Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs

Bo Lu; Yi Yan; Liting Dong; Lingling Han; Yawei Liu; Junping Yu; Jianjun Chen; Danyang Yi; Meiling Zhang; Xin Deng; Chao Wang; Runkun Wang; Depeng Wang; Hongping Wei; Di Liu; Chengqi Yi

doi:10.1038/s41421-021-00248-3

Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs

Bo Lu, Yi Yan, Liting Dong, Lingling Han, Yawei Liu, Junping Yu, Jianjun Chen, Danyang Yi, Meiling Zhang, Xin Deng, Chao Wang, Runkun Wang, Depeng Wang^*, Hongping Wei^*, Di Liu^*, Chengqi Yi^*

^*Corresponding author for this work

Department of Biomedical Sciences

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

15 Citations (Scopus)

41 Downloads (CityUHK Scholars)

Abstract

The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, poses a severe threat to humanity. Rapid and comprehensive analysis of both pathogen and host sequencing data is critical to track infection and inform therapies. In this study, we performed unbiased metatranscriptomic analysis of clinical samples from COVID-19 patients using a recently developed RNA-seq library construction method (TRACE-seq), which utilizes tagmentation activity of Tn5 on RNA/DNA hybrids. This approach avoids the laborious and time-consuming steps in traditional RNA-seq procedure, and hence is fast, sensitive, and convenient. We demonstrated that TRACE-seq allowed integrated characterization of full genome information of SARS-CoV-2, putative pathogens causing coinfection, antibiotic resistance, and host response from single throat swabs. We believe that the integrated information will deepen our understanding of pathogenesis and improve diagnostic accuracy for infectious diseases.

Original language	English
Article number	19
Journal	Cell Discovery
Volume	7
Online published	30 Mar 2021
DOIs	https://doi.org/10.1038/s41421-021-00248-3
Publication status	Published - 2021

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This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format.

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title = "Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs",

abstract = "The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, poses a severe threat to humanity. Rapid and comprehensive analysis of both pathogen and host sequencing data is critical to track infection and inform therapies. In this study, we performed unbiased metatranscriptomic analysis of clinical samples from COVID-19 patients using a recently developed RNA-seq library construction method (TRACE-seq), which utilizes tagmentation activity of Tn5 on RNA/DNA hybrids. This approach avoids the laborious and time-consuming steps in traditional RNA-seq procedure, and hence is fast, sensitive, and convenient. We demonstrated that TRACE-seq allowed integrated characterization of full genome information of SARS-CoV-2, putative pathogens causing coinfection, antibiotic resistance, and host response from single throat swabs. We believe that the integrated information will deepen our understanding of pathogenesis and improve diagnostic accuracy for infectious diseases.",

author = "Bo Lu and Yi Yan and Liting Dong and Lingling Han and Yawei Liu and Junping Yu and Jianjun Chen and Danyang Yi and Meiling Zhang and Xin Deng and Chao Wang and Runkun Wang and Depeng Wang and Hongping Wei and Di Liu and Chengqi Yi",

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doi = "10.1038/s41421-021-00248-3",

language = "English",

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TY - JOUR

T1 - Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs

AU - Lu, Bo

AU - Yan, Yi

AU - Dong, Liting

AU - Han, Lingling

AU - Liu, Yawei

AU - Yu, Junping

AU - Chen, Jianjun

AU - Yi, Danyang

AU - Zhang, Meiling

AU - Deng, Xin

AU - Wang, Chao

AU - Wang, Runkun

AU - Wang, Depeng

AU - Wei, Hongping

AU - Liu, Di

AU - Yi, Chengqi

PY - 2021

Y1 - 2021

N2 - The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, poses a severe threat to humanity. Rapid and comprehensive analysis of both pathogen and host sequencing data is critical to track infection and inform therapies. In this study, we performed unbiased metatranscriptomic analysis of clinical samples from COVID-19 patients using a recently developed RNA-seq library construction method (TRACE-seq), which utilizes tagmentation activity of Tn5 on RNA/DNA hybrids. This approach avoids the laborious and time-consuming steps in traditional RNA-seq procedure, and hence is fast, sensitive, and convenient. We demonstrated that TRACE-seq allowed integrated characterization of full genome information of SARS-CoV-2, putative pathogens causing coinfection, antibiotic resistance, and host response from single throat swabs. We believe that the integrated information will deepen our understanding of pathogenesis and improve diagnostic accuracy for infectious diseases.

AB - The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, poses a severe threat to humanity. Rapid and comprehensive analysis of both pathogen and host sequencing data is critical to track infection and inform therapies. In this study, we performed unbiased metatranscriptomic analysis of clinical samples from COVID-19 patients using a recently developed RNA-seq library construction method (TRACE-seq), which utilizes tagmentation activity of Tn5 on RNA/DNA hybrids. This approach avoids the laborious and time-consuming steps in traditional RNA-seq procedure, and hence is fast, sensitive, and convenient. We demonstrated that TRACE-seq allowed integrated characterization of full genome information of SARS-CoV-2, putative pathogens causing coinfection, antibiotic resistance, and host response from single throat swabs. We believe that the integrated information will deepen our understanding of pathogenesis and improve diagnostic accuracy for infectious diseases.

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U2 - 10.1038/s41421-021-00248-3

DO - 10.1038/s41421-021-00248-3

M3 - RGC 21 - Publication in refereed journal

C2 - 33785729

SN - 2056-5968

VL - 7

JO - Cell Discovery

JF - Cell Discovery

M1 - 19

ER -

Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs

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