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Detection and Genome Sequencing of SARS-CoV-2 Variants Belonging to the B.1.1.7 Lineage in the Philippines

DOI:10.1128/MRA.00219-21
Authors:
Francis A. Tablizo at University of the Philippines
Francis A. Tablizo
Cynthia Saloma at University of the Philippines
Cynthia Saloma
Marc Jerrone R. Castro
Marc Jerrone R. Castro
Marc Jerrone R. Castro
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Kenneth M. Kim
Kenneth M. Kim
Kenneth M. Kim
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Abstract

We report the sequencing and detection of 36 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples containing lineage-defining mutations specific to viruses belonging to the B.1.1.7 lineage in the Philippines.
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Detection and Genome Sequencing of SARS-CoV-2 Variants
Belonging to the B.1.1.7 Lineage in the Philippines
Francis A. Tablizo,
a
Cynthia P. Saloma,
b,g
Marc Jerrone R. Castro,
a
Kenneth M. Kim,
a
Maria Sofia L. Yangzon,
a
Carlo M. Lapid,
a
Benedict A. Maralit,
c
Marc Edsel C. Ayes,
d
Jan Michael C. Yap,
a
Jo-Hannah S. Llames,
c
Shiela Mae M. Araiza,
c
Kris P. Punayan,
c
Irish Coleen A. Asin,
c
Candice Francheska B. Tambaoan,
c
Asia Louisa U. Chong,
c
Karol Sophia Agape R. Padilla,
c
Rianna Patricia S. Cruz,
a
El King D. Morado,
a
Joshua Gregor A. Dizon,
a
Eva Maria Cutiongco-de la Paz,
b,g
Alethea R. de Guzman,
e
Razel Nikka M. Hao,
f
Arianne A. Zamora,
e
Devon Ray Pacial,
e
Juan Antonio R. Magalang,
e
Marissa Alejandria,
g
Celia Carlos,
g
Anna Ong-Lim,
g
Edsel Maurice Salvaña,
g
John Q. Wong,
g
Jaime C. Montoya,
g
Maria Rosario Singh-Vergeire
g
a
Core Facility for Bioinformatics, Philippine Genome Center, University of the Philippines System, Quezon City, Philippines
b
Philippine Genome Center, University of the Philippines System, Quezon City, Philippines
c
DNA Sequencing Core Facility, Philippine Genome Center, University of the Philippines System, Quezon City, Philippines
d
Clinical Genomics Laboratory, Philippine Genome Center, University of the Philippines System, Quezon City, Philippines
e
Epidemiology Bureau, Department of Health, Manila, Philippines
f
Disease Prevention and Control Bureau, Department of Health, Manila, Philippines
g
Inter-Agency Task Force on Emerging Infectious Diseases (IATF) Technical Working Group on COVID-19 Variants, Department of Health, Manila, Philippines
ABSTRACT We report the sequencing and detection of 36 severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2) samples containing lineage-defining mutations
specific to viruses belonging to the B.1.1.7 lineage in the Philippines.
Coronavirus disease 2019 (COVID-19) is an infectious disease that has gained pan-
demic status from the World Health Organization, with millions of cases and deaths
recorded worldwide. This global health crisis is caused by the virus referred to as
severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a member of the genus
Betacoronavirus (Coronaviridae), together with the causative agents of the first SARS
outbreak in 2003 and the Middle East respiratory syndrome (MERS) in 2012.
In this study, we present the genome sequences of 36 cases of COVID-19 in the
Philippines caused by viruses belonging to SARS-CoV-2 lineage B.1.1.7, also referred to
as 20I/501Y.V1 or the variant of concern (VOC) 202012/01. This particular SARS-CoV-2
variant was initially identified in the United Kingdom and has been reported to cause a
surge of COVID-19 infections in that country (1). Initial studies also suggest that the
B.1.1.7 viruses appear to have a replicative advantage (2) and are more transmissible
(3). The protocols used in this study were reviewed and approved by the Single Joint
Research Ethics Board of the Department of Health, with approval code SJREB-2021-11,
as part of a larger research program entitled “A retrospective study on the national
genomic surveillance of COVID-19 transmission in the Philippines by SARS-CoV-2 ge-
nome sequencing and bioinformatics analysis.”
In order to detect the entry of B.1.1.7 infection into the Philippines, nasopharyngeal
swabs were collected between 10 December 2020 and 31 January 2021 from COVID-
19 cases detected in returning overseas Filipinos, as well as from local case clusters,
mainly from the Cordillera Administrative Region of the country, among others. Only
reverse transcriptase PCR (RT-PCR)-positive cases with a cycle threshold (C
T
) value
below 30 in any gene target were considered for the subsequent sequence analysis.
The collected swab samples were then subjected to RNA extraction using the QIAamp
viral RNA minikit, the product of which was used as the template for the amplicon-
based Illumina COVIDSeq test sequencing workflow.
The resulting sequence reads were mapped to the reference SARS-CoV-2 genome
Citation Tablizo FA, Saloma CP, Castro MJR,
Kim KM, Yangzon MSL, Lapid CM, Maralit BA,
Ayes MEC, Yap JMC, Llames J-HS, Araiza SMM,
Punayan KP, Asin ICA, Tambaoan CFB, Chong
ALU, Padilla KSAR, Cruz RPS, Morado EKD,
Dizon JGA, Cutiongco-de la Paz EM, de
Guzman AR, Hao RNM, Zamora AA, Pacial DR,
Magalang JAR, Alejandria M, Carlos C, Ong-Lim
A, Salvaña EM, Wong JQ, Montoya JC, Singh-
Vergeire MR. 2021. Detection and genome
sequencing of SARS-CoV-2 variants belonging
to the B.1.1.7 lineage in the Philippines.
Microbiol Resour Announc 10:e00219-21.
https://doi.org/10.1128/MRA.00219-21.
Editor Simon Roux, DOE Joint Genome
Institute
Copyright © 2021 Tablizo et al. This is an
open-access article distributed under the terms
of the Creative Commons Attribution 4.0
International license.
Address correspondence to Cynthia P. Saloma,
cpsaloma@up.edu.ph.
Received 1 March 2021
Accepted 15 April 2021
Published 6 May 2021
Volume 10 Issue 18 e00219-21 mra.asm.org 1
GENOME SEQUENCES
(NCBI accession number NC_045512.2) using minimap2 version 2.17-r941 (4), with the
“–xsr”parameter for accurate genomic short-read alignment. Primer clipping and qual-
ity trimming, intrahost variant calling, removal of reads associated with mismatched
primer indices, and consensus sequence assembly were then performed following the
suggested workflow of iVar version 1.2.2 (5), using default parameters. The consensus
variants were identified by comparing the resulting assemblies with the reference
sequence using MUMmer (6), as implemented in RATT software (7). Lastly, SARS-CoV-2
lineage classifications (8) were assigned using PANGOLIN version 2.3.2 (https://github
.com/cov-lineages/pangolin).
A total of 36 Philippine SARS-CoV-2 samples were classified under the B.1.1.7 line-
age. Table 1 shows the primary consensus assembly metrics for these samples. The av-
erage depth of coverage across all the sequences is 1,183, with 26 of the samples car-
rying all 17 hallmark mutations of the B.1.1.7 lineage as listed in the PANGO lineages
report for the B.1.1.7 variant of concern (https://cov-lineages.org/global_report_B.1.1.7
.html).
The detection of B.1.1.7 from returning overseas Filipino workers and in the com-
munity highlights the need for genomic surveillance at the country’s ports of entry
and in the general population to monitor the importation and local transmission of
TABLE 1 Primary consensus sequence assembly metrics
Sample code
NCBI accession no. for:
Collection date
(day mo yr)
%GC
content
Sample
source
a
Mean
coverage
depth (×)
No. of
consensus
SNPs
b
No. of
B.1.1.7
SNPs % N
c
Length
(bp)GenBank SRA
PH-PGC-00315 MW735407 SRR13907363 29 Dec 20 37.32 ROF 1,201.27 52 17 1.76 29,884
PH-PGC-00317 MW735408 SRR13907362 29 Dec 20 37.48 ROF 1,194.12 50 17 1.30 29,884
PH-PGC-00401 MW735409 SRR13907351 10 Dec 20 37.22 ROF 996.07 51 17 2.12 29,884
PH-PGC-00986 MW735410 SRR13907340 7 Jan 21 37.14 ROF 1,164.12 50 17 2.26 29,884
PH-PGC-02005 MW735411 SRR13907330 4 Jan 21 31.86 CAR 508.19 44 14 16.82 29,884
PH-PGC-02008 MW735412 SRR13907329 3 Jan 21 35.45 CAR 740.89 48 17 6.87 29,884
PH-PGC-02009 MW735413 SRR13907328 3 Jan 21 34.31 CAR 689.44 45 14 10.19 29,884
PH-PGC-02033 MW735414 SRR13907327 5 Jan 21 37.38 CAR 1,362.04 49 17 1.52 29,884
PH-PGC-02127 MW735415 SRR13907326 7 Jan 21 33.83 CAR 973.77 45 14 11.36 29,884
PH-PGC-02131 MW735416 SRR13907325 7 Jan 21 36.53 CAR 1,326.01 49 17 3.77 29,885
PH-PGC-02133 MW735417 SRR13907361 7 Jan 21 34.19 CAR 892.30 49 16 10.20 29,884
PH-PGC-02152 MW735418 SRR13907360 9 Jan 21 36.16 CAR 1,086.44 38 16 4.80 29,884
PH-PGC-02181 MW735419 SRR13907359 8 Jan 21 36.40 CAR 882.19 50 17 4.18 29,884
PH-PGC-02183 MW735420 SRR13907358 8 Jan 21 37.06 CAR 1,210.23 51 17 2.42 29,884
PH-PGC-02184 MW735421 SRR13907357 8 Jan 21 35.20 CAR 891.29 48 16 7.54 29,884
PH-PGC-02185 MW735422 SRR13907356 8 Jan 21 37.33 CAR 1,131.33 49 17 1.69 29,884
PH-PGC-02225 MW735423 SRR13907355 8 Jan 21 37.13 CAR 1,303.29 51 17 2.14 29,884
PH-PGC-02408 MW735424 SRR13907354 7 Jan 21 37.92 ROF 1,652.89 51 17 0.10 29,884
PH-PGC-02434 MW735425 SRR13907353 12 Jan 21 37.70 ROF 1,168.26 53 17 0.78 29,884
PH-PGC-02630 MW735426 SRR13907352 16 Jan 21 37.83 ROF 1,307.23 48 17 0.41 29,884
PH-PGC-02725 MW735427 SRR13907350 14 Jan 21 37.16 ROF 1,140.03 52 17 2.04 29,884
PH-PGC-02730 MW735428 SRR13907349 16 Jan 21 37.87 ROF 1,620.34 52 17 0.13 29,884
PH-PGC-02732 MW735429 SRR13907348 17 Jan 21 37.89 ROF 724.58 52 17 0.25 29,884
PH-PGC-02733 MW735430 SRR13907347 17 Jan 21 37.88 ROF 1,499.29 51 17 0.15 29,884
PH-PGC-02745 MW735431 SRR13907345 19 Jan 21 30.64 ROF 679.99 32 12 19.71 29,894
PH-PGC-02756 MW735432 SRR13907344 15 Jan 21 37.01 CAR 1,037.94 50 17 2.23 29,884
PH-PGC-02770 MW735433 SRR13907343 15 Jan 21 35.34 ROF 971.34 44 14 6.34 29,885
PH-PGC-02793 MW735434 SRR13907342 19 Jan 21 37.65 ROF 1,290.90 50 17 0.90 29,884
PH-PGC-02812 MW735435 SRR13907341 24 Jan 21 37.91 CAR 1,654.09 50 17 0.18 29,884
PH-PGC-02826 MW735436 SRR13907339 21 Jan 21 37.85 CAR 1,346.54 52 17 0.31 29,884
PH-PGC-02845 MW735437 SRR13907338 13 Jan 21 37.74 CAR 1,454.34 51 17 0.58 29,884
PH-PGC-02851 MW735438 SRR13907337 11 Jan 21 37.87 CAR 1,563.14 49 17 0.28 29,884
PH-PGC-02886 MW735439 SRR13907336 16 Jan 21 37.67 CAR 1,411.43 51 17 0.86 29,884
PH-PGC-03846 MW735440 SRR13907334 24 Jan 21 37.87 ROF 1,458.88 49 17 0.16 29,884
PH-PGC-03939 MW735441 SRR13907333 31 Jan 21 37.89 ROF 2,082.45 50 16 0.27 29,885
PH-PGC-03978 MW735442 SRR13907332 25 Jan 21 37.25 NCR 990.68 53 16 2.01 29,884
a
ROF, returning overseas Filipino; CAR, Cordillera Administrative Region; NCR, National Capital Region.
b
SNPs, single nucleotide polymorphisms.
c
% N, percentage of ambiguous base calls (“N”content) in the consensus sequence assembly. High percent N values generally result in lower percent GC content.
Tablizo et al.
Volume 10 Issue 18 e00219-21 mra.asm.org 2
emerging variants of concern that may impact the public health response to the SARS-
CoV-2 pandemic in the Philippines.
Data availability. The consensus sequence assemblies reported in this study have
been deposited in the NCBI GenBank database, and their corresponding read align-
ments (BAM format) are in the NCBI Sequence Read Archive (SRA) database under
BioProject accession number PRJNA708134. The accession numbers for the GenBank
and SRA submissions are provided in Table 1.
ACKNOWLEDGMENTS
This project was supported by a Genomics Biosurveillance grant from the Philippine
Department of Health and a Department of Science and Technology–Philippine Council for
Health Research and Development grant to B.A.M. and the University of the Philippines. We
also thank the Philippine Genomic Biosurveillance Network contributing institutions.
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