Simultaneous Viral Whole-Genome Sequencing and Differential Expression Profiling in Respiratory Syncytial Virus Infection of Infants

Gu-Lung Lin; Tanya Golubchik; Simon Drysdale; Daniel O'Connor; Kimberley Jefferies; Anthony Brown; Mariateresa de Cesare; David Bonsall; M Azim Ansari; Jeroen Aerssens; Louis Bont; Peter Openshaw; Federico Martinón-Torres; Rory Bowden; Andrew J Pollard; RESCEU Investigators; Thea Kølsen Fischer

doi:10.1093/infdis/jiaa448

Simultaneous Viral Whole-Genome Sequencing and Differential Expression Profiling in Respiratory Syncytial Virus Infection of Infants

Gu-Lung Lin, Tanya Golubchik, Simon Drysdale, Daniel O'Connor, Kimberley Jefferies, Anthony Brown, Mariateresa de Cesare, David Bonsall, M Azim Ansari, Jeroen Aerssens, Louis Bont, Peter Openshaw, Federico Martinón-Torres, Rory Bowden, Andrew J Pollard, RESCEU Investigators , Thea Kølsen Fischer (Member of author group)

11 Citations (Scopus)

Abstract

Targeted metagenomics using strand-specific libraries with target enrichment is a sensitive, generalized approach to pathogen sequencing and transcriptome profiling. Using this method, we recovered 13 (76%) complete human respiratory syncytial virus (RSV) genomes from 17 clinical respiratory samples, reconstructed the phylogeny of the infecting viruses, and detected differential gene expression between 2 RSV subgroups, specifically, a lower expression of the P gene and a higher expression of the M2 gene in RSV-A than in RSV-B. This methodology can help to relate viral genetics to clinical phenotype and facilitate ongoing population-level RSV surveillance and vaccine development. Clinical Trials Registration. NCT03627572 and NCT03756766.

Original language	English
Journal	The Journal of infectious diseases
Volume	222
Issue number	Supplement_7
Pages (from-to)	S666-S671
ISSN	0022-1899
DOIs	https://doi.org/10.1093/infdis/jiaa448
Publication status	Published - 7 Oct 2020
Externally published	Yes

Keywords

differential gene expression
respiratory syncytial virus
RNA sequencing
transcriptome profiling
whole-genome sequencing

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10.1093/infdis/jiaa448

Cite this

Lin, G.-L., Golubchik, T., Drysdale, S., O'Connor, D., Jefferies, K., Brown, A., de Cesare, M., Bonsall, D., Ansari, M. A., Aerssens, J., Bont, L., Openshaw, P., Martinón-Torres, F., Bowden, R., Pollard, A. J., RESCEU Investigators , & Fischer, T. K. (2020). Simultaneous Viral Whole-Genome Sequencing and Differential Expression Profiling in Respiratory Syncytial Virus Infection of Infants. The Journal of infectious diseases, 222(Supplement_7), S666-S671. https://doi.org/10.1093/infdis/jiaa448

Simultaneous Viral Whole-Genome Sequencing and Differential Expression Profiling in Respiratory Syncytial Virus Infection of Infants. / Lin, Gu-Lung; Golubchik, Tanya; Drysdale, Simon et al.
In: The Journal of infectious diseases, Vol. 222, No. Supplement_7, 07.10.2020, p. S666-S671.

Research output: Contribution to journal › Journal article › Research › peer-review

Lin, G-L, Golubchik, T, Drysdale, S, O'Connor, D, Jefferies, K, Brown, A, de Cesare, M, Bonsall, D, Ansari, MA, Aerssens, J, Bont, L, Openshaw, P, Martinón-Torres, F, Bowden, R, Pollard, AJ, RESCEU Investigators & Fischer, TK 2020, 'Simultaneous Viral Whole-Genome Sequencing and Differential Expression Profiling in Respiratory Syncytial Virus Infection of Infants', The Journal of infectious diseases, vol. 222, no. Supplement_7, pp. S666-S671. https://doi.org/10.1093/infdis/jiaa448

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abstract = "Targeted metagenomics using strand-specific libraries with target enrichment is a sensitive, generalized approach to pathogen sequencing and transcriptome profiling. Using this method, we recovered 13 (76\%) complete human respiratory syncytial virus (RSV) genomes from 17 clinical respiratory samples, reconstructed the phylogeny of the infecting viruses, and detected differential gene expression between 2 RSV subgroups, specifically, a lower expression of the P gene and a higher expression of the M2 gene in RSV-A than in RSV-B. This methodology can help to relate viral genetics to clinical phenotype and facilitate ongoing population-level RSV surveillance and vaccine development. Clinical Trials Registration. NCT03627572 and NCT03756766.",

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AU - O'Connor, Daniel

AU - Jefferies, Kimberley

AU - Brown, Anthony

AU - de Cesare, Mariateresa

AU - Bonsall, David

AU - Ansari, M Azim

AU - Aerssens, Jeroen

AU - Bont, Louis

AU - Openshaw, Peter

AU - Martinón-Torres, Federico

AU - Bowden, Rory

AU - Pollard, Andrew J

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AB - Targeted metagenomics using strand-specific libraries with target enrichment is a sensitive, generalized approach to pathogen sequencing and transcriptome profiling. Using this method, we recovered 13 (76%) complete human respiratory syncytial virus (RSV) genomes from 17 clinical respiratory samples, reconstructed the phylogeny of the infecting viruses, and detected differential gene expression between 2 RSV subgroups, specifically, a lower expression of the P gene and a higher expression of the M2 gene in RSV-A than in RSV-B. This methodology can help to relate viral genetics to clinical phenotype and facilitate ongoing population-level RSV surveillance and vaccine development. Clinical Trials Registration. NCT03627572 and NCT03756766.

KW - differential gene expression

KW - respiratory syncytial virus

KW - RNA sequencing

KW - transcriptome profiling

KW - whole-genome sequencing

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Simultaneous Viral Whole-Genome Sequencing and Differential Expression Profiling in Respiratory Syncytial Virus Infection of Infants

Abstract

Keywords

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