Evidence map›Paper›PMID 42303613›Full record

ArticleNature communications2026

Longitudinal analysis of influenza A virus deletion-containing viral genomes reveals key determinants of co-evolutionary dynamics and interference.

Fadi G Alnaji, Mireille Farjo, Shu Ling Goh, Daryl Zheng Hao Aw, Paolo Alberto Lorenzini, Tongyu Liu, Rebekah Lin-Zhen Chan, Cornelius Lee, Marco Vignuzzi, Christopher B Brooke

Abstract read
In one paragraph

Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Fadi G AlnajiAgency for Science Technology and Research (A*STAR), Infectious Disease Labs, Singapore, Singapore.ORCID http://orcid.org/0000-0002-2893-9832
Mireille FarjoDepartment of Microbiology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
Shu Ling GohAgency for Science Technology and Research (A*STAR), Infectious Disease Labs, Singapore, Singapore.ORCID http://orcid.org/0000-0001-8575-6103
Daryl Zheng Hao AwAgency for Science Technology and Research (A*STAR), Infectious Disease Labs, Singapore, Singapore.
Paolo Alberto LorenziniAgency for Science Technology and Research (A*STAR), Infectious Disease Labs, Singapore, Singapore.
Tongyu LiuDepartment of Microbiology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
Rebekah Lin-Zhen ChanAgency for Science Technology and Research (A*STAR), Infectious Disease Labs, Singapore, Singapore.
Cornelius LeeAgency for Science Technology and Research (A*STAR), Infectious Disease Labs, Singapore, Singapore.
Marco VignuzziAgency for Science Technology and Research (A*STAR), Infectious Disease Labs, Singapore, Singapore. Marco_Vignuzzi@a-star.edu.sg.
Christopher B BrookeDepartment of Microbiology, University of Illinois at Urbana-Champaign, Champaign, IL, USA. cbrooke@illinois.edu.ORCID http://orcid.org/0000-0002-6815-1193

Funding

High resolution profiling and computational modeling of influenza virus-immune dynamics during natural infectionU01AI186993 · NIAID · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI Christopher Byron Brooke, Ruian Ke · 2025 to 2026
$2.7M
The effects of influenza virus genomic heterogeneity on replication dynamics and the host responseR01AI139246 · NIAID · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI BROOKE, CHRISTOPHER BYRON · 2018 to 2022
$1.9M
Dissecting the viral and host constraints that govern influenza virus antigenic evolutionR01AI179910 · NIAID · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI Christopher Byron Brooke · 2024 to 2026
$1.5M
NIAID NIH HHS R01 AI139246NIAID NIH HHS R01 AI179910NIAID NIH HHS U01 AI186993United States Department of Defense | Defense Advanced Research Projects Agency (DARPA) DOD DARPA INTERCEPT-W911NF-17-2-0034U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID) R01 AI139246U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID) R01 AI179910U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID) U01 AI186993
6 · The paper itself

Abstract

Influenza A virus populations contain substantial genetic diversity. A major contributor to this diversity is the ubiquitous production of deletion-containing viral genomes (DelVGs) - viral RNAs with large internal deletions. DelVGs directly compete with wild-type (WT) genomes and have been implicated in modulating disease severity. However, the specific functional and genetic interactions between DelVGs and WT genomes remain poorly understood. To examine how DelVGs and WT genomes co-evolve, we serially passage influenza A virus and use next-generation sequencing to build a longitudinal profile of DelVG emergence and dynamics. Highly diverse repertoires of DelVGs observed in early passages undergo sharp contractions in overall diversity, leaving only one or two DelVGs that persist at high frequency. We also identify a recurring substitution that significantly enhances DelVG replication and interference potency. These findings reveal DelVGs to be dynamic genomic elements that are subject to unique selection forces and actively shape viral population dynamics.

Indexed as

Evolution, MolecularGenome, ViralInfluenza A virusSequence DeletionAnimalsDogsGenetic VariationHigh-Throughput Nucleotide SequencingHumansMadin Darby Canine Kidney CellsRNA, ViralVirus ReplicationRNA, Viral

Identifiers

PMID42303613
PMCPMC13522585

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.