Jumpei Ito

[Please RT] Our new preprint is out! By rapidly quantifying interferon-stimulated genes (ISGs) expression across 220k RNA-seq data sets from diverse animals, we comprehensively identified “hidden viral infections” in wildlife and livestock (1/n). www.biorxiv.org/content/10.6...

biorxiv.orgQuantitative host-response mapping enables phenotypic profiling of viruses detected by virome sequencingAnimal-derived viruses have repeatedly caused human outbreaks, motivating efforts to identify and characterize viruses circulating in animals. Virome sequencing has accelerated animal virus discovery,...

New preprint! We developed ViroChart, a method that infers the properties of novel viruses detected in wildlife and livestock from host gene expression profiles. Fantastic work led by Junna @J_191206 ! See the quoted post for details: 🦠💻 (1/n) www.biorxiv.org/content/10.6...

Junna Kawasaki@junnakawasaki.bsky.social

Our latest work is now on bioRxiv! 🦠 ViroChart: Quantitative host-response mapping enables phenotypic profiling of viruses detected by virome sequencing. www.biorxiv.org/content/10.6... (1/9)

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sites.google.comVirus Informatics Lab（ウイルス情報科学）NEWS

Our lab works on AI for infectious diseases, with a focus on vaccine antigen design and the search for next pandemic viruses. We’re recruiting graduate students, JSPS PDs, postdocs, and project assistant professors — DM us anytime! (3/n) sites.google.com/view/virus-i...

biorxiv.orgHost innate immune response profiling reveals hidden viral infections across diverse animal speciesVirus discovery using RNA-seq data from wildlife and livestock offers a powerful strategy for identifying unknown pathogens with pandemic potential. However, conventional approaches rely on homology-b...

ISG Profiler: www.biorxiv.org/content/10.6...

Junna Kawasaki@junnakawasaki.bsky.social

Our latest work is now on bioRxiv! 🦠 ViroChart: Quantitative host-response mapping enables phenotypic profiling of viruses detected by virome sequencing. www.biorxiv.org/content/10.6... (1/9)

Our goal is to establish a new paradigm for virus discovery and characterization based on host transcriptional responses, aimed at finding the next pandemic virus. ISG Profiler (previous work) and ViroChart (this work) are the first steps, and we’re pushing this forward. (2/n)

biken.osaka-u.ac.jp生物情報解析分野ウイルス情報科学グループ特任助教（常勤）の公募について | NEWS&TOPICS | 大阪大学微生物病研究所 RIMD 文部科学省共同利用・共同研究拠点大阪大学微生物病研究所のウェブサイトです。

15 Sept

【拡散希望】当研究室では特任助教or特任研究員を若干名募集します。ワクチン抗原最適化AIや種間比較RNA-seq基盤モデルの開発など、深層学習関連のプロジェクトを進めてくれる方を募集します。ご興味のある方はお気軽にお問い合わせください！1/n www.biken.osaka-u.ac.jp/news_topics/... www.biken.osaka-u.ac.jp/news_topics/...

biken.osaka-u.ac.jp生物情報解析分野ウイルス情報科学グループ特任事務職員の公募について | NEWS&TOPICS | 大阪大学微生物病研究所 RIMD 文部科学省共同利用・共同研究拠点大阪大学微生物病研究所のウェブサイトです。

15 Sept

加えて、特任事務職員も1名募集しております。ご興味のありそうな方が近くにおりましたらぜひご共有いただけますと幸いです。 www.biken.osaka-u.ac.jp/news_topics/... 2/n

New preprint! We show that poxvirus gene repertoires are shaped by expansion-biased birth-and-death dynamics and genome architectural constraints. Led by Arnon Plianchaisuk (@chainorato) in our lab. Please share! (1/10) www.biorxiv.org/content/10.6...

Our lab (Viral Informatics Lab, RIMD, U. Osaka) pursues "AI for Viral Infectious Diseases": viral evolution, viral protein modeling for vaccine optimization, and AI to efficiently search for viruses that could cause the next pandemic. (9/10) sites.google.com/view/virus-i...

We are recruiting! Graduate students, postdocs, specially appointed assistant professors, and student research assistants. If our work interests you, please get in touch by email or DM. (10/10)

Poxvirus gene repertoire evolution thus rests on principles distinct from both small-genome viruses and cellular organisms. By mapping which genome regions vary and which are conserved in these viruses of public health concern, our work also informs vaccine design. (7/10)

Arnon Plianchaisuk performed all analyses. The work began at our former affiliation, Division of Systems Virology, IMSUT, University of Tokyo (Kei Sato lab). We thank Spyros Lytras, Hiroyuki Hikida, Yoichiro Nakatani, Emma Harding and Aris Katzourakis for their feedback. (8/10)

Gene gain and duplication were also strongly constrained by genome architecture. In most lineages, expansion was concentrated at both genome termini; in the most expanded lineages, amplification reached even the normally highly conserved central region. (5/10)

Phylogenetics and the origins of host-derived genes suggest that avian poxviruses (Avipoxvirus) may have arisen from a mammal-to-bird host switch. Avipoxvirus also underwent large-scale amplification, so adaptation to a new host may have triggered the expansion. (6/10)

Poxvirus genome size showed a strong linear relationship with the number of encoded viral genes. In other words, coding capacity increased proportionally with genome size. (3/10)

The poxvirus gene repertoire has evolved through a complex process of gain, duplication and loss. Across diverse lineages we found a consistent tendency toward expansion, marking its evolution as expansion-biased birth-and-death dynamics. (4/10)

Unlike most viruses, poxviruses carry genomes of several hundred kb with hundreds of genes. Across 59 genomes we integrated gene gain, loss and duplication, horizontal transfer from hosts, and synteny to reconstruct how the repertoire evolved. (2/10)

【拡散希望】プレプリントを公開しました！poxvirusが「拡大に偏ったbirth-and-death dynamics」と「ゲノム構造に制約された遺伝子増幅」により遺伝子レパトアを増大させてきたことを示しました。当研究室のArnon Plianchaisuk先生@chainoratoが主導した研究です（1/10） www.biorxiv.org/content/10.6...

阪大微研ウイルス情報科学（伊東研）は「AI for Viral Infectious Diseases」を掲げ、ウイルス進化研究、ワクチン最適化に向けたウイルスタンパク質モデリング、次のパンデミックを起こし得るウイルスを効率的に探索するAI技術の開発に取り組んでいます（9/10） sites.google.com/view/virus-i...

当研究室では、大学院生、ポスドク、特任助教、特任講師、学生アルバイトを絶賛募集中です！私たちの研究にご興味をお持ちの方は、ぜひメールやDMでお気軽にご連絡ください！（10/10）

以上から、poxvirusの遺伝子レパトア進化は、小型ゲノムのウイルスとも細胞性生物とも異なる原理に支えられていることが明らかになりました。公衆衛生上の懸念が大きいpoxvirusについて、ゲノムのどこが可変でどこが保存されるかを示した本研究は、ワクチン開発にも示唆を与えるものです（7/10）

解析はすべてArnon Plianchaisuk先生が実施しました。本研究は前職の東大医科研システムウイルス学分野（佐藤佳研究室）で開始したものです。Spyros Lytras先生、疋田弘之先生、中谷洋一郎先生、Emma F. Harding先生、Aris Katzourakis先生から貴重なご助言をいただきました（8/10）

また、遺伝子の獲得や重複はゲノム構造に強く制約されていました。多くの系統ではレパトアの拡大がゲノム両末端に集中する一方、特に大きく拡大した系統では、通常は高度に保存される中央領域にまで遺伝子増幅が及んでいました（5/10）

系統解析と宿主由来遺伝子の起源解析から、鳥類のpoxvirus（Avipoxvirus）が哺乳類から鳥類への宿主転換に由来する可能性が示されました。Avipoxvirusは大規模な遺伝子増幅を経た系統のひとつであり、新たな宿主への適応がレパトア拡大の契機になったのかもしれません（6/10）

poxvirusのゲノムサイズは、コードするウイルス遺伝子数と強い線形関係を示しました。すなわち、ゲノムが大きいほどコード可能な遺伝子数（coding capacity）も比例して増加することが明らかになりました（3/10）

poxvirusの遺伝子レパトアは、獲得・重複・喪失からなる複雑な過程を経て進化してきました。さらに、様々な系統で一貫して拡大する傾向がみられ、その進化は「拡大に偏ったbirth-and-death dynamics」に特徴づけられます（4/10）

大部分のウイルスがゲノムの小ささを特徴とするのとは対照的に、poxvirusは数百kbの巨大なゲノムと数百の遺伝子を持ちます。本研究では59種のゲノムを対象に、遺伝子の獲得・喪失・重複、宿主からの水平伝播、シンテニーを統合的に解析し、遺伝子レパトアの進化ダイナミクスを再構築しました（2/10）

Finally, I thank my current supervisor, Kei, for providing an environment that made this work possible. This study was primarily supported by JST PRESTO “Pandemic Social Infrastructure” (15/n).

sites.google.comITO Lab感染症制御に資するバイオインフォマティクス技術の創出 Development of bioinformatics technologies for infectious disease control

Bonus: From April, I will start a new lab at Osaka University. Virus discovery and phenotypic prediction based on host gene expression will remain a central topic—stay tuned! (16/n) sites.google.com/view/virus-i...

This work was driven by three outstanding young researchers: Luca led ISG Profiler, Hiroaki led ISG-VIP, and Kyoko conducted large-scale virus discovery and characterization together with me. I sincerely thank them for their exceptional efforts (13/n).

The large-scale analysis of 220k RNA-seq data sets was led by Mai. We also greatly benefited from in-depth discussions with Eddie, Spyros, and Junna (14/n).

We also uncovered key insights into viral evolution and infection risk, including rat viruses linked to the origins of highly pathogenic parvoviruses in pigs, dogs, and cats, and rodent colonies harboring PRRSV-related viruses at high prevalence (11/n).

In summary, ISG-based virus discovery complements conventional virome approaches and provides a scalable solution for comprehensive virus detection in the rapidly expanding landscape of animal RNA-seq data (12/n).

Notably, geNomad failed to detect viruses of the recently characterized and highly diverse genus Chaphamaparvovirus, whereas our method identified many, including highly divergent viral species (9/n).

These chaphamaparvoviruses were frequently detected in the livers of chickens and wild birds, and infected samples showed viral hepatitis-like transcriptomic signatures, suggesting a potential role in avian hepatitis (10/n).

Using this pre-screening strategy, we analyzed ~40k animal RNA-seq data sets released in 2024 and identified ~2,441 infections across diverse species, including 385 infections by novel viruses (7/n).

Importantly, our approach detected many viral infections missed by the widely used tool geNomad. These were enriched for highly divergent viruses with low sequence similarity to known viruses, highlighting the strength of our strategy for novel virus discovery (8/n).

In this study, we developed ISG Profiler for rapid ISG quantification from RNA-seq data and ISG-VIP for infection prediction. The framework applies to diverse avian and mammalian species, including those without reference genomes, and processes each sample in ~4 minutes (5/n).

ISG-VIP showed a positive prediction rate of ~8% and a recall of ~0.45. When used as a pre-screening step, it reduces the number of samples subjected to computationally intensive virome analysis to 8%, while still capturing ~45% of viral infections (6/n).

However, conventional virus discovery approaches based on homology searches are computationally expensive and have limited sensitivity for highly divergent viruses. As RNA-seq data continue to grow exponentially, more efficient and scalable strategies are needed (3/n).