An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes

ABSTRACT In numerous instances, tracking the biological significance of a nucleic acid sequence can be augmented through the identification of environmental niches in which the sequence of interest is present. Many metagenomic data sets are now available, with deep sequencing of samples from diverse...

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Autores principales:	Lamia Wahba, Nimit Jain, Andrew Z. Fire, Massa J. Shoura, Karen L. Artiles, Matthew J. McCoy, Dae-Eun Jeong
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	COVID SARS-nCoV-2 bioinformatics coronavirus metagenomics pangolin Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/7aff9710eb5d49ed861a7683854d9791
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spelling	oai:doaj.org-article:7aff9710eb5d49ed861a7683854d97912021-11-15T15:30:16ZAn Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes10.1128/mSphere.00160-202379-5042https://doaj.org/article/7aff9710eb5d49ed861a7683854d97912020-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00160-20https://doaj.org/toc/2379-5042ABSTRACT In numerous instances, tracking the biological significance of a nucleic acid sequence can be augmented through the identification of environmental niches in which the sequence of interest is present. Many metagenomic data sets are now available, with deep sequencing of samples from diverse biological niches. While any individual metagenomic data set can be readily queried using web-based tools, meta-searches through all such data sets are less accessible. In this brief communication, we demonstrate such a meta-metagenomic approach, examining close matches to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in all high-throughput sequencing data sets in the NCBI Sequence Read Archive accessible with the “virome” keyword. In addition to the homology to bat coronaviruses observed in descriptions of the SARS-CoV-2 sequence (F. Wu, S. Zhao, B. Yu, Y. M. Chen, et al., Nature 579:265–269, 2020, https://doi.org/10.1038/s41586-020-2008-3; P. Zhou, X. L. Yang, X. G. Wang, B. Hu, et al., Nature 579:270–273, 2020, https://doi.org/10.1038/s41586-020-2012-7), we note a strong homology to numerous sequence reads in metavirome data sets generated from the lungs of deceased pangolins reported by Liu et al. (P. Liu, W. Chen, and J. P. Chen, Viruses 11:979, 2019, https://doi.org/10.3390/v11110979). While analysis of these reads indicates the presence of a similar viral sequence in pangolin lung, the similarity is not sufficient to either confirm or rule out a role for pangolins as an intermediate host in the recent emergence of SARS-CoV-2. In addition to the implications for SARS-CoV-2 emergence, this study illustrates the utility and limitations of meta-metagenomic search tools in effective and rapid characterization of potentially significant nucleic acid sequences. IMPORTANCE Meta-metagenomic searches allow for high-speed, low-cost identification of potentially significant biological niches for sequences of interest.Lamia WahbaNimit JainAndrew Z. FireMassa J. ShouraKaren L. ArtilesMatthew J. McCoyDae-Eun JeongAmerican Society for MicrobiologyarticleCOVIDSARS-nCoV-2bioinformaticscoronavirusmetagenomicspangolinMicrobiologyQR1-502ENmSphere, Vol 5, Iss 3 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	COVID SARS-nCoV-2 bioinformatics coronavirus metagenomics pangolin Microbiology QR1-502
spellingShingle	COVID SARS-nCoV-2 bioinformatics coronavirus metagenomics pangolin Microbiology QR1-502 Lamia Wahba Nimit Jain Andrew Z. Fire Massa J. Shoura Karen L. Artiles Matthew J. McCoy Dae-Eun Jeong An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes
description	ABSTRACT In numerous instances, tracking the biological significance of a nucleic acid sequence can be augmented through the identification of environmental niches in which the sequence of interest is present. Many metagenomic data sets are now available, with deep sequencing of samples from diverse biological niches. While any individual metagenomic data set can be readily queried using web-based tools, meta-searches through all such data sets are less accessible. In this brief communication, we demonstrate such a meta-metagenomic approach, examining close matches to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in all high-throughput sequencing data sets in the NCBI Sequence Read Archive accessible with the “virome” keyword. In addition to the homology to bat coronaviruses observed in descriptions of the SARS-CoV-2 sequence (F. Wu, S. Zhao, B. Yu, Y. M. Chen, et al., Nature 579:265–269, 2020, https://doi.org/10.1038/s41586-020-2008-3; P. Zhou, X. L. Yang, X. G. Wang, B. Hu, et al., Nature 579:270–273, 2020, https://doi.org/10.1038/s41586-020-2012-7), we note a strong homology to numerous sequence reads in metavirome data sets generated from the lungs of deceased pangolins reported by Liu et al. (P. Liu, W. Chen, and J. P. Chen, Viruses 11:979, 2019, https://doi.org/10.3390/v11110979). While analysis of these reads indicates the presence of a similar viral sequence in pangolin lung, the similarity is not sufficient to either confirm or rule out a role for pangolins as an intermediate host in the recent emergence of SARS-CoV-2. In addition to the implications for SARS-CoV-2 emergence, this study illustrates the utility and limitations of meta-metagenomic search tools in effective and rapid characterization of potentially significant nucleic acid sequences. IMPORTANCE Meta-metagenomic searches allow for high-speed, low-cost identification of potentially significant biological niches for sequences of interest.
format	article
author	Lamia Wahba Nimit Jain Andrew Z. Fire Massa J. Shoura Karen L. Artiles Matthew J. McCoy Dae-Eun Jeong
author_facet	Lamia Wahba Nimit Jain Andrew Z. Fire Massa J. Shoura Karen L. Artiles Matthew J. McCoy Dae-Eun Jeong
author_sort	Lamia Wahba
title	An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes
title_short	An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes
title_full	An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes
title_fullStr	An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes
title_full_unstemmed	An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes
title_sort	extensive meta-metagenomic search identifies sars-cov-2-homologous sequences in pangolin lung viromes
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/7aff9710eb5d49ed861a7683854d9791
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An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes

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