challenges
Sequencing data must be carefully analyzed
to avoid errors or inaccuracies, which can
lead to incorrect conclusions and
misinterpretation of the data.
The cost of Oxford Nanopore sequencing
can be higher than other sequencing
technologies, which can limit its
widespread use in certain settings.
Future Implications and Conclusion

Improved outbreak Personalized

management
Oxford Nanopore sequencing technology has
the potential to revolutionize our ability to
respond to pandemics by providing real-time
data about viral outbreaks.
medicine
Oxford Nanopore sequencing technology can
also be used for personalized medicine,
allowing doctors to more effectively treat
diseases like cancer by analyzing patients’
genetic makeup and developing
individualized treatment plans.

Genomic surveillance has significant implications for our ability to manage pandemics like Covid-
19. By providing real-time data about the virus’s genomic makeup, this technology can help
researchers and public health officials better understand how the virus is spreading and how to
prevent further outbreaks.
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