Nature Search

A protein language model for exploring viral fitness landscapes

Ito et al. present CoVFit, an AI model that predicts variant fitness (transmissibility) from spike protein sequences alone. They further demonstrate its utility in forecasting viral evolution via single amino acid mutations.

Jumpei Ito
Adam Strange
Kei Sato
ResearchOpen Access13 May 2025
Nature Communications

Volume: 16, P: 1-16
Intratracheal trimerized nanobody cocktail administration suppresses weight loss and prolongs survival of SARS-CoV-2 infected mice

Nagata, Utsumi, Asaka, Maeda et al. describe a nanobody, TP86, that potently neutralizes both BA.1 and BA.2 Omicron SARS-CoV-2 variants, and, when combined with the TP17 nanobody, broadly neutralizes all SARS-CoV-2 variants. This nanobody cocktail also suppresses weight loss and prolongs survival of SARS-CoV-2 infected human ACE2 transgenic mice.

Kayoko Nagata
Daichi Utsumi
Akifumi Takaori-Kondo
ResearchOpen Access26 Nov 2022
Communications Medicine

Volume: 2, P: 1-6
Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation

The P681R mutation in the spike protein renders the Delta variant more pathogenic than prototypic SARS-CoV-2 in infected hamsters, and facilitates spike protein cleavage and enhances viral fusogenicity.

Akatsuki Saito
Takashi Irie
Kei Sato
ResearchOpen Access25 Nov 2021
Nature

Volume: 602, P: 300-306
SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion

A study of SARS-CoV-2 variants examining their transmission, infectivity, and potential resistance to therapies provides insights into the biology of the Delta variant and its role in the global pandemic.

Petra Mlcochova
Steven A. Kemp
Ravindra K. Gupta
ResearchOpen Access06 Sept 2021
Nature

Volume: 599, P: 114-119
Virological characteristics of the SARS-CoV-2 Omicron XBB.1.5 variant

XBB.1.5 of SARS-CoV-2 is a descendant of XBB.1 and has mutations in spike and ORF8, making it more infectious to humans. Here, the authors examined in detail the differences in virological properties of the two variants.

Tomokazu Tamura
Takashi Irie
Takasuke Fukuhara
ResearchOpen Access08 Feb 2024
Nature Communications

Volume: 15, P: 1-17
Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity

The spike protein of the Omicron variant of SARS-CoV-2 has a higher affinity for ACE2 than Delta, and a marked change in its antigenicity increases Omicron’s evasion of therapeutic and vaccine-elicited neutralizing antibodies.

Bo Meng
Adam Abdullahi
Ravindra K. Gupta
ResearchOpen Access01 Feb 2022
Nature

Volume: 603, P: 706-714
Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants

XBB is the first recombinant, globally dominant variant of SARS-CoV-2. Here, the authors examine the variant’s origins and virological properties, showing it is the first example of SARS-CoV-2 improving its fitness through recombination.

Tomokazu Tamura
Jumpei Ito
Kei Sato
ResearchOpen Access16 May 2023
Nature Communications

Volume: 14, P: 1-20
Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant

Recent Omicron SARS-CoV-2 subvariants independently acquire 5 key Spike mutations. Here, the authors evaluate the evolutionary importance of the 5 mutations and characterize the virological properties of variant BQ.1.1 harboring all 5 mutations.

Jumpei Ito
Rigel Suzuki
Kei Sato
ResearchOpen Access11 May 2023
Nature Communications

Volume: 14, P: 1-20
Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant

In vitro studies in human cell lines and in vivo studies in a hamster model show that the SARS-CoV-2 Omicron variant is less pathogenic than both the Delta variant and an ancestral strain of SARS-CoV-2.

Rigel Suzuki
Daichi Yamasoba
Kei Sato
ResearchOpen Access01 Feb 2022
Nature

Volume: 603, P: 700-705
Neutralizing immunity against coronaviruses in Tanzanian health care workers

Godfrey Barabona
Isaac Ngare
Takamasa Ueno
ResearchOpen Access06 Mar 2024
Scientific Reports

Volume: 14, P: 1-10
ILF2 enhances the DNA cytosine deaminase activity of tumor mutator APOBEC3B in multiple myeloma cells

Yasuhiro Kazuma
Kotaro Shirakawa
Akifumi Takaori-Kondo
ResearchOpen Access10 Feb 2022
Scientific Reports

Volume: 12, P: 1-10
Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5

The virological and pathological features of Omicron subvariants are compared in in vitro cellular and airway-on-a-chip and in vivo hamster models.

Tomokazu Tamura
Daichi Yamasoba
Takasuke Fukuhara
ResearchOpen Access24 Jul 2023
Communications Biology

Volume: 6, P: 1-12

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