Le Infezioni in Medicina, n.
2, 139-142, 2020
EDITORIAL 139
Genomic Epidemiology
and its importance in the study
of the COVID-19 pandemic
Alfonso J. Rodríguez-Morales1,2,3,4, Graciela J. Balbin-Ramon3,4,5, Ali A. Rabaan6, Ranjit Sah7,
Kuldeep Dhama8, Alberto Paniz-Mondolfi3,9,10,11,12, Pasquale Pagliano13, Silvano Esposito13
1
Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnológica de Pereira,
Pereira, Colombia;
2
Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Americas,
Pereira, Risaralda, Colombia;
3
Latin American Network of Coronavirus Disease 2019-COVID-19 Research (LANCOVID-19), Pereira,
Risaralda, Colombia;
4
Master in Clinical Epidemiology and Biostatistics, Universidad Cientifica del Sur, Lima, Peru;
5
Hospital de Emergencias Jose Casimiro Ulloa, Lima, Peru;
6
Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia;
7
Department of Microbiology, Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu, Nepal;
8
Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India;
9
Laboratory of Medical Microbiology, Department of Pathology, Molecular and Cell-based Medicine,
The Mount Sinai Hospital-Icahn School of Medicine at Mount Sinai, New York, USA;
10
Laboratorio de Señalización Celular y Bioquímica de Parásitos, Instituto de Estudios Avanzados (IDEA),
Caracas, Caracas, Venezuela;
11
Academia Nacional de Medicina, Caracas, Venezuela;
12
Instituto de Investigaciones Biomedicas IDB / Incubadora Venezolana de la Ciencia, Cabudare, Edo. Lara, Venezuela;
13
Department of Infectious Diseases, University of Salerno, Salerno, Italy
O ver the course of three months (December
2019-March 2020) the pandemic of the Coro-
navirus Disease 2019 (COVID-19), caused by a
and related outcomes, as well as their early detec-
tion, treatment, or prognosis.
From an instrumental viewpoint, the use in epi-
zoonotic virus, the Severe Acute Respiratory Syn- demiological research of molecular and cell biolo-
drome Coronavirus 2 (SARS-CoV-2), has raised gy techniques as well as the integration of genet-
multiple concerns and triggered an unprecedent- ics and systems biology into the interdisciplinary
ed and deep impact across multiple areas of bio- “omics” approach has revolutionized translation-
medical research, especially the disciplines of mo- al research and greatly contributed to the discov-
lecular biology, virology with particular empha- ery of novel biomarkers allowing tracing systems
sis on molecular epidemiology, and comparative through genome navigation, the so-called genom-
genomics [1-3]. ic epidemiology. Molecular epidemiology is mak-
According to the International Association of Ep- ing valuable contributions to biomedical, clinical,
idemiology, molecular epidemiology is defined and population sciences with exceptional impact
as the application of epidemiologic principles to on the role of gene-environment interactions, eti-
study the molecular, biochemical, cellular and ge- ology of diseases and the complex drivers of dis-
netic mechanisms that underlie the pathophysiol- ease progression by generating sound evidence
ogy, etiology and prevention of human diseases about the underlying biological mechanisms and
by providing knowledge with to potential prima-
ry prevention strategies [4].
Corresponding author Advances in sequencing technology has blos-
Alfonso J. Rodriguez-Morales somed into a new era of genomic epidemiology,
E-mail:
[email protected] where traditional molecular diagnostics and gen-
140 A.J. Rodríguez-Morales, G.J. Balbin-Ramon, A.A. Rabaan, et al.
otyping methods are being enhanced and even epidemics [6-8]. Such tools along with refined
replaced by novel throughput genomics-based methods of phylogenetic analysis provided fur-
methods to aid in the epidemiologic investiga- ther evidence that SARS-CoV-2 along with the
tions of communicable diseases. The ability to Bat-SARS-like coronavirus cluster is a distinct
analyze and compare entire pathogen genomes lineage within the subgenus of the Sarbecovirus
has allowed for unprecedented resolution into [9, 10].
how and why infectious diseases spread. As these Virology has embraced the next-generation se-
genomics-based methods continue to improve in quencing revolution, swiftly moving from the
speed, cost, and accuracy, they will be increasing- time of single genome sequencing to the age of
ly adopted to inform and guide infection control genomic epidemiology [11]. Hundreds and now
and public health practices [5]. even thousands of genomes are being processed
This emergence in novel genomic tools has been by massive parallel sequencing for detection of
key in understanding the many aspects of the multiple organism species, allowing unprece-
SARS-CoV-2/COVID-19 pandemic. The initial dented levels of resolution and insight in the
full-genome sequence analysis of SARS-CoV-2 evolution and epidemic diffusion of the main
revealed its taxonomic status as a member of the pathogens, currently including more than 2,220
betacoronavirus, with clear divergence from the full genomes included in the SARS-CoV-2 public
SARS-CoV and MERS-CoV both players of past database of the Global Initiative on Sharing All
Figure 1 - Full genome tree of all outbreak sequences analyzed by GISAID.
Available at: https://www.gisaid.org/hcov-19-analysis-update/
Genomic epidemiology of the COVID-19 pandemic 141
Influenza Data (GISAID) (Figure 1) [12]. GISAID ic epidemiology analyses allow recognition of
was originally developed for genomic data shar- transmission clusters, its biological evolutionary
ing on influenza, but now has extended its cov- rate, and finally the possibility of estimating the
erage to include a comprehensive, dynamic and magnitude of the potential pandemic. In multi-
constantly updated SARS-CoV-2 database [13]. ple countries of the world, obtaining new SARS-
The analyses show that the SARS-CoV-2 genomes CoV-2 genomes is ongoing, and this will allocate
sequenced are located mainly in three clades, in monitoring multiple aspects of this pandemic.
addition to others, S clade (541 genomes), G clade These include genetic diversity, association with
(931), V clade (208), and other additional clades clinical and epidemiological patterns and pro-
(548) (Figure 1). For example, the GISAID analyt- files, the usefulness of diagnostic methods, and
ical repository on the receptor binding surveil- the rational design of therapeutics and vaccine
lance for high quality genomes, up to March 28, candidates as mentioned above. Most countries
2020, revealed the presence of four different rare in Europe and North America have sequenced
variants near the binding interface: V483A in 16 their respective SARS-CoV-2 isolate genomes, but
USA/WA samples, L455I together with F456V in Asia, Middle East, Africa and Latin America,
in one Brazilian sample and G476S in 10 USA/ many countries still lack such capabilities.
WA samples [12]. Also, it has provided insights Fortunately, the ongoing COVID-19 pandemic
via comparative genomic analysis on potential has opened an era of open science where a num-
drug targets based on the degree of similarity of ber of publically available open-source projects
highly conserved between hCoV-19 and SARS. such as GISAID, and their related webs (https://
Both, the main protease and polymerase which nextstrain.org/ncov), have provided easy an ac-
are potential drug targets are highly conserved cessible tools to better understand and improve
between hCoV-19 and SARS with 96% and 97% outbreak response by capitalizing in pathogen
overall identity, respectively. Inhibitors devel- genomic data [12].
oped against the SARS-CoV main protease or pol-
ymerase have also shown the potential to bind in Funding
a similar fashion to hCoV-19 [12]. None.
As predicted, the evolving genomic revolution is
already having a profound impact on the practice Conflicts of Interest
of epidemiology, virology, infectious diseases, None.
and public health [14-16]. Molecular epidemiol-
ogy in all its ramifications allows reconstructing n REFERENCES
the evolutionary history of viruses, analyzing its
appearance and global spread such has been the [1] Rodriguez-Morales AJ, Cardona-Ospina JA, Gutiér-
recent experience with SARS-CoV-2. As its ge- rez-Ocampo E, et al. Clinical, laboratory and imaging
features of COVID-19: A systematic review and me-
nome continues to accumulate mutations (Figure
ta-analysis. Travel Med Infect Dis. 2020; 101623. [Online
1), the generation of distinct genetic traces helps ahead of print]
defining transmission chains and even rebuild [2] Rodriguez-Morales AJ, Bonilla-Aldana DK, Bal-
the links in a chain with individuals who ignore bin-Ramon GJ, et al. History is repeating itself, a prob-
their source of transmission, and even assess sce- able zoonotic spillover as a cause of an epidemic: the
narios such as community transmission. Com- case of 2019 novel Coronavirus. Infez Med. 2020; 28 (1),
parative genomics allows to infer the generation 3-5.
in a transmission chain, e.g. from imported case, [3] Bracken MB. Genomic epidemiology of complex
with full traceability and also allows to estimate disease: the need for an electronic evidence-based ap-
the most probable ancestor, and by comparison proach to research synthesis. Am J Epidemiol. 2005; 162
(4), 297-301.
and geographical location, where it originated.
[4] Porta M. Molecular epidemiology. In: Porta M, edi-
As new genomes of SARS-CoV-2 are being ob- tor. A Dictionary of Epidemiology. Oxford: Oxford Uni-
tained from imported cases, contacts and those of versity Press; 2014.
community transmission, in the next days, a bet- [5] Tang P, Croxen MA, Hasan MR, Hsiao WW, Hoang
ter understanding of the genomic epidemiology LM. Infection control in the new age of genomic epide-
of SARS-CoV-2 will become available. Genom- miology. Am J Infect Control. 2017; 45 (2), 170-9.
142 A.J. Rodríguez-Morales, G.J. Balbin-Ramon, A.A. Rabaan, et al.
[6] Al-Omari A, Rabaan AA, Salih S, Al-Tawfiq JA, [11] Gaiarsa S, De Marco L, Comandatore F, Marone
Memish ZA. MERS coronavirus outbreak: Implications P, Bandi C, Sassera D. Bacterial genomic epidemi-
for emerging viral infections. Diagn Microbiol Infect Dis. ology, from local outbreak characterization to spe-
2019; 93 (3), 265-85. cies-history reconstruction. Pathog Glob Health. 2015;
[7] Rabaan AA. Middle East respiratory syndrome coro- 109 (7), 319-27.
navirus: five years later. Expert Rev Respir Med. 2017; 11 [12] GISAID. Genomic epidemiology of novel corona-
(11), 901-12. virus. Available at https://nextstrain.org/ncov 2020
[8] Rizzardini G, Saporito T, Visconti A. What is new Last accessed 9th March 2020
in infectious diseases: Nipah virus, MERS-CoV and the [13] Shu Y, McCauley J. GISAID: Global initiative on
Blueprint List of the World Health Organization. Infez sharing all influenza data - from vision to reality. Euro
Med. 2018; 26 (3), 195-8. Surveill. 2017; 22 (13).
[9] Zhu N, Zhang D, Wang W, et al. A Novel Corona- [14] Traynor BJ. The era of genomic epidemiology. Neu-
virus from Patients with Pneumonia in China, 2019. N roepidemiol. 2009; 33 (3): 276-9.
Engl J Med. 2020 doi 10.1056/NEJMoa2001017. [15] Bastola A, Sah R, Rodriguez-Morales AJ, Lal BK,
[10] Paraskevis D, Kostaki EG, Magiorkinis G, Panay- Jha R, Ojha HC, et al. The first 2019 novel coronavirus
iotakopoulos G, Sourvinos G, Tsiodras S. Full-genome case in Nepal. Lancet Infect Dis. 2020; 20 (3), 279-80.
evolutionary analysis of the novel corona virus (2019- [16] Sah R, Rodriguez-Morales AJ, Jha R, et al. Com-
nCoV) rejects the hypothesis of emergence as a result plete genome sequence of a 2019 novel coronavirus
of a recent recombination event. Infect Genet Evol. 2020; (SARS-CoV-2) strain isolated in Nepal. Microbiol Resour
79, 104212. Announc. 2020; 9 (11).
