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DATE 2020-05-21
FROM Ruben Safir
SUBJECT Subject: [Learn] Generics and Computational power - the 21st century
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Genome Sequencing for Epidemiology, Surveillance and Molecular
contact-tracing in COVID-19
on April 25, 2020

Vinod Scaria

The declaration of COVID-19 as a global pandemic has necessitated the
acute need for tools to be deployed for epidemiology, surveillance and
molecular contact-tracing. The molecular tools for case detection have
been heavily dependent on RT-PCR based methodologies, which target
specific regions in the genome of SARS-nCoV-2, the viral pathogen
causing COVID-19. While RT-PCR methods offer modest sensitivity and high
specificity for case detection, they do not provide additional
opportunities for understanding the molecular evolution of the virus.

Whole genome sequencing of SARS-nCoV-2 is now widely used across the
globe to understand unique characteristics of the virus and also
understand the origin of the virus. This is possible due to the fact
that it is estimated that the virus has a modest mutation rate. As of
date, over 10,000 whole genome sequences of SARS-nCoV-2 have been
sequenced and deposited in public databases. The genome sequences
provide the following additional opportunities and obviates some of the
limitations of RT-PCR based assays.

Genome sequencing is not dependent on specific primers, and
therefore provides an opportunity to identify the pathogen. In fact the
identification of the unique virus which causes COVID-19 was through
genome sequencing (Wu, F., Zhao, S., Yu, B. et al.2020).
Allow the understanding of evolution of the SARS-nCoV-2 virus. The
evolution of the virus would be important to understand unique
properties of the virus including pathogenicity, which are of clinical
and epidemiological relevance and for public policy.
The mutation rate of the virus would allow effective tracing of the
origins of the virus through molecular phylogenetics. As of date, over
10 clades of the virus have been characterized, with strong geographical
affinities, thereby enabling identification of index cases, and contacts
in clusters of patients, especially in community infections. See Figure
1 for transmission of the 10 different clades of SARS-nCoV-2 virus
across geographies.
The genome map allows us to understand the genetic variants in
critical genomic regions identified by diagnostic primers (see Genome
Watchpost) as well as immunogenic sites - with implications in
development of better diagnostics and better vaccines.

Figure 1. SARS-nCoV-2 virus lineages and the global transmission across
geographies. Image from nextstrain retrieved 26/04/2020

The advent of high-throughput next generation sequencing (NGS)
technologies have made it possible to multiplex large numbers of viral
genomes for sequencing . Coupled with standard pipelines for the
analysis and assembly, this provides a unique opportunity to offer a
scalable and affordable solutions for epidemiology and contact tracing
across the country. An approach of sentinel surveillance using whole
genome sequencing could provide insights into contacts and origins of
disease in community infection, thereby providing the much required data
to contain the spread of the disease.


Wu, F., Zhao, S., Yu, B. et al. A new coronavirus associated with human
respiratory disease in China. Nature 579, 265=96269 (2020).

COVID-19 Genome Watchpost
The COVID-19 Genome Watchpost provides concise summaries of the analysis
of SARS-nCoV-2 genomes from around the world.

COVID-19 Genomepedia
The COVID-19 Genomepedia is a comprehesnive searchable resource on
SARS-nCoV-2 genomes available in public domain

COVID-19 Open Research, Data and Resources
More about the initiative could be found at

About the Author
Vinod Scaria is a Scientist at the CSIR Institute of Genomics and
Integrative Biology (CSIR-IGIB). All views expressed are personal. The
author can be contacted at

contact-tracing coronavirus covid-19 epidemiology Genome Genomics
molecular SARS-nCoV-2 surveillance
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From a possible isolated outbreak in a seafood market in Wuhan, China,
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  1. 2020-05-21 Ruben Safir <> Subject: [Learn] Generics and Computational power - the 21st century

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