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Sequence Analysis of 20,453 SARS-CoV-2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern

Scott Wesley Long1, Randall J. Olsen2, Randall J. Olsen1, Paul A. Christensen1, Sishir Subedi1, Robert Olson3, Robert Olson4, James J. Davis4, James J. Davis3, Matthew Ojeda Saavedra1, Prasanti Yerramilli1, Layne Pruitt1, Kristina Reppond1, Madison N. Shyer1, Jessica Cambric1, Ilya J. Finkelstein5, Jimmy Gollihar1, Jimmy Gollihar6, James M. Musser2, James M. Musser1 •
Houston Methodist Hospital1, Cornell University2, University of Chicago3, Argonne National Laboratory4, University of Texas at Austin5, United States Army Research Laboratory6
02 Mar 2021-medRxiv (Cold Spring Harbor Laboratory Press)-
TL;DR: Based on the extensive genome sequencing program involving 20,453 virus specimens from COVID-19 patients dating from March 2020, the authors report identification of all important SARS-CoV-2 variants among Houston Methodist Hospital patients residing in the greater metropolitan area.
Abstract: []Since the beginning of the SARS-CoV-2 pandemic, there has been international concern about the emergence of virus variants with mutations that increase transmissibility, enhance escape from the human immune response, or otherwise alter biologically important phenotypes. In late 2020, several "variants of concern" emerged globally, including the UK variant (B.1.1.7), South Africa variant (B.1.351), Brazil variants (P.1 and P.2), and two related California "variants of interest" (B.1.429 and B.1.427). These variants are believed to have enhanced transmissibility capacity. For the South Africa and Brazil variants, there is evidence that mutations in spike protein permit it to escape from some vaccines and therapeutic monoclonal antibodies. Based on our extensive genome sequencing program involving 20,453 virus specimens from COVID-19 patients dating from March 2020, we report identification of all important SARS-CoV-2 variants among Houston Methodist Hospital patients residing in the greater metropolitan area. Although these variants are currently at relatively low frequency in the population, they are geographically widespread. Houston is the first city in the United States to have all variants documented by genome sequencing. As vaccine deployment accelerates worldwide, increased genomic surveillance of SARS-CoV-2 is essential to understanding the presence and frequency of consequential variants and their patterns and trajectory of dissemination. This information is critical for medical and public health efforts to effectively address and mitigate this global crisis.

Summary (2 min read)

Jump to: [[Introduction]] – [SARS-CoV-2 Molecular Diagnostic Testing] – [SARS-CoV-2 Genome Sequencing] – [SARS-CoV-2 Genome Sequence Analysis] – [Geospatial Analysis] – [UK Variant of Concern (B.1.1.7)] – [Geospatial Distribution of Variants] and [Discussion]

[Introduction]

  • The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19).
  • 18, 21, 27, 28 Similarly, the South Africa and Brazil variants caused large disease outbreaks in their respective countries.
  • 40 The 2,400-bed Houston Methodist health system has eight hospitals and cares for a large, multiethnic, and geographically and socioeconomically diverse patient population throughout greater Houston.
  • The eight Houston Methodist hospitals have a single central molecular diagnostic laboratory, which means that all RT-PCR-specimens can readily be identified, banked, and subjected to further study as needed.
  • In the aggregate, strategic co-localization of these diagnostic attributes coupled with a contiguous research institute building seamlessly facilitates comprehensive population genomic studies of SARS-CoV-2 viruses causing infections in the Houston metropolitan region.

SARS-CoV-2 Molecular Diagnostic Testing

  • Specimens obtained from symptomatic patients with a high degree of suspicion for COVID-19 disease were tested in the Molecular Diagnostics Laboratory at Houston Methodist Hospital using assays granted Emergency Use Authorization (EUA) from the FDA (https://www.fda.gov/medical-devices/emergency-situations-medical-devices/faqs-diagnostictesting-sars-cov-2#offeringtests).
  • Multiple molecular testing platforms were used, including the COVID-19 test or RP2.1 test with BioFire Film Array instruments, the Xpert Xpress SARS-CoV-2 test using Cepheid GeneXpert Infinity or Cepheid GeneXpert Xpress IV instruments, the SARS-CoV-2 Assay using the Hologic Panther instrument, the Aptima SARS-CoV-2 Assay using the Hologic Panther Fusion system and the SARS-CoV-2 assay using Abbott Alinity m instruments.
  • All assays were performed according to the manufacturer's instructions.
  • Testing was performed on material obtained from nasopharyngeal, oropharyngeal, or nasal swabs immersed in universal transport media (UTM), bronchoalveolar lavage fluid, or sputum treated with dithiothreitol (DTT).
  • To standardize specimen collection, an instructional video was created for Houston Methodist healthcare workers (https://vimeo.com/396996468/2228335d56).

SARS-CoV-2 Genome Sequencing

  • Libraries for whole virus genome sequencing were prepared according to version 3 of the ARTIC nCoV-2019 sequencing protocol (https://artic.network/ncov-2019).
  • Long reads were generated with the LSK-109 sequencing kit, 24 native barcodes (NBD104 and NBD114 kits), and a GridION instrument (Oxford Nanopore).
  • Short sequence reads were generated with either a NextSeq 550 or NovaSeq 6000 instrument .

SARS-CoV-2 Genome Sequence Analysis

  • Viral genomes were assembled with the BV-BRC SARS-Cov2 assembly service (https://www.bvbrc.org/app/ComprehensiveSARS2Analysis).
  • 50 The One Codex SARS-CoV-2 variant calling and consensus assembly pipeline was chosen for assembling all sequences (https://github.com/onecodex/sars-cov-2.git) using default parameters and a minimum read depth of 3.
  • Briefly, the pipeline uses seqtk version 1.3-r116 for sequence trimming (https://github.com/lh3/seqtk.git); minimap version 2.1 51 for aligning reads against reference genome Wuhan-Hu-1 (NC_045512.2); samtools version 1.11 for sequence and file manipulation 52 ; and iVar version 1.2.2 for primer trimming and variant calling.

Geospatial Analysis

  • The patient home address zip codes were used to visualize the geospatial distribution of spread for each variant of concern.
  • Figures were generated using Tableau version 2020.

UK Variant of Concern (B.1.1.7)

  • It was strongly associated with a resurgence of SARS-CoV-2 infections in that region and rapidly became the dominant lineage.
  • Preliminary evidence indicates that immune sera from the Pfizer-BioNTech SARS-CoV-2 vaccine retain the ability to neutralize B.1.1.7 variants in vitro.
  • The P.1 variant of concern was reported to have originated in Manaus, Brazil, and like the South Africa B.1.351 variant, has numerous mutations in spike protein, including E484K and N501Y .
  • 16 Since November 2020, this variant has been detected in 42 states in the US, 63 and was first found in Houston Methodist Hospital patients in specimens obtained the last week of December, 2020.
  • 62 The California variants are noteworthy primarily for their emergence and very rapid spread in Los Angeles County and identification elsewhere in the US.

Geospatial Distribution of Variants

  • Given the importance of the identification of these SARS-CoV-2 variants in the Houston metropolitan area, the authors examined their geospatial distribution to investigate the extent of dissemination .
  • With the exception of the B.1.351 variant, patients infected with all other variants resided in widely dispersed areas of the metropolitan area.

Discussion

  • Here the authors report discovery of the UK (B.1.1.7), South Africa (B.1.351), and Brazil (P.1) SARS-CoV-2 variants of concern from patients in the Houston metropolitan region.
  • The authors also identified geographically-widespread dissemination of the Cal.20C California (B.1.429 and B.1.427) variants of interest.
  • These four SARS-CoV-2 variants are distributed across a large geospatial region in the metropolitan region , indicating successful patient-to-patient transmission among Houstonians.
  • None of the affected patients were from a common household or reported recent international travel, suggesting that every infection was independently acquired locally or during domestic travel.

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Content maybe subject to copyright    Report

Sequence Analysis of 20,453 SARS-CoV-2 Genomes from the Houston
1
Metropolitan Area Identifies the Emergence and Widespread
2
Distributi on of Multiple Isol ates of All Major Variant s of Concern
3
4
S. Wesley Long,
a,b,1
Randall J. Olsen,
a,b,1
Paul A. Christensen,
a
Sishir Subedi,
a
Robert Olson,
c,d
5
James J. Davis,
c,d
Matthew Ojeda Saavedra,
a
Prasanti Yerramilli,
a
Layne Pruitt,
a
Kristina 6
Reppond,
a
Madison N. Shyer,
a
Jessica Cambric,
a
Ilya J. Finkelstein,
e
Jimmy Gollihar,
a,f
and 7
James M. Musser
a,b#
8
9
From the
a
Center for Molecular and Translational Human Infectious Diseases Research,
10
Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and
11
Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas, 77030
12
b
Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill
13
Cornell Medical College, 1300 York Avenue, New York, New York, 10065
14
c
Consortium for Advanced Science and Engineering, 22 University of Chicago, 5801 South Ellis
15
Avenue, Chicago, Illinois, 60637
16
d
Computing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass
17
Avenue, Lemont, Illinois, 60439
18
e
Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of
19
Texas at Austin, Austin, Texas 78712
20
f
CCDC Army Research Laboratory-South, University of Texas, Austin, Texas 78712
21
. 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 March 2, 2021. ; https://doi.org/10.1101/2021.02.26.21252227doi: 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.
22
Number of text pages: 12 23
Number of tables: 1 24
Number of figures: 2 25
Running head (40 characters or less): SARS-CoV-2 variants of concern in Houston, TX 26
27
# Address correspondence to James M. Musser, M.D., Ph.D., Department of Pathology and 28
Genomic Medicine, Houston Methodist Research Institute, 6565 Fannin Street, Suite B490, 29
Houston, Texas 77030. Tel: 713.441.5 890, E- mail: jmmusser@houstonmethodist.org. 30
31
Disclosures: None. 32
33
34
35
36
37
38
39
40
41
42
43
. 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 March 2, 2021. ; https://doi.org/10.1101/2021.02.26.21252227doi: medRxiv preprint
[Abstract (220 words)] 44
Since the beginning of the SARS-CoV-2 pandemic, there has been international concern about 45
the emergence of virus variants with mutations that increase transmissibility, enhance escape 46
from the human immune response, or otherwise alter biologically important phenotypes. In 47
late 2020, several “variants of concern” emerged globally, including the UK variant (B.1.1.7), 48
South Africa variant (B.1.351), Brazil variants (P.1 and P.2), and two related California “variants 49
of interest” (B.1.429 and B.1.427). These variants are believed to have enhanced 50
transmissibility capacity. For the South Africa and Brazil variants, there is evidence that 51
mutations in spike protein permit it to escape from some vaccines and therapeutic monoclonal 52
antibodies. Based on our extensive genome sequencing program involving 20,453 virus 53
specimens from COVID-19 patients dating from March 2020, we report identification of all 54
important SARS-CoV-2 variants among Houston Methodist Hospital patients residing in the 55
greater metropolitan area. Although these variants are currently at relatively low frequency in 56
the population, they are geographically widespread. Houston is the first city in the United 57
States to have all variants documented by genome sequencing. As vaccine deployment 58
accelerates worldwide, increased genomic surveillance of SARS-CoV-2 is essential to 59
understanding the presence and frequency of consequential variants and their patterns and 60
trajectory of dissemination. This information is critical for medical and public health efforts to 61
effectively address and mitigate this global crisis. 62
63
64
. 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 March 2, 2021. ; https://doi.org/10.1101/2021.02.26.21252227doi: medRxiv preprint
[Introduction] 65
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of 66
coronavirus disease 2019 (COVID-19). Since first being identified in December 2019,
1-4
the virus 67
has spread globally and is responsible for massive human morbidity and mortality worldwide.
5-9
68
At the onset of the pandemic, effective treatments for COVID-19 were lacking. But as a result of 69
intense global research efforts, monoclonal antibody (mAbs) therapies
10, 11
and several 70
vaccines,
12, 13
primarily directed against the spike protein, have been developed to treat and 71
prevent SARS-CoV-2 infection. 72
In late 2020 the international research community described several SARS-CoV-2 73
“variants of concern” that warranted special scrutiny. These include the United Kingdom (UK) 74
variant (B.1.1.7), South Africa variant (B.1.351), Brazil variants (P.1 and P.2) and two California 75
variants (B.1.429/CAL.20C and B.1.427/CAL.20C).
14-22
These virus variants were designated as 76
“concerning” predominantly due to their reported enhanced person-to-person transmission in 77
some geographic areas, and they have since been detected in several countries worldwide. For 78
example, the UK B.1.1.7 variant spread rapidly in southeast England where it caused large 79
numbers of COVID-19 cases,
14
and was identified shortly thereafter in the United States (US) 80
[CDC; https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant.html].
23
More than 81
1,600 cases have since been documented in the US, and at least one large outbreak recently 82
was reported in a Michigan prison.
24, 25
There is concern at the Centers for Disease Control and 83
Prevention (CDC) that it could become the dominant variant causing disease in the US by 84
March.
23, 24, 26
Moreover, the UK B.1.1.7 variant may be linked to an increased death rate 85
compared to other virus types, adding further concern.
18, 21, 27, 28
86
. 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 March 2, 2021. ; https://doi.org/10.1101/2021.02.26.21252227doi: medRxiv preprint
Similarly, the South Africa and Brazil variants caused large disease outbreaks in their 87
respective countries.
19, 20
These variants also are of concern because they contain a mutation 88
(E484K) in the spike protein that decreases efficacy of some therapeutic mAbs, decreases
in
89
vitr
o virus neutralization, and may result in potential escape from immunity induced by natural 90
infection or vaccination.
29-37
All three variants (UK B.1.1.7, Brazil P.1, and South Africa B.1.351) 91
also have a N501Y mutation in spike protein that is associated with stronger binding to the 92
ACE2 receptor, possibly contributing to increased transmissibility.
38,39
93
The Houston metropolitan area is the fourth largest and most ethnically diverse city in 94
the US, with a population of approximately 7 million (https://www.houston.org/houston-
95
data
).
40
The 2,400-bed Houston Methodist health system has eight hospitals and cares for a 96
large, multiethnic, and geographically and socioeconomically diverse patient population 97
throughout greater Houston. The eight Houston Methodist hospitals have a single central 98
molecular diagnostic laboratory, which means that all RT-PCR-specimens can readily be 99
identified, banked, and subjected to further study as needed. In addition, the Department of 100
Pathology and Genomic Medicine has a long-standing record of integrating genome sequencing 101
efforts into clinical care and research, especially related to microbial pathogens infecting our 102
patients.
41-49
In the aggregate, strategic co-localization of these diagnostic attributes coupled 103
with a contiguous research institute building seamlessly facilitates comprehensive population 104
genomic studies of SARS-CoV-2 viruses causing infections in the Houston metropolitan region. 105
46, 49
106
Before the SARS-CoV-2 virus arrived in Houston, we planned an integrated strategy to 107
confront and mitigate this microbial threat to our patients. In addition to rapidly validating an 108
. 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 March 2, 2021. ; https://doi.org/10.1101/2021.02.26.21252227doi: medRxiv preprint
Citations
More filters
Journal Article•DOI•
Signals of Significantly Increased Vaccine Breakthrough, Decreased Hospitalization Rates, and Less Severe Disease in Patients with Coronavirus Disease 2019 Caused by the Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2 in Houston, Texas

[...]

Paul A. Christensen, Randall J. Olsen, S. Wesley Long, R. D. Snehal, James J. Davis, Matthew Ojeda Saavedra, K. Reppond, Madison N. Shyer, Jessica E. Cambric, Ryan D. H. Gadd, R. M. Thakur, A. Batajoo, R. Mangham, S Silva Peña, Tri Quang Trinh, Jacob C. Kinskey, Guy Williams, Robert Olson, Jimmy Gollihar, James M. Musser 
01 Feb 2022-American Journal of Pathology
TL;DR: In this article , a genome sequencing study of SARS-CoV-2 in the Houston Methodist health care system identified 4468 symptomatic patients with infections caused by Omicron (B.1.529) from late November 2021 through January 5, 2022.
Abstract: Genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to dramatically alter the landscape of the coronavirus disease 2019 (COVID-19) pandemic. The recently described variant of concern designated Omicron (B.1.1.529) has rapidly spread worldwide and is now responsible for the majority of COVID-19 cases in many countries. Because Omicron was recognized recently, many knowledge gaps exist about its epidemiology, clinical severity, and disease course. A genome sequencing study of SARS-CoV-2 in the Houston Methodist health care system identified 4468 symptomatic patients with infections caused by Omicron from late November 2021 through January 5, 2022. Omicron rapidly increased in only 3 weeks to cause 90% of all new COVID-19 cases, and at the end of the study period caused 98% of new cases. Compared with patients infected with either Alpha or Delta variants in our health care system, Omicron patients were significantly younger, had significantly increased vaccine breakthrough rates, and were significantly less likely to be hospitalized. Omicron patients required less intense respiratory support and had a shorter length of hospital stay, consistent with on average decreased disease severity. Two patients with Omicron stealth sublineage BA.2 also were identified. The data document the unusually rapid spread and increased occurrence of COVID-19 caused by the Omicron variant in metropolitan Houston, Texas, and address the lack of information about disease character among US patients.

148 citations

Journal Article•DOI•
Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies.

[...]

Chengchao Ding1, Jun He2, Xiangyu Zhang1, Chengcheng Jiang1, Yong Sun2, Yuqing Zhang1, Qingqing Chen2, Hongliang He1, Wenting Li1, Jiajia Xie1, Zhirong Liu2, Yong Gao1 •
University of Science and Technology of China1, Centers for Disease Control and Prevention2
01 Jan 2021-Frontiers in Immunology
TL;DR: In this paper, the authors evaluated the cross-neutralization of convalescent plasmas and RBD-specific monoclonal antibodies against various spike protein-based pseudoviruses.
Abstract: Small number of SARS-CoV-2 epidemic lineages did not efficiently exhibit a neutralization profile, while single amino acid mutation in the spike protein has not been confirmed in altering viral antigenicity resulting in immune escape. To identify crucial mutations in spike protein that escape humoral immune response, we evaluated the cross-neutralization of convalescent plasmas and RBD-specific monoclonal antibodies (mAbs) against various spike protein-based pseudoviruses. Three of 24 SARS-CoV-2 pseudoviruses containing different mutations in spike protein, including D614G, A475V, and E484Q, consistently showed an altered sensitivity to neutralization by convalescent plasmas. A475V and E484Q mutants are highly resistant to neutralization by mAb B38 and 2-4, suggesting that some crucial mutations in spike protein might evolve SARS-CoV-2 variants capable of escaping humoral immune response.

33 citations

Posted Content•DOI•
Early signals of significantly increased vaccine breakthrough, decreased hospitalization rates, and less severe disease in patients with COVID-19 caused by the Omicron variant of SARS-CoV-2 in Houston, Texas

[...]

P. and Christensen, Randall J. Olsen, S. Long, R. D. Snehal, J. Davis, Matthew Ojeda Saavedra, K. Reppond, Madison N. Shyer, Jessica E. Cambric, Ryan D. H. Gadd, R. M. Thakur, A. Batajoo, R. Mangham, S Silva Peña, Tinh H. Trinh, Jacob C. Kinskey, Graciëlle Williams, Ruth Olson, J. Golihar, James M. Musser 
01 Jan 2022-medRxiv
TL;DR: In the aggregate, the data document the unusually rapid spread and increased occurrence of COVID-19 caused by the Omicron variant in metropolitan Houston, and provide information about disease character.
Abstract: Genetic variants of SARS-CoV-2 continue to dramatically alter the landscape of the COVID-19 pandemic. The recently described variant of concern designated Omicron (B.1.1.529) has rapidly spread worldwide and is now responsible for the majority of COVID-19 cases in many countries. Because Omicron was recognized very recently, many knowledge gaps exist about its epidemiology and clinical severity and disease course. A comprehensive genome sequencing study of SARS-CoV-2 in the Houston Methodist healthcare system identified 862 symptomatic patients with infections caused by Omicron from late November 2021 through December 18, 2021. Omicron very rapidly increased in only three weeks to cause 90% of all new COVID-19 cases. Compared to patients infected with either Alpha or Delta variants in our healthcare system, Omicron patients were significantly younger, had significantly increased vaccine breakthrough rates, and were significantly less likely to be hospitalized. Omicron patients required less intense respiratory support and had a shorter length of hospital stay, consistent with decreased disease severity. Although the number of Omicron patients we studied is relatively small, in the aggregate the data document the unusually rapid spread and increased occurrence of COVID-19 caused by the Omicron variant in metropolitan Houston, and provide information about disease character.

26 citations

Journal Article•DOI•
The Emergence and Spread of Novel SARS-CoV-2 Variants.

[...]

Huaimin Yi1, Jin Wang1, Jiong Wang2, Yuying Lu1, Yali Zhang1, Ruihao Peng1, Jiahai Lu1, Zeliang Chen3, Zeliang Chen1 •
Sun Yat-sen University1, Southern Medical University2, Chinese Ministry of Education3
02 Aug 2021-Frontiers in Public Health
TL;DR: Wang et al. as discussed by the authors analyzed the distribution characteristics of prevalent SARS-CoV-2 variants and the frequency of mutant sites based on the data available from GISAID and PANGO by R 4.0.2 and ArcGIS 10.2.
Abstract: Since severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) began to spread in late 2019, laboratories around the world have widely used whole genome sequencing (WGS) to continuously monitor the changes in the viral genes and discovered multiple subtypes or branches evolved from SARS-CoV-2. Recently, several novel SARS-CoV-2 variants have been found to be more transmissible. They may affect the immune response caused by vaccines and natural infections and reduce the sensitivity to neutralizing antibodies. We analyze the distribution characteristics of prevalent SARS-CoV-2 variants and the frequency of mutant sites based on the data available from GISAID and PANGO by R 4.0.2 and ArcGIS 10.2. Our analysis suggests that B.1.1.7, B.1.351, and P.1 are more easily spreading than other variants, and the key mutations of S protein, including N501Y, E484K, and K417N/T, have high mutant frequencies, which may have become the main genotypes for the spread of SARS-CoV-2.

22 citations

Posted Content•DOI•
Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State

[...]

Garrett A. Perchetti1, Haiying Zhu1, Margaret G. Mills1, Lasata Shrestha1, Cassia Wagner2, Cassia Wagner1, Shah A Mohamed Bakhash1, Michelle J. Lin1, Hong Xie1, Meei-Li Huang1, Patrick C. Mathias1, Trevor Bedford1, Trevor Bedford2, Keith R. Jerome2, Keith R. Jerome1, Alexander L. Greninger1, Alexander L. Greninger2, Pavitra Roychoudhury2, Pavitra Roychoudhury1 •
University of Washington1, Fred Hutchinson Cancer Research Center2
12 Mar 2021-medRxiv
TL;DR: The first cases of the B.1.7 lineage of SARS-CoV-2 were detected in Washington State by using a combination of RT-PCR, RT-ddPCR and next-generation sequencing as discussed by the authors.
Abstract: Real-time epidemiological tracking of variants of interest can help limit the spread of more contagious forms of SARS-CoV-2, such as those containing the N501Y mutation. Typically, genetic sequencing is required to be able to track variants of interest in real-time. However, sequencing can take time and may not be accessible in all laboratories. Genotyping by RT-ddPCR offers an alternative to sequencing to rapidly detect variants of concern through discrimination of specific mutations such as N501Y that is associated with increased transmissibility. Here we describe the first cases of the B.1.1.7 lineage of SARS-CoV-2 detected in Washington State by using a combination of RT-PCR, RT-ddPCR, and next-generation sequencing. We screened 1,035 samples positive for SARS-CoV-2 by our CDC-based laboratory developed assay using ThermoFishers multiplex RT-PCR COVID-19 assay over four weeks from late December 2020 to early January 2021. S gene dropout candidates were subsequently assayed by RT-ddPCR to confirm four mutations within the S gene associated with the B.1.1.7 lineage: a deletion at amino acid (AA) 69-70 (ACATGT), deletion at AA 145, (TTA), N501Y mutation (TAT), and S982A mutation (GCA). All four targets were detected in two specimens, and follow-up sequencing revealed a total of 10 mutations in the S gene and phylogenetic clustering within the B.1.1.7 lineage. As variants of concern become increasingly prevalent, molecular diagnostic tools like RT-ddPCR can be utilized to quickly, accurately, and sensitively distinguish more contagious lineages of SARS-CoV-2.

14 citations

References
More filters
Journal Article•DOI•
The Sequence Alignment/Map format and SAMtools

[...]

Heng Li1, Bob Handsaker2, Alec Wysoker2, T. J. Fennell2, Jue Ruan3, Nils Homer2, Gabor T. Marth4, Gonçalo R. Abecasis2, Richard Durbin1 •
Wellcome Trust Sanger Institute1, University of California, Los Angeles2, Chinese Academy of Sciences3, Boston College4
01 Aug 2009-Bioinformatics
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Abstract: Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: [email protected]

45,957 citations

Journal Article•DOI•
Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

[...]

Chaolin Huang1, Yeming Wang2, Xingwang Li3, Lili Ren4, Jianping Zhao5, Yi Hu5, Li Zhang1, Guohui Fan2, Jiuyang Xu6, Xiaoying Gu2, Zhenshun Cheng7, Ting Yu1, Jia'an Xia1, Yuan Wei1, Wenjuan Wu1, Xuelei Xie1, Wen Yin5, Li Hui2, Min Liu2, Yan Xiao4, Hong Gao4, Li Guo4, Jungang Xie5, Guang-Fa Wang8, Rongmeng Jiang3, Zhancheng Gao8, Qi Jin4, Jianwei Wang4, Bin Cao2 •
Wuhan Jinyintan Hospital1, China-Japan Friendship Hospital2, Capital Medical University3, Peking Union Medical College4, Huazhong University of Science and Technology5, Tsinghua University6, Wuhan University7, Peking University8
24 Jan 2020-The Lancet
TL;DR: The epidemiological, clinical, laboratory, and radiological characteristics and treatment and clinical outcomes of patients with laboratory-confirmed 2019-nCoV infection in Wuhan, China, were reported.

36,578 citations

Journal Article•DOI•
A Novel Coronavirus from Patients with Pneumonia in China, 2019.

[...]

Na Zhu1, Dingyu Zhang, Wenling Wang1, Xingwang Li2, Bo Yang1, Jingdong Song1, Xiang Zhao1, Baoying Huang1, Weifeng Shi, Roujian Lu1, Peihua Niu1, Faxian Zhan1, Xuejun Ma1, Dayan Wang1, Wenbo Xu1, Wenbo Xu3, Guizhen Wu1, George F. Gao, Wenjie Tan1 •
Chinese Center for Disease Control and Prevention1, Capital Medical University2, Anhui University of Science and Technology3
24 Jan 2020-The New England Journal of Medicine
TL;DR: Human airway epithelial cells were used to isolate a novel coronavirus, named 2019-nCoV, which formed a clade within the subgenus sarbecovirus, Orthocoronavirinae subfamily, which is the seventh member of the family of coronaviruses that infect humans.
Abstract: In December 2019, a cluster of patients with pneumonia of unknown cause was linked to a seafood wholesale market in Wuhan, China. A previously unknown betacoronavirus was discovered through the use of unbiased sequencing in samples from patients with pneumonia. Human airway epithelial cells were used to isolate a novel coronavirus, named 2019-nCoV, which formed a clade within the subgenus sarbecovirus, Orthocoronavirinae subfamily. Different from both MERS-CoV and SARS-CoV, 2019-nCoV is the seventh member of the family of coronaviruses that infect humans. Enhanced surveillance and further investigation are ongoing. (Funded by the National Key Research and Development Program of China and the National Major Project for Control and Prevention of Infectious Disease in China.).

21,455 citations

Journal Article•DOI•
Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine.

[...]

Fernando P. Polack, Stephen J. Thomas1, Nicholas Kitchin2, Judith Absalon2, Alejandra Gurtman2, Stephen Lockhart2, John L. Perez2, Gonzalo Pérez Marc, Edson D. Moreira3, Cristiano Zerbini, Ruth Bailey2, Kena A. Swanson2, Satrajit Roychoudhury2, Kenneth Koury2, Ping Li2, Warren Kalina2, David A. Cooper2, Robert W. Frenck4, Laura L. Hammitt5, Özlem Türeci, Haylene Nell, Axel Schaefer, Serhat Ünal6, Dina B. Tresnan2, Susan Mather2, Philip R. Dormitzer2, Ugur Sahin, Kathrin U. Jansen2, William C. Gruber2 •
State University of New York Upstate Medical University1, Pfizer2, Oswaldo Cruz Foundation3, Cincinnati Children's Hospital Medical Center4, Johns Hopkins University5, Hacettepe University6
10 Dec 2020-The New England Journal of Medicine
TL;DR: A two-dose regimen of BNT162b2 conferred 95% protection against Covid-19 in persons 16 years of age or older and safety over a median of 2 months was similar to that of other viral vaccines.
Abstract: Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the resulting coronavirus disease 2019 (Covid-19) have afflicted tens of millions of people in a world...

10,274 citations

Journal Article•DOI•
A new coronavirus associated with human respiratory disease in China.

[...]

Fan Wu1, Su Zhao2, Bin Yu3, Yan-Mei Chen1, Wen Wang3, Zhi gang Song1, Yi Hu2, Zhao Wu Tao2, Jun Hua Tian3, Yuan Yuan Pei1, Ming Li Yuan2, Yu Ling Zhang1, Fa Hui Dai1, Yi Liu1, Qi Min Wang1, Jiao Jiao Zheng1, Lin Xu1, Edward C. Holmes4, Edward C. Holmes1, Yong-Zhen Zhang1, Yong-Zhen Zhang3 •
Fudan University1, Huazhong University of Science and Technology2, Centers for Disease Control and Prevention3, University of Sydney4
03 Feb 2020-Nature
TL;DR: Phylogenetic and metagenomic analyses of the complete viral genome of a new coronavirus from the family Coronaviridae reveal that the virus is closely related to a group of SARS-like coronaviruses found in bats in China.
Abstract: Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health1–3. Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing4 of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here ‘WH-Human 1’ coronavirus (and has also been referred to as ‘2019-nCoV’). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China5. This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans. Phylogenetic and metagenomic analyses of the complete viral genome of a new coronavirus from the family Coronaviridae reveal that the virus is closely related to a group of SARS-like coronaviruses found in bats in China.

9,231 citations

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Frequently Asked Questions (1)
Q1. What contributions have the authors mentioned in the paper "Sequence analysis of 20,453 sars-cov-2 genomes from the houston metropolitan area identifies the emergence and widespread distribution of multiple isolates of all major variants of concern" ?

Long et al. this paper presented the results of a study at the Center for Molecular and Translational Human Infectious Diseases Research ( CMTHIR ) at the University of Houston.