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Blood DNA virome associates with autoimmune diseases and COVID-19.

Publication ,  Journal Article
Sasa, N; Kojima, S; Koide, R; Hasegawa, T; Namkoong, H; Hirota, T; Watanabe, R; Nakamura, Y; Oguro-Igashira, E; Ogawa, K; Yata, T; Sonehara, K ...
Published in: Nature genetics
January 2025

Aberrant immune responses to viral pathogens contribute to pathogenesis, but our understanding of pathological immune responses caused by viruses within the human virome, especially at a population scale, remains limited. We analyzed whole-genome sequencing datasets of 6,321 Japanese individuals, including patients with autoimmune diseases (psoriasis vulgaris, rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), pulmonary alveolar proteinosis (PAP) or multiple sclerosis) and coronavirus disease 2019 (COVID-19), or healthy controls. We systematically quantified two constituents of the blood DNA virome, endogenous HHV-6 (eHHV-6) and anellovirus. Participants with eHHV-6B had higher risks of SLE and PAP; the former was validated in All of Us. eHHV-6B-positivity and high SLE disease activity index scores had strong correlations. Genome-wide association study and long-read sequencing mapped the integration of the HHV-6B genome to a locus on chromosome 22q. Epitope mapping and single-cell RNA sequencing revealed distinctive immune induction by eHHV-6B in patients with SLE. In addition, high anellovirus load correlated strongly with SLE, RA and COVID-19 status. Our analyses unveil relationships between the human virome and autoimmune and infectious diseases.

Duke Scholars

Published In

Nature genetics

DOI

EISSN

1546-1718

ISSN

1061-4036

Publication Date

January 2025

Volume

57

Issue

1

Start / End Page

65 / 79

Related Subject Headings

  • Whole Genome Sequencing
  • Virome
  • SARS-CoV-2
  • Middle Aged
  • Male
  • Lupus Erythematosus, Systemic
  • Humans
  • Herpesvirus 6, Human
  • Genome-Wide Association Study
  • Female
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Sasa, N., Kojima, S., Koide, R., Hasegawa, T., Namkoong, H., Hirota, T., … Okada, Y. (2025). Blood DNA virome associates with autoimmune diseases and COVID-19. Nature Genetics, 57(1), 65–79. https://doi.org/10.1038/s41588-024-02022-z
Sasa, Noah, Shohei Kojima, Rie Koide, Takanori Hasegawa, Ho Namkoong, Tomomitsu Hirota, Rei Watanabe, et al. “Blood DNA virome associates with autoimmune diseases and COVID-19.Nature Genetics 57, no. 1 (January 2025): 65–79. https://doi.org/10.1038/s41588-024-02022-z.
Sasa N, Kojima S, Koide R, Hasegawa T, Namkoong H, Hirota T, et al. Blood DNA virome associates with autoimmune diseases and COVID-19. Nature genetics. 2025 Jan;57(1):65–79.
Sasa, Noah, et al. “Blood DNA virome associates with autoimmune diseases and COVID-19.Nature Genetics, vol. 57, no. 1, Jan. 2025, pp. 65–79. Epmc, doi:10.1038/s41588-024-02022-z.
Sasa N, Kojima S, Koide R, Hasegawa T, Namkoong H, Hirota T, Watanabe R, Nakamura Y, Oguro-Igashira E, Ogawa K, Yata T, Sonehara K, Yamamoto K, Kishikawa T, Sakaue S, Edahiro R, Shirai Y, Maeda Y, Nii T, Chubachi S, Tanaka H, Yabukami H, Suzuki A, Nakajima K, Arase N, Okamoto T, Nishikawa R, Namba S, Naito T, Miyagawa I, Ueno M, Ishitsuka Y, Furuta J, Kunimoto K, Kajihara I, Fukushima S, Miyachi H, Matsue H, Kamata M, Momose M, Bito T, Nagai H, Ikeda T, Horikawa T, Adachi A, Matsubara T, Ikumi K, Nishida E, Nakagawa I, Yagita-Sakamaki M, Yoshimura M, Ohshima S, Kinoshita M, Ito S, Arai T, Hirose M, Tanino Y, Nikaido T, Ichiwata T, Ohkouchi S, Hirano T, Takada T, Tazawa R, Morimoto K, Takaki M, Konno S, Suzuki M, Tomii K, Nakagawa A, Handa T, Tanizawa K, Ishii H, Ishida M, Kato T, Takeda N, Yokomura K, Matsui T, Uchida A, Inoue H, Imaizumi K, Goto Y, Kida H, Fujisawa T, Suda T, Yamada T, Satake Y, Ibata H, Saigusa M, Shirai T, Hizawa N, Nakata K, Japan COVID-19 Task Force, Imafuku S, Tada Y, Asano Y, Sato S, Nishigori C, Jinnin M, Ihn H, Asahina A, Saeki H, Kawamura T, Shimada S, Katayama I, Poisner HM, Mack TM, Bick AG, Higasa K, Okuno T, Mochizuki H, Ishii M, Koike R, Kimura A, Noguchi E, Sano S, Inohara H, Fujimoto M, Inoue Y, Yamaguchi E, Ogawa S, Kanai T, Morita A, Matsuda F, Tamari M, Kumanogoh A, Tanaka Y, Ohmura K, Fukunaga K, Imoto S, Miyano S, Parrish NF, Okada Y. Blood DNA virome associates with autoimmune diseases and COVID-19. Nature genetics. 2025 Jan;57(1):65–79.

Published In

Nature genetics

DOI

EISSN

1546-1718

ISSN

1061-4036

Publication Date

January 2025

Volume

57

Issue

1

Start / End Page

65 / 79

Related Subject Headings

  • Whole Genome Sequencing
  • Virome
  • SARS-CoV-2
  • Middle Aged
  • Male
  • Lupus Erythematosus, Systemic
  • Humans
  • Herpesvirus 6, Human
  • Genome-Wide Association Study
  • Female