Nature Search

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

SARS-CoV-2 Omicron XEC variant, a recombinant of JN.1 progeny, shows increased viral fitness and pathogenicity. Here, the authors show that the nucleocapsid mutation R204P enhances inflammation and suggest a growing role of non-spike mutations in viral evolution.

Shuhei Tsujino
Masumi Tsuda
Miki Kawano
ResearchOpen Access14 Dec 2025
Nature Communications

Volume: 17, P: 1-13
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
The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

Genetic mechanisms influencing COVID-19 susceptibility are not well understood. Here, the authors analyzed whole blood RNA-seq data of 465 Japanese individuals with COVID-19, highlighting thousands of fine-mapped variants affecting expression and splicing of genes, as well as the presence of COVID-19 severity-interaction eQTLs.

Qingbo S. Wang
Ryuya Edahiro
Yukinori Okada
ResearchOpen Access22 Aug 2022
Nature Communications

Volume: 13, P: 1-19
DOCK2 is involved in the host genetics and biology of severe COVID-19

A genome-wide association study highlights a variant in DOCK2, which is common in East Asian populations but rare in Europeans, as a host genetic risk factor for severe COVID-19.

Ho Namkoong
Ryuya Edahiro
Yukinori Okada
ResearchOpen Access08 Aug 2022
Nature

Volume: 609, P: 754-760
Deciphering state-dependent immune features from multi-layer omics data at single-cell resolution

A single-cell multiomic immune cell atlas from 235 Japanese, including patients with COVID-19 and healthy individuals, linked with host genetics including germline and somatic mutation, plasma proteomics and metagenomics data reveals that immune cells are dynamically regulated in a cell state-dependent manner.

Ryuya Edahiro
Go Sato
Yukinori Okada
ResearchOpen Access28 Jul 2025
Nature Genetics

Volume: 57, P: 1905-1921
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
Genome-wide association meta-analysis identifies GP2 gene risk variants for pancreatic cancer

Previous genome-wide association studies have identified risk loci for pancreatic cancer but were centered on individuals of European ancestry. Here the authors identify GP2 gene variants associated with pancreatic cancer susceptibility in populations of East Asian ancestry.

Yingsong Lin
Masahiro Nakatochi
Keitaro Matsuo
ResearchOpen Access24 Jun 2020
Nature Communications

Volume: 11, P: 1-12
Blood DNA virome associates with autoimmune diseases and COVID-19

Analysis of the blood DNA virome in patients with COVID-19 and autoimmune disease associates endogenous HHV-6 (eHHV-6) and high anellovirus load with increased disease risk, most notably for systemic lupus erythematosus. eHHV-6 carriers show a distinct immune response.

Noah Sasa
Shohei Kojima
Yukinori Okada
ResearchOpen Access03 Jan 2025
Nature Genetics

Volume: 57, P: 65-79
Mapping the human genetic architecture of COVID-19

A global network of researchers was formed to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity; this paper reports 13 genome-wide significant loci and potentially actionable mechanisms in response to infection.

Mari E. K. Niemi
Juha Karjalainen
Chloe Donohue
ResearchOpen Access08 Jul 2021
Nature

Volume: 600, P: 472-477
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
Single-cell analyses and host genetics highlight the role of innate immune cells in COVID-19 severity

Peripheral blood mononuclear cells from 73 Japanese patients with coronavirus disease 2019 (COVID-19) and 75 healthy controls were analyzed using single-cell transcriptomics. Combining these data with genotyping data highlights the interplay between host genetics and the immune response in modulating disease severity.

Ryuya Edahiro
Yuya Shirai
Yukinori Okada
ResearchOpen Access24 Apr 2023
Nature Genetics

Volume: 55, P: 753-767
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
Development and characterization of a dedicated dose monitor for ultrahigh-dose-rate scanned carbon-ion beams

Masashi Yagi
Shinichi Shimizu
Tatsuaki Kanai
ResearchOpen Access21 May 2024
Scientific Reports

Volume: 14, P: 1-11
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
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
Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1

JN.1 lineage is a globally dominant variant of SARS-CoV-2. Here, the authors examine structural insights into the BA.2.86 and JN.1 spike dynamics to help understand the mechanisms underlying SARS-CoV-2 infection and its neutralizing-antibody evasion.

Hisano Yajima
Yuki Anraku
Takao Hashiguchi
ResearchOpen Access07 Oct 2024
Nature Communications

Volume: 15, P: 1-14
Structure and function of a β-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium

A β-galactosidase acting specifically on β-1,2-galactooligosaccharides was found from an intestinal bacterium.

Yutaka Nakazawa
Masumi Kageyama
Masahiro Nakajima
ResearchOpen Access16 Jan 2025
Communications Biology

Volume: 8, P: 1-12
A second update on mapping the human genetic architecture of COVID-19

Masahiro Kanai
Shea J. Andrews
Matthew Solomonson
ResearchOpen Access06 Sept 2023
Nature

Volume: 621, P: E7-E26
Multicenter study on caries risk assessment in adults using survival Classification and Regression Trees

Masumi Arino
Ataru Ito
Mikako Hayashi
ResearchOpen Access06 Jul 2016
Scientific Reports

Volume: 6, P: 1-7
Author Correction: Structure and function of a β-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium

Yutaka Nakazawa
Masumi Kageyama
Masahiro Nakajima
Amendments and CorrectionsOpen Access07 Feb 2025
Communications Biology

Volume: 8, P: 1
Dysregulated type I/III interferon system in circulation from patients with anti-MDA5-positive dermatomyositis

Akira Yoshida
Takahisa Gono
Masataka Kuwana
ResearchOpen Access15 Jul 2025
Scientific Reports

Volume: 15, P: 1-16
Profiling of runs of homozygosity from whole-genome sequence data in Japanese biobank

Aye Ko Ko Minn
Motomichi Matsuzaki
Gen Tamiya
ResearchOpen Access03 Apr 2025
Journal of Human Genetics

Volume: 70, P: 287-296
Simulating metabolic pathways to enhance interpretations of metabolome genome-wide association studies

Shun Kodate
Mitsuharu Sato
Kengo Kinoshita
ResearchOpen Access16 May 2025
Scientific Reports

Volume: 15, P: 1-11
Indirect CRISPR screening with photoconversion revealed key factors of drug resistance with cell–cell interactions

An indirect CRISPR screening system based on the photoconvertible fluorescent protein, Dendra2, enables the discovery of elements responsible for drug resistance from cell–cell interactions.

Keisuke Sugita
Iichiroh Onishi
Morito Kurata
ResearchOpen Access01 Jun 2023
Communications Biology

Volume: 6, P: 1-13
Identification and replication of sex-dimorphic protein quantitative trait loci across multiple ancestries and their associations with diseases

Youngjune Bhak
Vasilis Raptis
Albert Tenesa
ResearchOpen Access28 Aug 2025
Scientific Reports

Volume: 15, P: 1-16
Freeze-dried fecal microorganisms as an effective biomaterial for the treatment of calves suffering from diarrhea

Jahidul Islam
Natsuki Ohtani
Tomonori Nochi
ResearchOpen Access14 Nov 2024
Scientific Reports

Volume: 14, P: 1-15
Supramolecular nanofiber formation from commercially available arginine and a bola-type diacetylenic diacid via hydrogelation

A diacetylenic-acid arginine salt gelated water. The properties of the supramolecular hydrogel were examined by optical microscopy, electron microscopy, X-ray diffraction and ultraviolet (UV)-absorption and circular dichroism (CD) spectroscopies. Microscopic images showed that 10, 12-docosadiynedioic acid arginine salt formed a fibrous structure. Upon UV irradiation, the gel polymerized to diacetylene oligomers fibers. After the removal of arginine, CD spectra indicated that the diacetylene oligomers maintained chirality.

Masaru Mukai
Masaki Kogiso
Hiroyuki Minamikawa
Research04 Apr 2012
Polymer Journal

Volume: 44, P: 646-650
Gelsolin alleviates rheumatoid arthritis by negatively regulating NLRP3 inflammasome activation

Jiyeon Lee
Fumiyuki Sasaki
Lark Kyun Kim
ResearchOpen Access24 Aug 2024
Cell Death & Differentiation

Volume: 31, P: 1679-1694
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
Molecular hydrogen attenuates gefitinib-induced exacerbation of naphthalene-evoked acute lung injury through a reduction in oxidative stress and inflammation

Yasuhiro Terasaki
Tetsuya Suzuki
Ikuroh Ohsawa
Research01 Feb 2019
Laboratory Investigation

Volume: 99, P: 793-806
HMGB1 released from intestinal epithelia damaged by cholera toxin adjuvant contributes to activation of mucosal dendritic cells and induction of intestinal cytotoxic T lymphocytes and IgA

Ayako Wakabayashi
Masumi Shimizu
Hidemi Takahashi
ResearchOpen Access24 May 2018
Cell Death & Disease

Volume: 9, P: 1-17
Suppression of R5-type of HIV-1 in CD4⁺ NKT cells by Vδ1⁺ T cells activated by flavonoid glycosides, hesperidin and linarin

Michiyuki Yonekawa
Masumi Shimizu
Hidemi Takahashi
ResearchOpen Access17 May 2019
Scientific Reports

Volume: 9, P: 1-12
Comparative analysis of necrotizing enterocolitis in preterm infants born in Japan and born to mothers of Japanese ethnicity in California

Satoshi Kusuda
Mihoko V. Bennett
Asao Yara
ResearchOpen Access22 Mar 2025
Scientific Reports

Volume: 15, P: 1-11
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

Search

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

Virological characteristics of the SARS-CoV-2 Omicron XBB.1.5 variant

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

DOCK2 is involved in the host genetics and biology of severe COVID-19

Deciphering state-dependent immune features from multi-layer omics data at single-cell resolution

Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation

Genome-wide association meta-analysis identifies GP2 gene risk variants for pancreatic cancer

Blood DNA virome associates with autoimmune diseases and COVID-19

Mapping the human genetic architecture of COVID-19

Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant

Single-cell analyses and host genetics highlight the role of innate immune cells in COVID-19 severity

Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants

Development and characterization of a dedicated dose monitor for ultrahigh-dose-rate scanned carbon-ion beams

A protein language model for exploring viral fitness landscapes

Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant

Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1

Structure and function of a β-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium

A second update on mapping the human genetic architecture of COVID-19

Multicenter study on caries risk assessment in adults using survival Classification and Regression Trees

Author Correction: Structure and function of a β-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium

Dysregulated type I/III interferon system in circulation from patients with anti-MDA5-positive dermatomyositis

Profiling of runs of homozygosity from whole-genome sequence data in Japanese biobank

Simulating metabolic pathways to enhance interpretations of metabolome genome-wide association studies

Indirect CRISPR screening with photoconversion revealed key factors of drug resistance with cell–cell interactions

Identification and replication of sex-dimorphic protein quantitative trait loci across multiple ancestries and their associations with diseases

Freeze-dried fecal microorganisms as an effective biomaterial for the treatment of calves suffering from diarrhea

Supramolecular nanofiber formation from commercially available arginine and a bola-type diacetylenic diacid via hydrogelation

Gelsolin alleviates rheumatoid arthritis by negatively regulating NLRP3 inflammasome activation

Neutralizing immunity against coronaviruses in Tanzanian health care workers

Molecular hydrogen attenuates gefitinib-induced exacerbation of naphthalene-evoked acute lung injury through a reduction in oxidative stress and inflammation

HMGB1 released from intestinal epithelia damaged by cholera toxin adjuvant contributes to activation of mucosal dendritic cells and induction of intestinal cytotoxic T lymphocytes and IgA

Suppression of R5-type of HIV-1 in CD4⁺ NKT cells by Vδ1⁺ T cells activated by flavonoid glycosides, hesperidin and linarin

Comparative analysis of necrotizing enterocolitis in preterm infants born in Japan and born to mothers of Japanese ethnicity in California

Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5

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