A rapid and label-free platform for virus capture and identification from clinical samples

Yin Ting Yeh, Kristen Gulino, Yu He Zhang, Aswathy Sabestien, Tsui Wen Chou, Bin Zhou, Zhong Lin, Istvan Albert, Huaguang Lu, Venkataraman Swaminathan, Elodie Ghedin, Mauricio Terrones

Research output: Contribution to journalArticle

Abstract

Emerging and reemerging viruses are responsible for a number of recent epidemic outbreaks. A crucial step in predicting and controlling outbreaks is the timely and accurate characterization of emerging virus strains. We present a portable microfluidic platform containing carbon nanotube arrays with differential filtration porosity for the rapid enrichment and optical identification of viruses. Different emerging strains (or unknown viruses) can be enriched and identified in real time through a multivirus capture component in conjunction with surface-enhanced Raman spectroscopy. More importantly, after viral capture and detection on a chip, viruses remain viable and get purified in a microdevice that permits subsequent in-depth characterizations by various conventional methods. We validated this platform using different subtypes of avian influenza A viruses and human samples with respiratory infections. This technology successfully enriched rhinovirus, influenza virus, and parainfluenza viruses, and maintained the stoichiometric viral proportions when the samples contained more than one type of virus, thus emulating coinfection. Viral capture and detection took only a few minutes with a 70-fold enrichment enhancement; detection could be achieved with as little as 102 EID50/mL (50% egg infective dose per microliter), with a virus specificity of 90%. After enrichment using the device, we demonstrated by sequencing that the abundance of viral-specific reads significantly increased from 4.1 to 31.8% for parainfluenza and from 0.08 to 0.44% for influenza virus. This enrichment method coupled to Raman virus identification constitutes an innovative system that could be used to quickly track and monitor viral outbreaks in real time.

Original languageEnglish (US)
Pages (from-to)895-901
Number of pages7
JournalProceedings of the National Academy of Sciences of the United States of America
Volume117
Issue number2
DOIs
StatePublished - Jan 14 2020

Fingerprint

Viruses
Disease Outbreaks
Paramyxoviridae Infections
Orthomyxoviridae
Rhinovirus
Carbon Nanotubes
Influenza in Birds
Microfluidics
Raman Spectrum Analysis
Porosity
Influenza A virus
Coinfection
Respiratory Tract Infections
Ovum
Technology
Equipment and Supplies

All Science Journal Classification (ASJC) codes

  • General

Cite this

Yeh, Yin Ting ; Gulino, Kristen ; Zhang, Yu He ; Sabestien, Aswathy ; Chou, Tsui Wen ; Zhou, Bin ; Lin, Zhong ; Albert, Istvan ; Lu, Huaguang ; Swaminathan, Venkataraman ; Ghedin, Elodie ; Terrones, Mauricio. / A rapid and label-free platform for virus capture and identification from clinical samples. In: Proceedings of the National Academy of Sciences of the United States of America. 2020 ; Vol. 117, No. 2. pp. 895-901.
@article{da31796741e74aee9861e97db43ad9c1,
title = "A rapid and label-free platform for virus capture and identification from clinical samples",
abstract = "Emerging and reemerging viruses are responsible for a number of recent epidemic outbreaks. A crucial step in predicting and controlling outbreaks is the timely and accurate characterization of emerging virus strains. We present a portable microfluidic platform containing carbon nanotube arrays with differential filtration porosity for the rapid enrichment and optical identification of viruses. Different emerging strains (or unknown viruses) can be enriched and identified in real time through a multivirus capture component in conjunction with surface-enhanced Raman spectroscopy. More importantly, after viral capture and detection on a chip, viruses remain viable and get purified in a microdevice that permits subsequent in-depth characterizations by various conventional methods. We validated this platform using different subtypes of avian influenza A viruses and human samples with respiratory infections. This technology successfully enriched rhinovirus, influenza virus, and parainfluenza viruses, and maintained the stoichiometric viral proportions when the samples contained more than one type of virus, thus emulating coinfection. Viral capture and detection took only a few minutes with a 70-fold enrichment enhancement; detection could be achieved with as little as 102 EID50/mL (50{\%} egg infective dose per microliter), with a virus specificity of 90{\%}. After enrichment using the device, we demonstrated by sequencing that the abundance of viral-specific reads significantly increased from 4.1 to 31.8{\%} for parainfluenza and from 0.08 to 0.44{\%} for influenza virus. This enrichment method coupled to Raman virus identification constitutes an innovative system that could be used to quickly track and monitor viral outbreaks in real time.",
author = "Yeh, {Yin Ting} and Kristen Gulino and Zhang, {Yu He} and Aswathy Sabestien and Chou, {Tsui Wen} and Bin Zhou and Zhong Lin and Istvan Albert and Huaguang Lu and Venkataraman Swaminathan and Elodie Ghedin and Mauricio Terrones",
year = "2020",
month = "1",
day = "14",
doi = "10.1073/pnas.1910113117",
language = "English (US)",
volume = "117",
pages = "895--901",
journal = "Proceedings of the National Academy of Sciences of the United States of America",
issn = "0027-8424",
number = "2",

}

A rapid and label-free platform for virus capture and identification from clinical samples. / Yeh, Yin Ting; Gulino, Kristen; Zhang, Yu He; Sabestien, Aswathy; Chou, Tsui Wen; Zhou, Bin; Lin, Zhong; Albert, Istvan; Lu, Huaguang; Swaminathan, Venkataraman; Ghedin, Elodie; Terrones, Mauricio.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 117, No. 2, 14.01.2020, p. 895-901.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A rapid and label-free platform for virus capture and identification from clinical samples

AU - Yeh, Yin Ting

AU - Gulino, Kristen

AU - Zhang, Yu He

AU - Sabestien, Aswathy

AU - Chou, Tsui Wen

AU - Zhou, Bin

AU - Lin, Zhong

AU - Albert, Istvan

AU - Lu, Huaguang

AU - Swaminathan, Venkataraman

AU - Ghedin, Elodie

AU - Terrones, Mauricio

PY - 2020/1/14

Y1 - 2020/1/14

N2 - Emerging and reemerging viruses are responsible for a number of recent epidemic outbreaks. A crucial step in predicting and controlling outbreaks is the timely and accurate characterization of emerging virus strains. We present a portable microfluidic platform containing carbon nanotube arrays with differential filtration porosity for the rapid enrichment and optical identification of viruses. Different emerging strains (or unknown viruses) can be enriched and identified in real time through a multivirus capture component in conjunction with surface-enhanced Raman spectroscopy. More importantly, after viral capture and detection on a chip, viruses remain viable and get purified in a microdevice that permits subsequent in-depth characterizations by various conventional methods. We validated this platform using different subtypes of avian influenza A viruses and human samples with respiratory infections. This technology successfully enriched rhinovirus, influenza virus, and parainfluenza viruses, and maintained the stoichiometric viral proportions when the samples contained more than one type of virus, thus emulating coinfection. Viral capture and detection took only a few minutes with a 70-fold enrichment enhancement; detection could be achieved with as little as 102 EID50/mL (50% egg infective dose per microliter), with a virus specificity of 90%. After enrichment using the device, we demonstrated by sequencing that the abundance of viral-specific reads significantly increased from 4.1 to 31.8% for parainfluenza and from 0.08 to 0.44% for influenza virus. This enrichment method coupled to Raman virus identification constitutes an innovative system that could be used to quickly track and monitor viral outbreaks in real time.

AB - Emerging and reemerging viruses are responsible for a number of recent epidemic outbreaks. A crucial step in predicting and controlling outbreaks is the timely and accurate characterization of emerging virus strains. We present a portable microfluidic platform containing carbon nanotube arrays with differential filtration porosity for the rapid enrichment and optical identification of viruses. Different emerging strains (or unknown viruses) can be enriched and identified in real time through a multivirus capture component in conjunction with surface-enhanced Raman spectroscopy. More importantly, after viral capture and detection on a chip, viruses remain viable and get purified in a microdevice that permits subsequent in-depth characterizations by various conventional methods. We validated this platform using different subtypes of avian influenza A viruses and human samples with respiratory infections. This technology successfully enriched rhinovirus, influenza virus, and parainfluenza viruses, and maintained the stoichiometric viral proportions when the samples contained more than one type of virus, thus emulating coinfection. Viral capture and detection took only a few minutes with a 70-fold enrichment enhancement; detection could be achieved with as little as 102 EID50/mL (50% egg infective dose per microliter), with a virus specificity of 90%. After enrichment using the device, we demonstrated by sequencing that the abundance of viral-specific reads significantly increased from 4.1 to 31.8% for parainfluenza and from 0.08 to 0.44% for influenza virus. This enrichment method coupled to Raman virus identification constitutes an innovative system that could be used to quickly track and monitor viral outbreaks in real time.

UR - http://www.scopus.com/inward/record.url?scp=85077937753&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85077937753&partnerID=8YFLogxK

U2 - 10.1073/pnas.1910113117

DO - 10.1073/pnas.1910113117

M3 - Article

C2 - 31882450

AN - SCOPUS:85077937753

VL - 117

SP - 895

EP - 901

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

SN - 0027-8424

IS - 2

ER -