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



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.
Detection and Genome Sequencing of SARS-CoV-2 Variants
Belonging to the B.1.1.7 Lineage in the Philippines
Francis A. Tablizo,
Cynthia P. Saloma,
Marc Jerrone R. Castro,
Kenneth M. Kim,
Maria Soa L. Yangzon,
Carlo M. Lapid,
Benedict A. Maralit,
Marc Edsel C. Ayes,
Jan Michael C. Yap,
Jo-Hannah S. Llames,
Shiela Mae M. Araiza,
Kris P. Punayan,
Irish Coleen A. Asin,
Candice Francheska B. Tambaoan,
Asia Louisa U. Chong,
Karol Sophia Agape R. Padilla,
Rianna Patricia S. Cruz,
El King D. Morado,
Joshua Gregor A. Dizon,
Eva Maria Cutiongco-de la Paz,
Alethea R. de Guzman,
Razel Nikka M. Hao,
Arianne A. Zamora,
Devon Ray Pacial,
Juan Antonio R. Magalang,
Marissa Alejandria,
Celia Carlos,
Anna Ong-Lim,
Edsel Maurice Salvaña,
John Q. Wong,
Jaime C. Montoya,
Maria Rosario Singh-Vergeire
Core Facility for Bioinformatics, Philippine Genome Center, University of the Philippines System, Quezon City, Philippines
Philippine Genome Center, University of the Philippines System, Quezon City, Philippines
DNA Sequencing Core Facility, Philippine Genome Center, University of the Philippines System, Quezon City, Philippines
Clinical Genomics Laboratory, Philippine Genome Center, University of the Philippines System, Quezon City, Philippines
Epidemiology Bureau, Department of Health, Manila, Philippines
Disease Prevention and Control Bureau, Department of Health, Manila, Philippines
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-dening mutations
specic 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 rst 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 identied 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
) 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 workow.
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.
Editor Simon Roux, DOE Joint Genome
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,
Received 1 March 2021
Accepted 15 April 2021
Published 6 May 2021
Volume 10 Issue 18 e00219-21 1
(NCBI accession number NC_045512.2) using minimap2 version 2.17-r941 (4), with the
“–xsrparameter 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 workow of iVar version 1.2.2 (5), using default parameters. The consensus
variants were identied by comparing the resulting assemblies with the reference
sequence using MUMmer (6), as implemented in RATT software (7). Lastly, SARS-CoV-2
lineage classications (8) were assigned using PANGOLIN version 2.3.2 (https://github
A total of 36 Philippine SARS-CoV-2 samples were classied 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 (
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 countrys 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)
depth (×)
No. of
No. of
SNPs % N
(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
ROF, returning overseas Filipino; CAR, Cordillera Administrative Region; NCR, National Capital Region.
SNPs, single nucleotide polymorphisms.
% N, percentage of ambiguous base calls (Ncontent) 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 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.
This project was supported by a Genomics Biosurveillance grant from the Philippine
Department of Health and a Department of Science and TechnologyPhilippine 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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Microbiology Resource Announcement
Volume 10 Issue 18 e00219-21 3
Full-text available
During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing.
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The alpha/B.1.1.7 SARS-CoV-2 lineage emerged in autumn 2020 in the United Kingdom and transmitted rapidly until winter 2021 when it was responsible for most new COVID-19 cases in many European countries. The incidence domination was likely due to a fitness advantage that could be driven by the RBD residue change (N501Y), which also emerged independently in other Variants of Concern such as the beta/B.1.351 and gamma/P.1 strains. Here we present a functional characterization of the alpha/B.1.1.7 variant and show an eight-fold affinity increase towards human ACE-2. In accordance with this, transgenic hACE-2 mice showed a faster disease progression and severity after infection with a low dose of B.1.1.7, compared to an early 2020 SARS-CoV-2 isolate. When challenged with sera from convalescent individuals or anti-RBD monoclonal antibodies, the N501Y variant showed a minor, but significant elevated evasion potential of ACE-2/RBD antibody neutralization. The data suggest that the single asparagine to tyrosine substitution remarkable rise in affinity may be responsible for the higher transmission rate and severity of the B.1.1.7 variant.
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Background COVID-19 initially caused less severe outbreaks in many low- and middle-income countries (LMIC) compared with many high-income countries, possibly because of differing demographics, socioeconomics, surveillance, and policy responses. Here, we investigate the role of multiple factors on COVID-19 dynamics in the Philippines, a LMIC that has had a relatively severe COVID-19 outbreak. Methods We applied an age-structured compartmental model that incorporated time-varying mobility, testing, and personal protective behaviors (through a “Minimum Health Standards” policy, MHS) to represent the first wave of the Philippines COVID-19 epidemic nationally and for three highly affected regions (Calabarzon, Central Visayas, and the National Capital Region). We estimated effects of control measures, key epidemiological parameters, and interventions. Findings Population age structure, contact rates, mobility, testing, and MHS were sufficient to explain the Philippines epidemic based on the good fit between modelled and reported cases, hospitalisations, and deaths. The model indicated that MHS reduced the probability of transmission per contact by 13-27%. The February 2021 case detection rate was estimated at ~8%, population recovered at ~9%, and scenario projections indicated high sensitivity to MHS adherence. Interpretation COVID-19 dynamics in the Philippines are driven by age, contact structure, mobility, and MHS adherence. Continued compliance with low-cost MHS should help the Philippines control the epidemic until vaccines are widely distributed, but disease resurgence may be occurring due to a combination of low population immunity and detection rates and new variants of concern.
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The novel SARS-CoV-2 Variant of Concern (VOC)-202012/01 (also known as B.1.1.7), first collected in United Kingdom on 20 September 2020, is a rapidly growing lineage that in January 2021 constituted 86% of all SARS-CoV-2 genomes sequenced in England. The VOC has been detected in 40 out of 46 countries that reported at least 50 genomes in January 2021. We have estimated that the replicative advantage of the VOC is in the range 1.83–2.18 [95% CI: 1.71–2.40] with respect to the 20A.EU1 variant that dominated in England in November 2020, and in range 1.65–1.72 [95% CI: 1.46–2.04] in Wales, Scotland, Denmark, and USA. As the VOC strain will likely spread globally towards fixation, it is important to monitor its molecular evolution. We have estimated growth rates of expanding mutations acquired by the VOC lineage to find that the L18F substitution in spike has initiated a fast growing VOC substrain. The L18F substitution is of significance because it has been found to compromise binding of neutralizing antibodies. Of concern are immune escape mutations acquired by the VOC: E484K, F490S, S494P (in the receptor binding motif of spike) and Q677H, Q675H (in the proximity of the polybasic cleavage site at the S1/S2 boundary). These mutants may hinder efficiency of existing vaccines and expand in response to the increasing after-infection or vaccine-induced seroprevalence.
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Two new SARS-CoV-2 lineages with the N501Y mutation in the receptor-binding domain of the spike protein spread rapidly in the United Kingdom. We estimated that the earlier 501Y lineage without amino acid deletion Δ69/Δ70, circulating mainly between early September and mid-November, was 10% (6-13%) more transmissible than the 501N lineage, and the 501Y lineage with amino acid deletion Δ69/Δ70, circulating since late September, was 75% (70-80%) more transmissible than the 501N lineage. Two new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages carrying the amino acid substitution N501Y in the receptor-binding domain (RBD) of the spike protein have spread rapidly in the United Kingdom (UK) during late autumn 2020. Assessing the public health threat of these lineages (e.g. the potential for them to increase herd immunity thresholds if they displace other circulating SARS-CoV-2 strains) requires quantification of their comparative transmissibility. Here we adopted our previous epidemiological framework for relative fitness inference of co-circulating pathogen strains, which has been applied on influenza viruses [1] and SARS-CoV-2 D614G strains [2], to characterise the comparative transmissibility of the 501Y lineages.
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The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is associated with severe pneumonia/disease (COVID-19), has resulted in the generation of tens of thousands of virus genome sequences. The rate of genome generation is unprecedented, yet there is currently no coherent nor accepted scheme for naming the expanding phylogenetic diversity of SARS-CoV-2. Here, we present a rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread. Our system is made tractable by constraining the number and depth of hierarchical lineage labels and by flagging and delabelling virus lineages that become unobserved and hence are probably inactive. By focusing on active virus lineages and those spreading to new locations, this nomenclature will assist in tracking and understanding the patterns and determinants of the global spread of SARS-CoV-2.
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Motivation: Recent advances in sequencing technologies promise ultra-long reads of ∼100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms. Results: Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥ 100bp in length, ≥1kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads, and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions (INDELs) and introduces new heuristics to reduce spurious alignments. It is 3-4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or cDNA mappers at higher accuracy, surpassing most aligners specialized in one type of alignment. Availability and implementation: Contact:
The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes. Two new graphical viewing tools provide alternative ways to analyze genome alignments. The new system is the first version of MUMmer to be released as open-source software. This allows other developers to contribute to the code base and freely redistribute the code. The MUMmer sources are available at
Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom
  • K Leung
  • Mhh Shum
  • G M Leung
  • Tty Lam
  • J T Wu
Leung K, Shum MHH, Leung GM, Lam TTY, Wu JT. 2021. Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. Euro Surveill 26:2002106. https://