Nature Search

Engineered ACE2 receptor therapy overcomes mutational escape of SARS-CoV-2

Hoshino et al., engineer a human virus receptor, hACE2, and demonstrate its potential for overcoming SARS-CoV-2 mutations that otherwise hinder therapeutic interventions. Overall, the data provide insights in to the therapeutic potential of engineered receptors.

Yusuke Higuchi
Tatsuya Suzuki
Atsushi Hoshino
ResearchOpen Access21 Jun 2021
Nature Communications

Volume: 12, 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
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
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
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
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
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
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
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
Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants

In this study, the authors isolated SARS-CoV-2 receptor binding site monoclonal antibodies resistant to Omicron mutations. An amino acid in the receptor binding domain, tyrosine-489, is a virus-vulnerable site and a common footprint of broadly neutralizing antibodies.

Saya Moriyama
Yuki Anraku
Yoshimasa Takahashi
ResearchOpen Access14 Jul 2023
Nature Communications

Volume: 14, P: 1-17
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
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
Metagenomics-enabled reverse-genetics assembly and characterization of myotis bat morbillivirus

Characterization of the myotis bat morbillivirus shows that infection in human cells is restricted by innate immune responses in vitro and cross-neutralization by sera from measles, mumps and rubella vaccinees.

Satoshi Ikegame
Jillian C. Carmichael
Benhur Lee
Research04 May 2023
Nature Microbiology

Volume: 8, P: 1108-1122
Structural and virological identification of neutralizing antibody footprint provides insights into therapeutic antibody design against SARS-CoV-2 variants

A SARS-CoV-2 antibody, NT-108, exhibits potent therapeutic effects in vivo. Cryo-EM structure of the spike complexed with single-chain Fv of NT108 reveals its neutralizing mechanism, providing insight into antibody therapeutic design.

Yuki Anraku
Shunsuke Kita
Katsumi Maenaka
ResearchOpen Access22 Mar 2025
Communications Biology

Volume: 8, P: 1-12
Structure of the measles virus hemagglutinin bound to its cellular receptor SLAM

The measles virus hemagglutinin (MVH) promotes viral attachment to host cells via interaction with signaling lymphocyte activation molecule (SLAM). Now the crystal structure of MVH head domain in complex with the distal domain of SLAM, together with functional work, reveals the details of this interaction and explains the effectiveness of the currently used vaccine.

Takao Hashiguchi
Toyoyuki Ose
Yusuke Yanagi
Research09 Jan 2011
Nature Structural & Molecular Biology

Volume: 18, P: 135-141
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
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
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
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
Immune response and protective efficacy of the SARS-CoV-2 recombinant spike protein vaccine S-268019-b in mice

Tomoyuki Homma
Noriyo Nagata
Hideki Hasegawa
ResearchOpen Access02 Dec 2022
Scientific Reports

Volume: 12, P: 1-17
Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants

Broadly neutralizing antibodies to SARS-CoV-2 variants including Omicron were isolated from long-term hospitalized convalescent patients with early SARS-CoV-2 strain B.1.1, and the mechanisms are identified from crystal structures.

Kiyomi Shitaoka
Akifumi Higashiura
Tomoharu Yasuda
ResearchOpen Access11 Apr 2023
Communications Biology

Volume: 6, P: 1-14
Structural basis for Glycan-receptor binding by mumps virus hemagglutinin-neuraminidase

Rosa Ester Forgione
Cristina Di Carluccio
Alba Silipo
ResearchOpen Access31 Jan 2020
Scientific Reports

Volume: 10, P: 1-13
Author Correction: Immune response and protective efficacy of the SARS-CoV-2 recombinant spike protein vaccine S-268019-b in mice

Tomoyuki Homma
Noriyo Nagata
Hideki Hasegawa
Amendments and CorrectionsOpen Access31 Jan 2024
Scientific Reports

Volume: 14, P: 1-3
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
High-mobility group box-1 protein promotes granulomatous nephritis in adenine-induced nephropathy

Yoko Oyama
Teruto Hashiguchi
Ikuro Maruyama
Research15 Mar 2010
Laboratory Investigation

Volume: 90, P: 853-866

Search

Engineered ACE2 receptor therapy overcomes mutational escape of SARS-CoV-2

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

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

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

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

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

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

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

Blood DNA virome associates with autoimmune diseases and COVID-19

Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants

A protein language model for exploring viral fitness landscapes

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

Metagenomics-enabled reverse-genetics assembly and characterization of myotis bat morbillivirus

Structural and virological identification of neutralizing antibody footprint provides insights into therapeutic antibody design against SARS-CoV-2 variants

Structure of the measles virus hemagglutinin bound to its cellular receptor SLAM

Mapping the human genetic architecture of COVID-19

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

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

Neutralizing immunity against coronaviruses in Tanzanian health care workers

Immune response and protective efficacy of the SARS-CoV-2 recombinant spike protein vaccine S-268019-b in mice

Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants

Structural basis for Glycan-receptor binding by mumps virus hemagglutinin-neuraminidase

Author Correction: Immune response and protective efficacy of the SARS-CoV-2 recombinant spike protein vaccine S-268019-b in mice

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

High-mobility group box-1 protein promotes granulomatous nephritis in adenine-induced nephropathy

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