Full genome sequence of the first SARS-CoV-2 detected in Mexico

Abstract

SARS-CoV-2 was first detected in the city of Wuhan, Hubei Province, China. In this report, we describe the complete genome sequence of the first imported SARS-CoV-2, detected in a Mexican patient who had traveled to Bergamo, Italy. Phylogenetic analysis showed that this isolate belongs to subclade A2a (lineage G) and is closely related to isolates from Finland, Germany and Brazil, all of which were from patients with a history of travel to Italy. This is the first report of the complete genome sequence of this virus in Mexico.

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Archives of Virology
https://doi.org/10.1007/s00705-020-04695-3
ANNOTATED SEQUENCE RECORD
Full genome sequence oftherst SARS‑CoV‑2 detected inMexico
FabiolaGarcés‑Ayala1· AdnanAraiza‑Rodríguez1· EdgarMendieta‑Condado1·
AbrilPaulinaRodríguez‑Maldonado1· ClaudiaWong‑Arámbula1· MagalyLanda‑Flores1·
JuanCarlosdelMazo‑López1· MaribelGonzález‑Villa1· NoéEscobar‑Escamilla1 · DavidEsaúFragoso‑Fonseca1 ·
Maríadel CarmenEsteban‑Valencia1· LourdesLloret‑Sánchez1· DayaniraSarithArellano‑Suarez1·
TatianaErnestinaNuñez‑García1· NervainBenjaminContreras‑González1· NatividadCruz‑Ortiz1·
AdrianaRuiz‑López1· MiguelÁngelFierro‑Valdez1· DanielRegalado‑Santiago1· NancyMartínez‑Velázquez1·
MireyaMederos‑Michel1· JoelVázquez‑Pérez2· JoséArturoMartínez‑Orozco2· EduardoBecerril‑Vargas2·
JorgeSalas2· LucíaHernández‑Rivas1· IrmaLópez‑Martínez1· JoséLuisAlomía‑Zegarra3· HugoLópez‑Gatell4·
GiselaBarrera‑Badillo1 · JoséErnestoRamírez‑González1
Received: 16 March 2020 / Accepted: 11 May 2020
© Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract
SARS-CoV-2 was first detected in the city of Wuhan, Hubei Province, China. In this report, we describe the complete genome
sequence of the first imported SARS-CoV-2, detected in a Mexican patient who had traveled to Bergamo, Italy. Phylogenetic
analysis showed that this isolate belongs to subclade A2a (lineage G) and is closely related to isolates from Finland, Germany
and Brazil, all of which were from patients with a history of travel to Italy. This is the first report of the complete genome
sequence of this virus in Mexico.
Virus name: hCoV/Mexico/CDMX/InDRE_01/2020
GISAID accession ID: EPI_ISL_412972
A novel coronavirus, recently named severe acute respiratory
syndrome-related coronavirus type 2 (SARS-CoV-2), was
identified in the city of Wuhan, Hubei Province, China, in
December of 2019 It is betacoronavirus that affects the lower
respiratory tract and manifests as pneumonia in humans [1,
2]. According to the Johns Hopkins University Coronavi-
rus Resource Center and the Daily Technical Statement on
New Coronavirus Cases Worldwide (COVID-19) issued by
the Secretary of Health of Mexico, as of March 20, 2020,
234,072 confirmed cases have been reported worldwide with
9840 deaths. In Mexico, 203 cases have been confirmed,
with two deaths reported [3, 4]. At the time of this writ-
ing, 768 complete genomic sequences of SARS Cov-2 have
been obtained and deposited in the GISAID database, and
10 clades have been defined from phylogenetic studies car-
ried out with these sequences (A1, A1a, A2, A2a, A3, A5,
B, B1, B2 and B4) [5].
Here, we report the complete genome sequence of SARS-
CoV-2 from the first imported case of COVID-19 detected in
Mexico. The sample hCoV/Mexico/CDMX/InDRE_01/2020
was obtained directly from a nasopharyngeal swab from a
35-year-old male patient (InDRE 1198) residing in Mex-
ico City who had a confirmed diagnosis of SARS-CoV-2
on February 27, 2020 and had traveled to Bergamo, Italy,
between February 16 and 22, 2020.
A diagnostic test for COVID-19 was first conducted
at the Instituto Nacional de Enfermedades Respiratorias,
Mexico City, on February 27, 2020. Following the national
guidelines of the Mexican Ministry of Health [6], a sample
was sent to the National Influenza Center at the Instituto
de Diagnostico y Referencia Epidemiologicos (InDRE); the
Handling Editor: Yue Wang.
* Gisela Barrera-Badillo
gisela.barrera20@yahoo.com.mx
* José Ernesto Ramírez-González
ernesto.ramirez@salud.gob.mx
1 Instituto de Diagnóstico y Referencia Epidemiológicos “Dr.
Manuel Martínez Báez”, MexicoCity, Mexico
2 Instituto Nacional de Enfermedades Respiratorias,
MexicoCity, Mexico
3 Dirección General de Epidemiología, MexicoCity, Mexico
4 Subsecretaría de Prevención y Promoción de la Salud,
MexicoCity, Mexico

F. Garcés-Ayala etal.
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confirmatory diagnosis was conducted using a real-time RT-
PCR protocol to detect SARS-CoV-2 [7], and of a 221-bp
fragment of the region coding for the orf1ab polyprotein
was sequenced by the Sanger method and will be published
elsewhere. The sample from the patient had a cycle threshold
value of 19.5 for the E gene and 20.4 for the RdRP gene.
The complete virus genome from the positive case was
amplified using the novel coronavirus sequencing multiplex
primers [8] (https ://artic .netwo rk/ncov-2019). cDNA syn-
thesis was conducted using Super Script IV Reverse Tran-
scriptase (Invitrogen) and the concentration of PCR the
product was measured using a Qubit dsDNA High Sensitiv-
ity Kit on a Qubit 3.0 fluorometer (Thermo Fisher) and an
Agilent 2100 Bioanalyzer (Agilent Technologies).
A library without barcodes was generated and
sequenced using an Ion Torrent system, using an Ion
Xpress™ Plus Fragment Library Kit for sequencing on
an Ion 318™ v2 chip. A total of 1,445,751 reads were
obtained for hCov/Mexico/CDMX/InDRE_01/2020. The
complete genome sequence was assembled using CLC
Genomics Workbench 20 (QIAGEN) and SPAdes [9] and
mapped against the reference sequence Wuhan-Hu-1 (Gen-
Bank accession number NC_045512.2).
The consensus sequence was assembled into a single
contig with a total length of 29,849 bp, corresponding to
99.8% of genome, and a deep average coverage of 3,983X.
The sequence was deposited in the GISAID database [5]
under accession ID EPI_ISL_412972.
A database was constructed including 178 genomic
sequences available on the GISAID platform, obtained
from December 31, 2019 to March 05, 2020, reported
in 22 countries. A phylogenetic tree was constructed in
MEGA 6 software using the neighbor-joining method and
the Kimura 2-parameter evolution model with 100 boot-
strap replicates [10]. The strain hCoV/Mexico/CDMX/
InDRE_01/2020 was grouped in the clade A2 subclade
A2a (also called lineage G) and is closely related to iso-
lates from Finland, Italy, and Germany as well as an iso-
late from the first imported SARS-CoV-2 case in Brazil
[11] (Fig.1).
Fig. 1 Neighbor-joining tree constructed in MEGA using the Kimura
2-parameter evolution model with 100 bootstrap replicates. hCoV/
Mexico/CDMX/InDRE_01/2020 (indicated by an arrow) is grouped
in clade A2a with sequences previously reported from Brazil, Ger-
many, Italy, and Finland. The 14408C>T substitution is characteristic
of subclade A2a

Genome sequence of the first SARS-CoV-2 detected in Mexico
1 3
Genetic analysis showed that the hCoV/Mexico/CDMX/
InDRE_01/2020 genome differs by seven nucleotide sub-
stitutions compared to the Wuhan-Hu-1 reference strain:
241C>T, 3037C>T, 14408C>T, 23403A>G, 28881G>A,
28882G>A, and 28883G>C. We confirmed the presence of
the 14408C>T substitution, which is characteristic of the
sequences clustered in subclade A2a.
A second database of 768 sequences deposited until
March 20, 2020, was used to construct a phylogenetic
tree. This analysis showed that hCoV/Mexico/CDMX/
InDRE_01/2020 clusters with European lineage G
sequences, mainly from Belgium, Switzerland, and Eng-
land (Fig.2). This finding correlates with the transmission
events reported by GISAID [5], which suggest that this strain
was first introduced into Belgium, then England, and finally,
Italy, where the Mexican patient had been traveling.
This is the first report of the complete genome of this
virus in our country, and these data will contribute to the
molecular epidemiology of the SARS-CoV-2.
Acknowledgements We thank all the staff of the Technological Devel-
opment and Molecular Research Unit (Susana Serrano, Lidia García,
Estela Corona, América Mandujano, Araceli Rodríguez, Isaura Mar-
tinez, Elizabeth Andrade, Juan Luis Tellez Mario Torres, Claudia
Gómez, Guadalupe Montiel, Aída García), Virology Department, and
Sample Control and Services Department at InDRE for technical assis-
tance; we also thank Blanca Taboada for bioinformatical assistance,
and Nuno Faria for sharing multiplex primers. No external funding
was received for this work.
The findings and conclusions in this report are those of the authors
and do not necessarily represent the official opinion of the Ministry of
Health of Mexico.
Funding None.
Compliance with ethical standards
Conflict of interest The authors declare no conflict of interest.
Ethical approval This article does not contain any studies with human
participants or animals performed by any of the authors.
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