TY - JOUR
T1 - Influenza A Virus Defective Viral Genomes Are Inefficiently Packaged into Virions Relative to Wild-Type Genomic RNAs
AU - Alnaji, Fadi G.
AU - Reiser, William K.
AU - Rivera-Cardona, Joel
AU - te Velthuis, Aartjan J.W.
AU - Brooke, Christopher B.
N1 - Funding Information:
This study was generously funded by the Defense Advanced Research Projects Agency under contract DARPA-16-35-INTERCEPT-FP-018 and by National Institute of Allergy and Infectious Diseases grant 1R01AI139246. A.T.V. is supported by joint Wellcome Trust and Royal Society grant 206579/Z/17/Z.
Funding Information:
We are grateful to other members of the lab for helpful comments and critical readings of the manuscript, as well as to Tanja Laske from Max Planck Institute and Prerna Arora from Georg-August-University G?ttingen for helpful discussion. This study was generously funded by the Defense Advanced Research Projects Agency under contract DARPA-16-35-INTERCEPT-FP-018 and by National Institute of Allergy and Infectious Diseases grant 1R01AI139246. A.T.V. is supported by joint Wellcome Trust and Royal Society grant 206579/Z/17/Z.
Publisher Copyright:
Copyright © 2021 Alnaji et al.
PY - 2021/12/1
Y1 - 2021/12/1
N2 - Deletion-containing viral genomes (DelVGs) are commonly produced during influenza A virus infection and have been implicated in influencing clinical infection outcomes. Despite their ubiquity, the specific molecular mechanisms that govern DelVG formation and their packaging into defective interfering particles (DIPs) remain poorly understood. Here, we utilized next-generation sequencing to analyze DelVGs that form de novo early during infection, prior to packaging. Analysis of these early DelVGs revealed that deletion formation occurs in clearly defined hot spots and is significantly associated with both direct sequence repeats and enrichment of adenosine and uridine bases. By comparing intracellular DelVGs with those packaged into extracellular virions, we discovered that DelVGs face a significant bottleneck during genome packaging relative to wild-type genomic RNAs. Interestingly, packaged DelVGs exhibited signs of enrichment for larger DelVGs suggesting that size is an important determinant of packaging efficiency. Our data provide the first unbiased, high-resolution portrait of the diversity of DelVGs that are generated by the influenza A virus replication machinery and shed light on the mechanisms that underly DelVG formation and packaging.
AB - Deletion-containing viral genomes (DelVGs) are commonly produced during influenza A virus infection and have been implicated in influencing clinical infection outcomes. Despite their ubiquity, the specific molecular mechanisms that govern DelVG formation and their packaging into defective interfering particles (DIPs) remain poorly understood. Here, we utilized next-generation sequencing to analyze DelVGs that form de novo early during infection, prior to packaging. Analysis of these early DelVGs revealed that deletion formation occurs in clearly defined hot spots and is significantly associated with both direct sequence repeats and enrichment of adenosine and uridine bases. By comparing intracellular DelVGs with those packaged into extracellular virions, we discovered that DelVGs face a significant bottleneck during genome packaging relative to wild-type genomic RNAs. Interestingly, packaged DelVGs exhibited signs of enrichment for larger DelVGs suggesting that size is an important determinant of packaging efficiency. Our data provide the first unbiased, high-resolution portrait of the diversity of DelVGs that are generated by the influenza A virus replication machinery and shed light on the mechanisms that underly DelVG formation and packaging.
KW - Defective interfering particles
KW - Genome packaging
KW - Influenza
KW - Sequencing
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U2 - 10.1128/mBio.02959-21
DO - 10.1128/mBio.02959-21
M3 - Article
C2 - 34809454
AN - SCOPUS:85122074718
SN - 2161-2129
VL - 12
JO - mBio
JF - mBio
IS - 6
M1 - e02959-21
ER -