Publications

• Host innate immune response profiling reveals hidden viral infections across diverse animal species.

Nishimura L*, Unno H*, Kurihara K*, Suganami M, Kawasaki J, Lytras S, Okumura K, Holmes EC, Ito J†, Sato K†. bioRxiv 2026.03.16.711951; doi: https://doi.org/10.64898/2026.03.16.711951

• Combined Effects of Severe Immunocompromise and Prolonged Virus Shedding on Within-Host SARS-CoV-2 Evolution in COVID-19.

Hirata Y, Takahashi K, Iwamoto N, Jeong YD, Miyamoto S, Kawasaki J, Harrison MT, Mine S, Iida S, Saito S, Ainai A, Kanno T, Katano H, Sasaki N, Horiba K, Tsunoi T, Ishikane M, Kamegai K, Itoh N, Akazawa-Kai N, Okumura N, Haraguchi M, Sakoh T, Morishima M, Araoka H, Uchida N, Hase R, Marumo Y, Adachi T, Matsue K, Saito T, Ohmagari N, Iwami S, Suzuki T. bioRxiv 2026.04.14.26350918; doi: https://doi.org/10.64898/2026.04.14.26350918

• Rising vaccine hesitancy in a future pandemic after COVID-19 and its decision drivers in Japan.

Kawasaki J*, Hamada M*, Machida M, Komorizono R, Kobayashi-Ishihara M, Fujita N, Tabuchi T, Furuse Y†. medRxiv 2026.01.18.26344375; doi: https://doi.org/10.64898/2026.01.18.26344375

• Integrative modeling of seasonal influenza evolution via AI-powered antigenic cartography
  Ito J*†, Kawakubo S*, Unno H, Strange A, Lytras S, Okumura K, Lilley A, Harvey R, Lewis N, Sato K†. bioRxiv 2025.08.04.668423; doi: https://doi.org/10.1101/2025.08.04.668423

• A protein language model for exploring viral fitness landscapes.

Ito J*†, Strange A, Liu W, Joas G, Lytras S; Genotype to Phenotype Japan (G2P-Japan) Consortium; Sato K†. Nat Commun. 2025 May 13;16(1):4236. doi:10.1038/s41467-025-59422-w. PMID: 40360496; PMCID: PMC12075601.

• Pathogen genomic surveillance and the AI revolution. 

Lytras S, Lamb KD, Ito J, Grove J, Yuan K, Sato K, Hughes J, Robertson DL. J Virol. 2025 Feb 25;99(2):e0160124. doi: 10.1128/jvi.01601-24. Epub 2025 Jan 29. PMID: 39878472; PMCID: PMC11852828.

• Hidden challenges in evaluating spillover risk of zoonotic viruses using machine learning models. 

Kawasaki J*†, Suzuki T, Hamada M†. Commun Med (Lond). 2025 May 20;5(1):187. doi: 10.1038/s43856-025-00903-w. PMID: 40394176; PMCID: PMC12092720.

• Virological characteristics of the SARS-CoV-2 LP.8.1 variant. 

Chen L, Kaku Y, Okumura K, Uriu K, Zhu Y; Genotype to Phenotype Japan (G2P-Japan) Consortium; Ito J, Sato K. Lancet Infect Dis. 2025 Apr;25(4):e193. doi: 10.1016/S1473-3099(25)00079-9. Epub 2025 Feb 10. PMID: 39947218.

• Evolution of BA.2.86 to JN.1 reveals that functional changes in non-structural viral proteins are required for fitness of SARS-CoV-2. 

Tsujino S, Tsuda M, Nao N, Okumura K, Wang L, Oda Y, Mimura Y, Li J, Hashimoto R, Matsumura Y, Suzuki R, Suzuki S, Yoshimatsu K, Nagao M, Ito J, Takayama K, Sato K, Matsuno K, Tamura T, Tanaka S, Fukuhara T; Genotype to Phenotype Japan (G2P-Japan) Consortium. J Virol. 2025 Oct 23;99(10):e0090825. doi: 10.1128/jvi.00908-25. Epub 2025 Sep 23. PMID: 40985731; PMCID: PMC12548449.

• A non-spike nucleocapsid R204P mutation in SARS-CoV-2 Omicron XEC enhances inflammation and pathogenicity. 

Tsujino S, Tsuda M, Deguchi S, Ito J, Taha TY, Nasser H, Wang L, Rosecrans J, Suzuki R, Suzuki S, Yoshimatsu K, Ott M, Ikeda T, Sato K, Takayama K, Tanaka S, Tamura T, Fukuhara T; Genotype to Phenotype Japan (G2P-Japan) Consortium. Nat Commun. 2025 Dec 14;17(1):735. doi: 10.1038/s41467-025-67455-4. PMID: 41392175; PMCID: PMC12819382.