TY - JOUR

T1 - Deep sequencing analysis of defective genomes of parainfluenza virus 5 and their role in interferon induction

AU - Killip, M. J.

AU - Young, D. F.

AU - Gatherer, Derek

AU - Ross, C. S.

AU - Short, J. A. L.

AU - Davison, A. J.

AU - Goodbourn, S.

AU - Randall, R. E.

PY - 2013/5

Y1 - 2013/5

N2 - Preparations of parainfluenza virus 5 (PIV5) that are potent activators of the interferon (IFN) induction cascade were generated by high-multiplicity passage in order to accumulate defective interfering virus genomes (DIs). Nucleocapsid RNA from these virus preparations was extracted and subjected to deep sequencing. Sequencing data were analyzed using methods designed to detect internal deletion and “copyback” DIs in order to identify and characterize the different DIs present and to approximately quantify the ratio of defective to nondefective genomes. Trailer copybacks dominated the DI populations in IFN-inducing preparations of both the PIV5 wild type (wt) and PIV5-VΔC (a recombinant virus that does not encode a functional V protein). Although the PIV5 V protein is an efficient inhibitor of the IFN induction cascade, we show that nondefective PIV5 wt is unable to prevent activation of the IFN response by coinfecting copyback DIs due to the interfering effects of copyback DIs on nondefective virus protein expression. As a result, copyback DIs are able to very rapidly activate the IFN induction cascade prior to the expression of detectable levels of V protein by coinfecting nondefective virus.

AB - Preparations of parainfluenza virus 5 (PIV5) that are potent activators of the interferon (IFN) induction cascade were generated by high-multiplicity passage in order to accumulate defective interfering virus genomes (DIs). Nucleocapsid RNA from these virus preparations was extracted and subjected to deep sequencing. Sequencing data were analyzed using methods designed to detect internal deletion and “copyback” DIs in order to identify and characterize the different DIs present and to approximately quantify the ratio of defective to nondefective genomes. Trailer copybacks dominated the DI populations in IFN-inducing preparations of both the PIV5 wild type (wt) and PIV5-VΔC (a recombinant virus that does not encode a functional V protein). Although the PIV5 V protein is an efficient inhibitor of the IFN induction cascade, we show that nondefective PIV5 wt is unable to prevent activation of the IFN response by coinfecting copyback DIs due to the interfering effects of copyback DIs on nondefective virus protein expression. As a result, copyback DIs are able to very rapidly activate the IFN induction cascade prior to the expression of detectable levels of V protein by coinfecting nondefective virus.

KW - Animals

KW - Cell Line

KW - Defective Viruses

KW - Genome, Viral

KW - High-Throughput Nucleotide Sequencing

KW - Humans

KW - Interferons

KW - Rubulavirus

KW - Rubulavirus Infections

KW - Viral Proteins

UR - http://www.scopus.com/inward/record.url?scp=84876318226&partnerID=8YFLogxK

U2 - 10.1128/JVI.03383-12

DO - 10.1128/JVI.03383-12

M3 - Journal article

C2 - 23449801

AN - SCOPUS:84876318226

VL - 87

SP - 4798

EP - 4807

JO - Journal of Virology

JF - Journal of Virology

SN - 0022-538X

IS - 9

ER -