Investigating the Global Spread of SARS-CoV-2 Leveraging Next-Gen Sequencing and Principal Component Analysis

Christiane Scherer; James Grover; Darby Kammeraad; Gabe Rudy; Andreas Scherer

doi:doi:10.11648/j.ejcbs.20200604.11

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Investigating the Global Spread of SARS-CoV-2 Leveraging Next-Gen Sequencing and Principal Component Analysis

Christiane Scherer, James Grover, Darby Kammeraad, Gabe Rudy, Andreas Scherer

Published in European Journal of Clinical and Biomedical Sciences (Volume 6, Issue 4)

Received: 15 June 2020 Accepted: 3 July 2020 Published: 13 August 2020

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Abstract

As COVID-19 has spread from the first reported cases into a global pandemic, there has been a number of efforts to understand the mutations and clusters of genetic lineages of the SARS-CoV-2 virus. The high mutation rate and rapid spread makes this analysis capable of tracking chains of infections as well as putting individual sequences in context. Whole genomes of the SARS-CoV-2 virus are being collected and shared from across the globe. With the advent of affordable and prolific Next Generation Sequencing, this is the first pandemic in which the genomic evolution of the pathogen can be tracked in near real-time. So far, phylogenetic analysis methods have recently found a broader application in this regard. Here we demonstrate that Principal Component Analysis (PCA), used heavily in population genetics, corroborates the existing findings while providing unique new capabilities to understand our public repositories of complete virus sequences. This novel application of PCA is demonstrated on all publicly available SARS-CoV-2 samples from GenBank and other open-access databases until mid-April. We show that PCA is a useful and easy-to-use tool to analyze SARS-CoV-2 genomes in addition to phylogenetic analytics. It offers a previously untapped opportunity to analyze the dynamics of the current SARS-CoV-2 pandemic in a new way.

Published in	European Journal of Clinical and Biomedical Sciences (Volume 6, Issue 4)
DOI	10.11648/j.ejcbs.20200604.11
Page(s)	49-55
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2024. Published by Science Publishing Group

Keywords

SARS-CoV-2, COVID-19, Principal Component Analysis, Next-Generation Sequencing

References

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[5]	A. Scherer, "Leveraging Next-Generation Sequencing Technology in the Fight Against COVID-19," Clinical Lab Manager, vol. May 4, 2020.
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APA Style

Christiane Scherer, James Grover, Darby Kammeraad, Gabe Rudy, Andreas Scherer. (2020). Investigating the Global Spread of SARS-CoV-2 Leveraging Next-Gen Sequencing and Principal Component Analysis. European Journal of Clinical and Biomedical Sciences, 6(4), 49-55. https://doi.org/10.11648/j.ejcbs.20200604.11

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ACS Style

Christiane Scherer; James Grover; Darby Kammeraad; Gabe Rudy; Andreas Scherer. Investigating the Global Spread of SARS-CoV-2 Leveraging Next-Gen Sequencing and Principal Component Analysis. Eur. J. Clin. Biomed. Sci. 2020, 6(4), 49-55. doi: 10.11648/j.ejcbs.20200604.11

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AMA Style

Christiane Scherer, James Grover, Darby Kammeraad, Gabe Rudy, Andreas Scherer. Investigating the Global Spread of SARS-CoV-2 Leveraging Next-Gen Sequencing and Principal Component Analysis. Eur J Clin Biomed Sci. 2020;6(4):49-55. doi: 10.11648/j.ejcbs.20200604.11

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@article{10.11648/j.ejcbs.20200604.11,
  author = {Christiane Scherer and James Grover and Darby Kammeraad and Gabe Rudy and Andreas Scherer},
  title = {Investigating the Global Spread of SARS-CoV-2 Leveraging Next-Gen Sequencing and Principal Component Analysis},
  journal = {European Journal of Clinical and Biomedical Sciences},
  volume = {6},
  number = {4},
  pages = {49-55},
  doi = {10.11648/j.ejcbs.20200604.11},
  url = {https://doi.org/10.11648/j.ejcbs.20200604.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ejcbs.20200604.11},
  abstract = {As COVID-19 has spread from the first reported cases into a global pandemic, there has been a number of efforts to understand the mutations and clusters of genetic lineages of the SARS-CoV-2 virus. The high mutation rate and rapid spread makes this analysis capable of tracking chains of infections as well as putting individual sequences in context. Whole genomes of the SARS-CoV-2 virus are being collected and shared from across the globe. With the advent of affordable and prolific Next Generation Sequencing, this is the first pandemic in which the genomic evolution of the pathogen can be tracked in near real-time. So far, phylogenetic analysis methods have recently found a broader application in this regard. Here we demonstrate that Principal Component Analysis (PCA), used heavily in population genetics, corroborates the existing findings while providing unique new capabilities to understand our public repositories of complete virus sequences. This novel application of PCA is demonstrated on all publicly available SARS-CoV-2 samples from GenBank and other open-access databases until mid-April. We show that PCA is a useful and easy-to-use tool to analyze SARS-CoV-2 genomes in addition to phylogenetic analytics. It offers a previously untapped opportunity to analyze the dynamics of the current SARS-CoV-2 pandemic in a new way.},
 year = {2020}
}

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TY  - JOUR
T1  - Investigating the Global Spread of SARS-CoV-2 Leveraging Next-Gen Sequencing and Principal Component Analysis
AU  - Christiane Scherer
AU  - James Grover
AU  - Darby Kammeraad
AU  - Gabe Rudy
AU  - Andreas Scherer
Y1  - 2020/08/13
PY  - 2020
N1  - https://doi.org/10.11648/j.ejcbs.20200604.11
DO  - 10.11648/j.ejcbs.20200604.11
T2  - European Journal of Clinical and Biomedical Sciences
JF  - European Journal of Clinical and Biomedical Sciences
JO  - European Journal of Clinical and Biomedical Sciences
SP  - 49
EP  - 55
PB  - Science Publishing Group
SN  - 2575-5005
UR  - https://doi.org/10.11648/j.ejcbs.20200604.11
AB  - As COVID-19 has spread from the first reported cases into a global pandemic, there has been a number of efforts to understand the mutations and clusters of genetic lineages of the SARS-CoV-2 virus. The high mutation rate and rapid spread makes this analysis capable of tracking chains of infections as well as putting individual sequences in context. Whole genomes of the SARS-CoV-2 virus are being collected and shared from across the globe. With the advent of affordable and prolific Next Generation Sequencing, this is the first pandemic in which the genomic evolution of the pathogen can be tracked in near real-time. So far, phylogenetic analysis methods have recently found a broader application in this regard. Here we demonstrate that Principal Component Analysis (PCA), used heavily in population genetics, corroborates the existing findings while providing unique new capabilities to understand our public repositories of complete virus sequences. This novel application of PCA is demonstrated on all publicly available SARS-CoV-2 samples from GenBank and other open-access databases until mid-April. We show that PCA is a useful and easy-to-use tool to analyze SARS-CoV-2 genomes in addition to phylogenetic analytics. It offers a previously untapped opportunity to analyze the dynamics of the current SARS-CoV-2 pandemic in a new way.
VL  - 6
IS  - 4
ER  -

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Author Information

Christiane Scherer

Department of Microbiology and Hygiene, Institute of Laboratory Medicine, Evangelical Clinical Bethel, Bielefeld, Germany
James Grover

Golden Helix, Inc, Bozeman, Montana, United States
Darby Kammeraad

Golden Helix, Inc, Bozeman, Montana, United States
Gabe Rudy

Golden Helix, Inc, Bozeman, Montana, United States
Andreas Scherer

Golden Helix, Inc, Bozeman, Montana, United States

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Plain Text BibTeX RIS

APA Style

Christiane Scherer, James Grover, Darby Kammeraad, Gabe Rudy, Andreas Scherer. (2020). Investigating the Global Spread of SARS-CoV-2 Leveraging Next-Gen Sequencing and Principal Component Analysis. European Journal of Clinical and Biomedical Sciences, 6(4), 49-55. https://doi.org/10.11648/j.ejcbs.20200604.11

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ACS Style

Christiane Scherer; James Grover; Darby Kammeraad; Gabe Rudy; Andreas Scherer. Investigating the Global Spread of SARS-CoV-2 Leveraging Next-Gen Sequencing and Principal Component Analysis. Eur. J. Clin. Biomed. Sci. 2020, 6(4), 49-55. doi: 10.11648/j.ejcbs.20200604.11

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AMA Style

Christiane Scherer, James Grover, Darby Kammeraad, Gabe Rudy, Andreas Scherer. Investigating the Global Spread of SARS-CoV-2 Leveraging Next-Gen Sequencing and Principal Component Analysis. Eur J Clin Biomed Sci. 2020;6(4):49-55. doi: 10.11648/j.ejcbs.20200604.11

Copy | Download

@article{10.11648/j.ejcbs.20200604.11,
  author = {Christiane Scherer and James Grover and Darby Kammeraad and Gabe Rudy and Andreas Scherer},
  title = {Investigating the Global Spread of SARS-CoV-2 Leveraging Next-Gen Sequencing and Principal Component Analysis},
  journal = {European Journal of Clinical and Biomedical Sciences},
  volume = {6},
  number = {4},
  pages = {49-55},
  doi = {10.11648/j.ejcbs.20200604.11},
  url = {https://doi.org/10.11648/j.ejcbs.20200604.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ejcbs.20200604.11},
  abstract = {As COVID-19 has spread from the first reported cases into a global pandemic, there has been a number of efforts to understand the mutations and clusters of genetic lineages of the SARS-CoV-2 virus. The high mutation rate and rapid spread makes this analysis capable of tracking chains of infections as well as putting individual sequences in context. Whole genomes of the SARS-CoV-2 virus are being collected and shared from across the globe. With the advent of affordable and prolific Next Generation Sequencing, this is the first pandemic in which the genomic evolution of the pathogen can be tracked in near real-time. So far, phylogenetic analysis methods have recently found a broader application in this regard. Here we demonstrate that Principal Component Analysis (PCA), used heavily in population genetics, corroborates the existing findings while providing unique new capabilities to understand our public repositories of complete virus sequences. This novel application of PCA is demonstrated on all publicly available SARS-CoV-2 samples from GenBank and other open-access databases until mid-April. We show that PCA is a useful and easy-to-use tool to analyze SARS-CoV-2 genomes in addition to phylogenetic analytics. It offers a previously untapped opportunity to analyze the dynamics of the current SARS-CoV-2 pandemic in a new way.},
 year = {2020}
}

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TY  - JOUR
T1  - Investigating the Global Spread of SARS-CoV-2 Leveraging Next-Gen Sequencing and Principal Component Analysis
AU  - Christiane Scherer
AU  - James Grover
AU  - Darby Kammeraad
AU  - Gabe Rudy
AU  - Andreas Scherer
Y1  - 2020/08/13
PY  - 2020
N1  - https://doi.org/10.11648/j.ejcbs.20200604.11
DO  - 10.11648/j.ejcbs.20200604.11
T2  - European Journal of Clinical and Biomedical Sciences
JF  - European Journal of Clinical and Biomedical Sciences
JO  - European Journal of Clinical and Biomedical Sciences
SP  - 49
EP  - 55
PB  - Science Publishing Group
SN  - 2575-5005
UR  - https://doi.org/10.11648/j.ejcbs.20200604.11
AB  - As COVID-19 has spread from the first reported cases into a global pandemic, there has been a number of efforts to understand the mutations and clusters of genetic lineages of the SARS-CoV-2 virus. The high mutation rate and rapid spread makes this analysis capable of tracking chains of infections as well as putting individual sequences in context. Whole genomes of the SARS-CoV-2 virus are being collected and shared from across the globe. With the advent of affordable and prolific Next Generation Sequencing, this is the first pandemic in which the genomic evolution of the pathogen can be tracked in near real-time. So far, phylogenetic analysis methods have recently found a broader application in this regard. Here we demonstrate that Principal Component Analysis (PCA), used heavily in population genetics, corroborates the existing findings while providing unique new capabilities to understand our public repositories of complete virus sequences. This novel application of PCA is demonstrated on all publicly available SARS-CoV-2 samples from GenBank and other open-access databases until mid-April. We show that PCA is a useful and easy-to-use tool to analyze SARS-CoV-2 genomes in addition to phylogenetic analytics. It offers a previously untapped opportunity to analyze the dynamics of the current SARS-CoV-2 pandemic in a new way.
VL  - 6
IS  - 4
ER  -

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