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SARS-CoV-2 B.1.1.7 lineage rapidly spreads and overwhelms R.1 lineage in Japan: serial and stationary observation in a community

Yosuke Hirotsu, Masao Omata1•
University of Tokyo1
06 Jul 2021-medRxiv (Cold Spring Harbor Laboratory Press)-
TL;DR: In this paper, the transition of viral lineage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was determined by stationary genome analysis in Yamanashi, Japan.
Abstract: Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) circulates in the world and acquires mutations during evolution. To identify the new emergent variants, the surveillance of the variants of concern (VOC) and variants of interest (VOI) is ongoing. This study aimed to determine how the transition of viral lineage occurred by stationary genome analysis in Yamanashi, Japan. Methods We performed the whole genome sequencing using SARS-CoV-2 positive samples (n=325) collected from February 2020 to the end of June 2021. The number of analyzed samples accounted for 15.4% of the total 2,109 samples identified in our community. Viral lineage was defined by the Phylogenetic Assignment of Named Global Outbreak (PANGO) lineages. Results We identified 13 types of viral lineages including R.1, P.1, B.1.1.7 (Alpha) and B.1.617.2 (Delta) These virus lineages had distinct periods of expansion and decline. After the emerging of the R.1 lineage harboring E484K variant (designated VOI in Japan), the prevalent B.1.1.214 lineage were no longer identified. The R.1 lineages were temporarily prevalent afterwards, but the influx of B.1.1.7 lineage (designated VOC) led to a decline in R.1. Currently, B.1.1.7 has become dominant after mid-April, 2021. Conclusion We clearly elucidated the transition and replacement of viral lineage by the community-based analysis. The virus completely replaced by more infectious lineages, therefore, it will be necessary to continue to monitor the VOC and VOI.

Summary (1 min read)

Jump to: [Introduction] – [Ethics statement] – [Nucleic acid extraction] – [Whole-genome sequencing] and [Clade and lineage classification]

Introduction

  • The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) circulates in the world and acquires mutations during evolution.
  • Meantime, various types of viral lineage have emerged during the virus evolution.
  • To prevent the spread of SARS-CoV-2, these VOCs and VOIs continue to be under surveillance in many countries.
  • The B.1.1.7 lineage was first identified in the United Kingdom at September 2020 and detected at airport quarantine in Japan at December 2020.

Ethics statement

  • The Institutional Review Board of the Clinical Research and Genome Research Committee at Yamanashi Central Hospital approved this study and the use of an opt-out consent method (Approval No. C2019-30).
  • The requirement for written informed consent was waived owing to it being an observational study and the urgent need to collect COVID-19 data.

Nucleic acid extraction

  • Nasopharyngeal swab samples were collected by using cotton swabs and placed in 3 ml of viral transport media (VTM) purchased from Copan Diagnostics (Murrieta, CA, United States).
  • The authors used 200 µl of VTM for nucleic acid extraction, performed within 2 h of sample collection.
  • Screening of spike protein mutation with TaqMan assay.
  • The authors also used a TaqMan SARS-CoV-2 Mutation Panel for detecting spike 69-70 deletion, N501Y and E484K (Thermo Fisher Scientific).
  • Master Mix CG was used as the master mix.

Whole-genome sequencing

  • Sequencing reads were processed, and their quality was assessed by using Genexus Software with SARS-CoV-2 plugins.
  • After initial mapping, a variant call was performed by using the Torrent Variant Caller.
  • The COVID19AnnotateSnpEff plugin was used for the annotation of variants.
  • Assembly was performed with the Iterative Refinement Meta-Assembler [20].

Clade and lineage classification

  • The viral clade and lineage classifications were conducted by using Nextstrain [14], and Phylogenetic Assignment of Named Global Outbreak Lineages [21].
  • As a result, sequencing analysis could successfully determine viral sequence from 325 individuals, excluding 10 individuals due to the very low viral load.
  • European Centre for Disease Prevention and Control: SARS-CoV-2 variants of concern.

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Figures (2)

Content maybe subject to copyright    Report

1
SARS-CoV-2 B.1.1.7 lineage rapidly spreads and
overwhelms R.1 lineage in Japan: serial and stationary
observation in a community
Yosuke Hirotsu
1
* and Masao Omata
2,3
1
Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi,
Japan
2
Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu,
Yamanashi, Japan
3
The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
*Corresponding author: Yosuke Hirotsu, Genome Analysis Center, Yamanashi Central
Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
Email: hirotsu-bdyu@ych.pref.yamanashi.jp
Tel: +81-55-253-7111, Fax: +81-55-253-8011
ORCID ID: 0000-0002-8002-834X
Short title: SARS-CoV-2 B.1.1.7 overwhelms R.1
. CC-BY-NC-ND 4.0 International licenseIt is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
The copyright holder for this preprint this version posted July 6, 2021. ; https://doi.org/10.1101/2021.06.30.21259820doi: medRxiv preprint
NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice.
2
Abstract
Background
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) circulates in the world
and acquires mutations during evolution. To identify the new emergent variants, the
surveillance of the variants of concern (VOC) and variants of interest (VOI) is ongoing. This
study aimed to determine how the transition of viral lineage occurred by stationary genome
analysis in Yamanashi, Japan.
Methods
We performed the whole genome sequencing using SARS-CoV-2 positive samples (n=325)
collected from February 2020 to the end of June 2021. The number of analyzed samples
accounted for 15.4% of the total 2,109 samples identified in our community. Viral lineage was
defined by the Phylogenetic Assignment of Named Global Outbreak (PANGO) lineages.
Results
We identified 13 types of viral lineages including R.1, P.1, B.1.1.7 (Alpha) and B.1.617.2
(Delta) These virus lineages had distinct periods of expansion and decline. After the
emerging of the R.1 lineage harboring E484K variant (designated VOI in Japan), the
prevalent B.1.1.214 lineage were no longer identified. The R.1 lineages were temporarily
prevalent afterwards, but the influx of B.1.1.7 lineage (designated VOC) led to a decline in
R.1. Currently, B.1.1.7 has become dominant after mid-April, 2021.
Conclusion
We clearly elucidated the transition and replacement of viral lineage by the community-based
analysis. The virus completely replaced by more infectious lineages, therefore, it will be
necessary to continue to monitor the VOC and VOI.
. CC-BY-NC-ND 4.0 International licenseIt is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
The copyright holder for this preprint this version posted July 6, 2021. ; https://doi.org/10.1101/2021.06.30.21259820doi: medRxiv preprint
3
Introduction
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is spreading
worldwide and threatening human health. In countries where vaccination is widely available,
the number of infected cases and deaths turned to be decreasing, giving a hope for the virus
under the control. Meantime, various types of viral lineage have emerged during the virus
evolution. In particular, mutations in receptor binding domain (RBD) of spike protein are of
interest for possible changes in the nature of the virus. The several viral lineages have been
designated as variant of concern (VOC) or variant of interest (VOI).
On May 31, 2021, World Health Organization (WHO) proposed a new designation,
Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1) and Delta (B.1.617.2) as the four VOCs and
Epsilon (B.1.427/B.1.429), Zeta (P.2), Eta (B.1.525), Theta (B.1.525) Lota (B.1.526), Kappa
(B.1.617.1) and Lambda (C.37) as the seven VOIs [1]. The U.S. Centers for Disease Control
and Prevention (CDC) [2], the European Centre for Disease Prevention and Control (ECDC)
[3], the Public Health England (PHE) [4] and National Institute of Infectious Diseases (NIID)
in Japan also have their own designations for VOCs and VOIs [5]. These lineages have
hallmark mutations in spike protein, which was suggested to affect the transmissibility,
immunity, and disease severity [6]. To prevent the spread of SARS-CoV-2, these VOCs and
VOIs continue to be under surveillance in many countries.
In January 2021, we started to conduct genomic surveillance of SARS-CoV-2 [7-9].
We previously reported on the SARS-CoV-2 R.1 lineage harboring spike W152L, E484K and
G769V mutations [8]. In Japan, the R.1 lineage was first registered in Global Initiative on
Sharing All Influenza Data (GISAID) database in November 2020 and showed an increase
around January 2021 [8, 10, 11]. Although the NIID in Japan has designated R.1 lineage as
a VOC, it is not clear there are associations with increased infectivity and transmissibility [5].
The B.1.1.7 lineage was first identified in the United Kingdom at September 2020
and detected at airport quarantine in Japan at December 2020. The B.1.1.7 was reported to
be highly transmissible and increase the disease severity [12, 13]. Actually, the B.1.1.7
spreads rapidly and is identified in 150 countries as of June 30, 2021 [14, 15]. Although
B.1.1.7 is reported to be highly transmissible, the transition of other virus lineage in Japan
has not been fully elucidated after the influx of B.1.1.7.
In this study, we conducted whole genome analysis of SARS-CoV-2 in 325 samples
. CC-BY-NC-ND 4.0 International licenseIt is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
The copyright holder for this preprint this version posted July 6, 2021. ; https://doi.org/10.1101/2021.06.30.21259820doi: medRxiv preprint
4
collected from February 2020 to June 2021 in Kofu, Japan. The lineages other than VOC and
VOI were observed until mid-January 2021, afterward, the R.1 lineage was dominant.
However, the subsequent influx of B.1.1.7 increased rapidly, suggesting a rapid replacement
of R.1 with B.1.1.7. We elucidated that the two major lineages have different infectivity based
on genomic surveillance.
Materials and Methods
Ethics statement
The Institutional Review Board of the Clinical Research and Genome Research Committee
at Yamanashi Central Hospital approved this study and the use of an opt-out consent
method (Approval No. C2019-30). The requirement for written informed consent was
waived owing to it being an observational study and the urgent need to collect COVID-19
data.
Nucleic acid extraction
Nasopharyngeal swab samples were collected by using cotton swabs and placed in 3 ml of
viral transport media (VTM) purchased from Copan Diagnostics (Murrieta, CA, United States).
We used 200 µl of VTM for nucleic acid extraction, performed within 2 h of sample collection.
Total nucleic acid was isolated using the MagMAX Viral/Pathogen Nucleic Acid Isolation Kit
(Thermo Fisher Scientific; Waltham, MA, United States) as previously described [16].
Screening of spike protein mutation with TaqMan assay
To detect hallmark mutations found in VOC and VOI, we performed allelic discrimination
analysis with a TaqMan assay. We also used a TaqMan SARS-CoV-2 Mutation Panel for
detecting spike 69-70 deletion, N501Y and E484K (Thermo Fisher Scientific). We also
designed a Custom TaqMan assay (Thermo Fisher Scientific) for detecting SARS-CoV-2
spike protein with the W152L and G769V mutations as previously described [8]. TaqPath 1-
Step RT-qPCR Master Mix CG was used as the master mix. The TaqMan Minor Groove
Binder probes for the wild-type and variant alleles were labelled with VIC dye and FAM dye
fluorescence, respectively.
. CC-BY-NC-ND 4.0 International licenseIt is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
The copyright holder for this preprint this version posted July 6, 2021. ; https://doi.org/10.1101/2021.06.30.21259820doi: medRxiv preprint
5
Whole-genome sequencing
We studied a total of 335 patients who were infected with SARS-CoV-2 determined by real-
time quantitative PCR and/or quantitative antigen test from February 15, 2020 to June 30,
2021 [16-19]. We subjected all these samples to whole genome analysis and successfully
obtained 325 sequence data, except for 10 samples with very low viral load.
SARS-CoV-2 genomic RNA was reverse transcribed into cDNA and amplified by
using the Ion AmpliSeq SARS-CoV-2 Research Panel (Thermo Fisher Scientific) on the Ion
Torrent Genexus System in accordance with the manufacturer’s instructions [8, 9].
Sequencing reads were processed, and their quality was assessed by using Genexus
Software with SARS-CoV-2 plugins. The sequencing reads were mapped and aligned by
using the torrent mapping alignment program. After initial mapping, a variant call was
performed by using the Torrent Variant Caller. The COVID19AnnotateSnpEff plugin was
used for the annotation of variants. Assembly was performed with the Iterative Refinement
Meta-Assembler [20].
Clade and lineage classification
The viral clade and lineage classifications were conducted by using Nextstrain [14], and
Phylogenetic Assignment of Named Global Outbreak (PANGO) Lineages [21]. The
sequences data was deposited in the Global Initiative on Sharing Avian Influenza Data
(GISAID) EpiCoV database [22].
Results
From February 2020 to the end of June 2021, we collected 335 SARS-CoV-2 positive
samples determined by RT-qPCR and/or quantitative antigen tests [16-19]. We subjected
these samples to the whole genome analysis and TaqMan mutation screening assay. As a
result, sequencing analysis could successfully determine viral sequence from 325 individuals,
excluding 10 individuals due to the very low viral load. As of June 30, this represented 15.4%
of the 2,109 infected individuals identified in our district.
To characterize the viral lineage, the yielded sequence data were analyzed by
PANGO lineage [15, 21]. The result showed the 325 samples were classified into 13 types of
lineage (B, B.1, B.1.1, B.1.149, B.1.1.284, B.1.1.214, B.1.411, B.1.346, R.1, P.1, B.1.1.220
. CC-BY-NC-ND 4.0 International licenseIt is made available under a
is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
The copyright holder for this preprint this version posted July 6, 2021. ; https://doi.org/10.1101/2021.06.30.21259820doi: medRxiv preprint
Citations
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Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections

[...]

Yuki Kurahashi, Silvia Sutandhio, Koichi Furukawa, Lidya Handayani Tjan, Sachiyo Iwata, Shigeru Sano, Yoshiki Tohma, Hiroyuki Ohkita, Sachiko Nakamura, Mitsuhiro Nishimura, Jun Arii, Tatsunori Kiriu, E. Yamamoto, Tatsuya Nagano, Yoshihiro Nishimura, Yasuko Mori 
24 Feb 2022-Frontiers in Immunology
TL;DR: The results indicate that neutralizing antibodies that recognize the common epitope for several variants may be maintained for a long time, whileneutralizing antibodies having specific epitopes for a variant, produced in large quantities immediately after infection, may decrease quite rapidly.
Abstract: Background Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic. The emergence of variants of concern (VOCs) has become one of the most pressing issues in public health. To control VOCs, it is important to know which COVID-19 convalescent sera have cross-neutralizing activity against VOCs and how long the sera maintain this protective activity. Methods Sera of patients infected with SARS-CoV-2 from March 2020 to January 2021 and admitted to Hyogo Prefectural Kakogawa Medical Center were selected. Blood was drawn from patients at 1-3, 3-6, and 6-8 months post onset. Then, a virus neutralization assay against SARS-CoV-2 variants (D614G mutation as conventional strain; B.1.1.7, P.1, and B.1.351 as VOCs) was performed using authentic viruses. Results We assessed 97 sera from 42 patients. Sera from 28 patients showed neutralizing activity that was sustained for 3-8 months post onset. The neutralizing antibody titer against D614G significantly decreased in sera of 6-8 months post onset compared to those of 1-3 months post onset. However, the neutralizing antibody titers against the three VOCs were not significantly different among 1-3, 3-6, and 6-8 months post onset. Discussion Our results indicate that neutralizing antibodies that recognize the common epitope for several variants may be maintained for a long time, while neutralizing antibodies having specific epitopes for a variant, produced in large quantities immediately after infection, may decrease quite rapidly.

8 citations

Journal Article•DOI•
Identification and Analysis of SARS-CoV-2 Alpha Variants in the Largest Taiwan COVID-19 Outbreak in 2021

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Li-Teh Liu, Jih-Jin Tsai, Ko Chang, Chun-Hong Chen, Ping Lin, Ching-Yi Tsai, Yan-Yi Tsai, M C Hsu, Wan-Long Chuang, Jer-Ming Chang, Shang-Jyh Hwang, Inn-Wen Chong 
25 Apr 2022-Frontiers in Medicine
TL;DR: It is concluded that the largest COVID-19 outbreak in Taiwan between May and June 2021 was initially caused by the alpha/B.1.
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is believed to have originated in Wuhan City, Hubei Province, China, in December 2019. Infection with this highly dangerous human-infecting coronavirus via inhalation of respiratory droplets from SARS-CoV-2 carriers results in coronavirus disease 2019 (COVID-19), which features clinical symptoms such as fever, dry cough, shortness of breath, and life-threatening pneumonia. Several COVID-19 waves arose in Taiwan from January 2020 to March 2021, with the largest outbreak ever having a high case fatality rate (CFR) (5.95%) between May and June 2021. In this study, we identified five 20I (alpha, V1)/B.1.1.7/GR SARS-CoV-2 (KMUH-3 to 7) lineage viruses from COVID-19 patients in this largest COVID-19 outbreak. Sequence placement analysis using the existing SARS-CoV-2 phylogenetic tree revealed that KMUH-3 originated from Japan and that KMUH-4 to KMUH-7 possibly originated via local transmission. Spike mutations M1237I and D614G were identified in KMUH-4 to KMUH-7 as well as in 43 other alpha/B.1.1.7 sequences of 48 alpha/B.1.1.7 sequences deposited in GISAID derived from clinical samples collected in Taiwan between 20 April and July. However, M1237I mutation was not observed in the other 12 alpha/B.1.1.7 sequences collected between 26 December 2020, and 12 April 2021. We conclude that the largest COVID-19 outbreak in Taiwan between May and June 2021 was initially caused by the alpha/B.1.1.7 variant harboring spike D614G + M1237I mutations, which was introduced to Taiwan by China Airlines cargo crew members. To our knowledge, this is the first documented COVID-19 outbreak caused by alpha/B.1.1.7 variant harboring spike M1237I mutation thus far. The largest COVID-19 outbreak in Taiwan resulted in 13,795 cases and 820 deaths, with a high CFR, at 5.95%, accounting for 80.90% of all cases and 96.47% of all deaths during the first 2 years. The high CFR caused by SARS-CoV-2 alpha variants in Taiwan can be attributable to comorbidities and low herd immunity. We also suggest that timely SARS-CoV-2 isolation and/or sequencing are of importance in real-time epidemiological investigations and in epidemic prevention. The impact of G614G + M1237I mutations in the spike gene on the SARS-CoV-2 virus spreading as well as on high CFR remains to be elucidated.

4 citations

Journal Article•DOI•
Lung tropism in hospitalized patients following infection with SARS-CoV-2 variants from D614G to Omicron BA.2

[...]

Yosuke Hirotsu, Yumiko Kakizaki, Akitoshi Saito, Toshiharu Tsutsui, Syunya Hanawa, Haruna Yamaki, Syuichiro Ide, Makoto Kawaguchi, Hiroaki Kobayashi, Yoshihiro Miyashita, Masao Omata 
25 Feb 2023-Communications medicine
TL;DR: In this paper , the authors analyzed the association between the severity of the pathogenesis of pneumonia in humans and SARS-CoV-2 variants that have been prevalent to date and found that there was a marked decrease in pneumonia prevalence and lung involvement in patients infected with Omicron owing to decreased tropism in the lungs.
Abstract: Abstract Background The genetic and pathogenic characteristics of SARS-CoV-2 have evolved from the original isolated strains; however, the changes in viral virulence have not been fully defined. In this study, we analyzed the association between the severity of the pathogenesis of pneumonia in humans and SARS-CoV-2 variants that have been prevalent to date. Methods We examined changes in the variants and tropism of SARS-CoV-2. A total of 514 patients admitted between February 2020 and August 2022 were included and evaluated for pneumonia by computed tomography (CT) as a surrogate of viral tropism. Results The prevalence of pneumonia for each variant was as follows: D614G (57%, 65/114), Alpha (67%, 41/61), Delta (49%, 41/84), Omicron BA.1.1 (26%, 43/163), and Omicron BA.2 (11%, 10/92). The pneumonia prevalence in unvaccinated patients progressively declined from 70% to 11% as the variants changed: D614G (56%, 61/108), Alpha (70%, 26/37), Delta (60%, 38/63), BA.1.1 (52%, 15/29), and BA.2 (11%, 2/19). The presence of pneumonia in vaccinated patients was as follows: Delta (16%, 3/19), BA.1.1 (21%, 27/129), and BA.2 (11%, 8/73). Compared with D614G, the areas of lung involvement were also significantly reduced in BA.1.1 and BA.2 variants. Conclusions Compared with previous variants, there was a marked decrease in pneumonia prevalence and lung involvement in patients infected with Omicron owing to decreased tropism in the lungs that hindered viral proliferation in the alveolar epithelial tissue. Nevertheless, older, high-risk patients with comorbidities who are infected with an Omicron variant can still develop pneumonia and require early treatment.

1 citations

References
More filters
Journal Article•DOI•
GISAID: Global initiative on sharing all influenza data - from vision to reality.

[...]

Yuelong Shu1, John W. McCauley2•
Chinese Center for Disease Control and Prevention1, Francis Crick Institute2
30 Mar 2017-Eurosurveillance
TL;DR: This poster presents a poster presenting a poster presented at the 2016 International Conference of the Association for the Study of Viral Influenza and its Disruption in China, where it was presented for the first time.
Abstract: Yuelong Shu1, John McCauley2 1. WHO Collaborating Center for Reference and Research on Influenza, Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China 2. WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, the Francis Crick Institute, London, United Kingdom

2,306 citations

Journal Article•DOI•
Nextstrain: real-time tracking of pathogen evolution.

[...]

James Hadfield1, Colin Megill1, Sidney M Bell2, Sidney M Bell1, John Huddleston1, John Huddleston2, Barney Potter1, Charlton Callender1, Pavel Sagulenko3, Trevor Bedford1, Richard A. Neher4, Richard A. Neher5, Richard A. Neher3 •
Fred Hutchinson Cancer Research Center1, University of Washington2, Max Planck Society3, University of Basel4, Swiss Institute of Bioinformatics5
01 Dec 2018-Bioinformatics
TL;DR: Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualization platform that presents a real-time view into the evolution and spread of a range of viral pathogens of high public health importance.
Abstract: Summary Understanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualization platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species. Nextstrain compiles our current understanding into a single accessible location, open to health professionals, epidemiologists, virologists and the public alike. Availability and implementation All code (predominantly JavaScript and Python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org.

2,305 citations

Journal Article•DOI•
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.

[...]

Andrew Rambaut1, Edward C. Holmes2, Áine O'Toole1, Verity Hill1, John T. McCrone1, Christopher Ruis3, Louis du Plessis4, Oliver G. Pybus4 •
University of Edinburgh1, University of Sydney2, University of Cambridge3, University of Oxford4
15 Jul 2020-Nature microbiology
TL;DR: A rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread and is designed to provide a real-time bird’s-eye view of the diversity of the hundreds of thousands of genome sequences collected worldwide.
Abstract: 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.

2,093 citations

Journal Article•DOI•
Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant.

[...]

Leonid Yurkovetskiy1, Xue Wang2, Kristen E. Pascal3, Christopher Tomkins-Tinch4, Thomas Nyalile1, Yetao Wang1, Alina Baum3, William E. Diehl1, Ann Dauphin1, Claudia Carbone1, Kristen Veinotte1, Shawn B. Egri1, Stephen F. Schaffner4, Stephen F. Schaffner5, Jacob E. Lemieux4, James B. Munro1, Ashique Rafique3, Abhi Barve2, Pardis C. Sabeti, Christos A. Kyratsous3, Natalya Dudkina2, Kuang Shen1, Jeremy Luban •
University of Massachusetts Medical School1, Thermo Fisher Scientific2, Regeneron3, Harvard University4, Broad Institute5
29 Oct 2020-Cell
TL;DR: It is shown that D614G was more infectious than the ancestral form on human lung cells, colon cells, and on cells rendered permissive by ectopic expression of human ACE2 or of ACE2 orthologs from various mammals, including Chinese rufous horseshoe bat and Malayan pangolin.

840 citations

Journal Article•DOI•
Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England.

[...]

Erik M. Volz1, Swapnil Mishra1, Meera Chand2, Jeffrey C. Barrett3, Robert Johnson1, Lily Geidelberg1, Wes Hinsley1, Daniel J. Laydon1, Gavin Dabrera2, Áine O'Toole4, Roberto Amato3, Manon Ragonnet-Cronin1, Ian Harrison2, Ben Jackson4, Cristina V. Ariani3, Olivia Boyd1, Nicholas J. Loman5, Nicholas J. Loman2, John T. McCrone4, Sónia Gonçalves3, David Jorgensen1, Richard M. Myers2, Verity Hill4, David K. Jackson3, Katy A. M. Gaythorpe1, Natalie Groves2, John Sillitoe3, Dominic P. Kwiatkowski3, Seth Flaxman1, Oliver Ratmann1, Samir Bhatt6, Samir Bhatt1, Susan Hopkins2, Axel Gandy1, Andrew Rambaut4, Neil M. Ferguson1 •
Imperial College London1, Public Health England2, Wellcome Trust Sanger Institute3, University of Edinburgh4, University of Birmingham5, University of Copenhagen6
25 Mar 2021-Nature
TL;DR: In this paper, the authors show that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S gene target failures (SGTF) in community-based diagnostic PCR testing.
Abstract: The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England1, was first identified in the UK in late summer to early autumn 20202. Whole-genome SARS-CoV-2 sequence data collected from community-based diagnostic testing for COVID-19 show an extremely rapid expansion of the B.1.1.7 lineage during autumn 2020, suggesting that it has a selective advantage. Here we show that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S gene target failures (SGTF) in community-based diagnostic PCR testing. Analysis of trends in SGTF and non-SGTF case numbers in local areas across England shows that B.1.1.7 has higher transmissibility than non-VOC lineages, even if it has a different latent period or generation time. The SGTF data indicate a transient shift in the age composition of reported cases, with cases of B.1.1.7 including a larger share of under 20-year-olds than non-VOC cases. We estimated time-varying reproduction numbers for B.1.1.7 and co-circulating lineages using SGTF and genomic data. The best-supported models did not indicate a substantial difference in VOC transmissibility among different age groups, but all analyses agreed that B.1.1.7 has a substantial transmission advantage over other lineages, with a 50% to 100% higher reproduction number.

827 citations

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[...]

13 Mar 2021-bioRxiv
Paola Cristina Resende, Tiago Gräf, Anna Carolina Dias Paixão, Luciana Appolinario, Renata Serrano Lopes, Ana Carolina da Fonseca Mendonça, Alice Sampaio Barreto da Rocha, Fernando Couto Motta, Lidio Gonçalves Lima Neto, Ricardo Khouri, Pedro Santos-Muccillo, João Felipe Bezerra, Dalane Loudal Florentino Teixeira, Irina Nastassja Riediger, Maria do Carmo Debur, Rodrigo Ribeiro-Rodrigues, Anderson Brandao Leite, Cliomar Alves do Santos, Tatiana Schäffer Gregianini, Sandra Fernandes, A Bernardes, Andrea Cony Cavalcanti, Fabio Miyajima, Claudio Sachhi, Tirza Mattos, Cristiano Fernandes da Costa, Edson Delatorre, Gabriel Luz Wallau, Felipe Gomes Naveca, Gonzalo Bello, Marilda M. Siqueira 
Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations.

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12 May 2021
Rokshana Parvin, Sultana Zahura Afrin, Jahan Ara Begum, Salma Ahmed, Mohammed Nooruzzaman, Emdadul Haque Chowdhury, Anne Pohlmann, Shyamal Kumar Paul 
The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil.

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01 Oct 2021-Frontiers in Public Health
Cíntia Bittar, Fábio Sossai Possebon, Leila Sabrina Ullmann, Dayla Bott Geraldini, Vivaldo Gomes da Costa, Luiz Gonzaga Paula de Almeida, Paulo R. S. Sanches, Nailton M. Nascimento-Júnior, Eduardo Maffud Cilli, Cecilia Artico Banho, Guilherme Campos, Helena Lage Ferreira, Lívia Sacchetto, Gislaine Celestino Dutra da Silva, Maisa Carla Pereira Parra, Marilia Mazzi Moraes, Paulo Inácio da Costa, Ana Tereza Ribeiro de Vasconcelos, Fernando Rosado Spilki, Maurício Lacerda Nogueira, Paula Rahal, João Pessoa Araújo 
Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level

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05 Mar 2021-Pathogenetics
Malik Sallam, Azmi Mahafzah
Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany.

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29 Jul 2021-Viruses
Sébastien Calvignac-Spencer, Matthias Budt, Matthew Huska, Hugues Richard, Luca Leipold, Linus Grabenhenrich, Torsten Semmler, Max von Kleist, Stefan Kröger, Thorsten Wolff, Martin Hölzer 
Frequently Asked Questions (3)
Q1. Why was the requirement for written informed consent waived?

The requirement for written informed consent was waived owing to it being an observational study and the urgent need to collect COVID-19 data. 

The authors studied a total of 335 patients who were infected with SARS-CoV-2 determined by realtime quantitative PCR and/or quantitative antigen test from February 15, 2020 to June 30, 2021 [16-19]. 

Hirotsu Y, Mochizuki H, Omata M: Double-quencher probes improve detectionsensitivity toward Severe Acute Respiratory Syndrome Coronavirus 2 (SARSCoV-2) in a reverse-transcription polymerase chain reaction (RT-PCR) assay J Virol Methods 2020, 284:113926.18.