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. 2022 Mar;603(7902):687-692.
doi: 10.1038/s41586-022-04441-6. Epub 2022 Jan 21.

SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters

Peter J Halfmann #  1 Shun Iida #  2 Kiyoko Iwatsuki-Horimoto #  3 Tadashi Maemura #  1 Maki Kiso #  3 Suzanne M Scheaffer  4 Tamarand L Darling  4 Astha Joshi  4 Samantha Loeber  5 Gagandeep Singh  6   7 Stephanie L Foster  8 Baoling Ying  4 James Brett Case  4 Zhenlu Chong  4 Bradley Whitener  4 Juan Moliva  9 Katharine Floyd  8 Michiko Ujie  3 Noriko Nakajima  2 Mutsumi Ito  3 Ryan Wright  1 Ryuta Uraki  3   10 Prajakta Warang  6   7 Matthew Gagne  9 Rong Li  11 Yuko Sakai-Tagawa  3 Yanan Liu  11 Deanna Larson  11 Jorge E Osorio  12   13 Juan P Hernandez-Ortiz  13 Amy R Henry  9 Karl Ciuoderis  13 Kelsey R Florek  14 Mit Patel  8 Abby Odle  15 Lok-Yin Roy Wong  15 Allen C Bateman  14 Zhongde Wang  11 Venkata-Viswanadh Edara  8 Zhenlu Chong  4 John Franks  16 Trushar Jeevan  16 Thomas Fabrizio  16 Jennifer DeBeauchamp  16 Lisa Kercher  16 Patrick Seiler  16 Ana Silvia Gonzalez-Reiche  17 Emilia Mia Sordillo  18 Lauren A Chang  6   7   19 Harm van Bakel  17 Viviana Simon  6   17   18   20 Consortium Mount Sinai Pathogen Surveillance (PSP) study groupDaniel C Douek  9 Nancy J Sullivan  9 Larissa B Thackray  4 Hiroshi Ueki  3   10 Seiya Yamayoshi  3   10 Masaki Imai  3   10 Stanley Perlman  15 Richard J Webby  16 Robert A Seder  9 Mehul S Suthar  8   21 Adolfo García-Sastre  6   7   18   20   22 Michael Schotsaert  6   7 Tadaki Suzuki  2 Adrianus C M Boon  23   24   25 Michael S Diamond  26   27   28   29 Yoshihiro Kawaoka  30   31   32
Collaborators, Affiliations

SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters

Peter J Halfmann et al. Nature. 2022 Mar.

Abstract

The recent emergence of B.1.1.529, the Omicron variant1,2, has raised concerns of escape from protection by vaccines and therapeutic antibodies. A key test for potential countermeasures against B.1.1.529 is their activity in preclinical rodent models of respiratory tract disease. Here, using the collaborative network of the SARS-CoV-2 Assessment of Viral Evolution (SAVE) programme of the National Institute of Allergy and Infectious Diseases (NIAID), we evaluated the ability of several B.1.1.529 isolates to cause infection and disease in immunocompetent and human ACE2 (hACE2)-expressing mice and hamsters. Despite modelling data indicating that B.1.1.529 spike can bind more avidly to mouse ACE2 (refs. 3,4), we observed less infection by B.1.1.529 in 129, C57BL/6, BALB/c and K18-hACE2 transgenic mice than by previous SARS-CoV-2 variants, with limited weight loss and lower viral burden in the upper and lower respiratory tracts. In wild-type and hACE2 transgenic hamsters, lung infection, clinical disease and pathology with B.1.1.529 were also milder than with historical isolates or other SARS-CoV-2 variants of concern. Overall, experiments from the SAVE/NIAID network with several B.1.1.529 isolates demonstrate attenuated lung disease in rodents, which parallels preliminary human clinical data.

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Conflict of interest statement

M.S.D. is a consultant for Inbios, Vir Biotechnology, Senda Biosciences, and Carnival Corporation, and on the Scientific Advisory Boards of Moderna and Immunome. The Diamond laboratory has received funding support in sponsored research agreements from Moderna, Vir Biotechnology, and Emergent BioSolutions. The Boon laboratory has received unrelated funding support in sponsored research agreements from AI Therapeutics, AbbVie Inc., GreenLight Biosciences Inc., and Nano targeting & Therapy Biopharma Inc. M.S.S. serves on Advisory boards for Moderna and Ocugen. Y.K. has received unrelated funding support from Daiichi Sankyo Pharmaceutical, Toyama Chemical, Tauns Laboratories, Inc., Shionogi & Co. Ltd, Otsuka Pharmaceutical, KM Biologics, Kyoritsu Seiyaku, Shinya Corporation and Fuji Rebio. The A.G.-S. laboratory has received unrelated research support from Pfizer, Senhwa Biosciences, Kenall Manufacturing, Avimex, Johnson & Johnson, Dynavax, 7Hills Pharma, Pharmamar, ImmunityBio, Accurius, Nanocomposix, Hexamer, N-fold LLC, Model Medicines, Atea Pharma and Merck. A.G.-S. has paid or equity-based consulting agreements for the following companies: Vivaldi Biosciences, Contrafect, 7Hills Pharma, Avimex, Vaxalto, Pagoda, Accurius, Esperovax, Farmak, Applied Biological Laboratories, Pharmamar, Paratus, CureLab Oncology, CureLab Veterinary and Pfizer, outside the reported work. A.G.-S. is inventor on patents and patent applications on the use of antivirals and vaccines for the treatment and prevention of virus infections and cancer, owned by the Icahn School of Medicine at Mount Sinai, New York, outside the reported work. Icahn School of Medicine at Mount Sinai has filed patent applications relating to SARS-CoV-2 serological assays that list Viviana Simon as co-inventor. S.P. has received unrelated research support from BioAge Laboratories and Autonomous Therapeutics Inc. The remaining authors declare no competing interests.

Figures

Fig. 1
Fig. 1. B.1.1.529 is less pathogenic in mice.
a, Left: weight change in mock-infected mice (n = 4) or mice inoculated with B.1.1.529 + A701V (n = 5), B.1.1.529 (n = 3) or B.1.351 (n = 3). Middle: weight change in mice inoculated with B.1.1.529 or B.1.351 (n = 5) (**P = 0.0075, ***P = 0.0006, ****P < 0.0001). Right: weight change in mice inoculated with B.1.1.529 (n = 4), B.1.1.7 (n = 10) or B.1.351 (n = 18). Comparison between B.1.351 and B.1.1.529: *P = 0.0151, ***P = 0.0003 (3 dpi) and 0.0006 (4 dpi). Mean ± s.e.m. b, Viral RNA level in mice inoculated with B.1.1.529 or B.1.351 (n = 5) (**P = 0.0079). c, Infectious virus titre in mice inoculated with B.1.1.529 + A701V, B.1.1.529 or B.1.351 (n = 3). d, Infectious virus titre in mice inoculated with B.1.1.529 or B.1.351 (n = 5) (**P = 0.0079). e, Pulmonary function analysis as measured by whole-body plethysmography. Mean ± s.e.m. Comparison between B.1.617.2 and B.1.351: **P = 0.0095 (n = 5 each). f, Left, weight change in mice inoculated with WA1/2020 D614G (103 FFU; n = 6), B.1.1.529 (103 FFU; n = 3), B.1.1.529 (104 PFU; n = 6) or B.1.1.529 (105 FFU; n = 3). Right, weight change in mice inoculated with 104 PFU of B.1.1.529 +A701V (n = 6) or B.1.351 (n = 6), or mock-infected, age-matched mice (n = 4). Mean ± s.e.m. g, Infectious virus titre in lungs of mice inoculated with WA1/2020 D614G (n = 8) or B.1.1.529 (n = 7) (****P < 0.0001). h, Infectious virus titre in mice inoculated with B.1.1.529 + A701V or B.1.351 (n = 3). i, Heat map of concentration of cytokines and chemokines in lungs of infected mice. Results are from one (af, h, i) or two (g) experiments. The dotted line is the limit of detection. Statistical analysis (a, e: two-way analysis of variance (ANOVA) with multiple comparisons test; b, d, g: two-tailed Mann–Whitney test) was performed on datasets with four or more data points. See Supplementary Table 1 for more information. CCL4, chemokine (C-C motif) ligand 4; IL-18, interleukin-18; CXCL2, chemokine (C-X-C motif) ligand 2; TNF, tumour necrosis factor; GM-CSF, granulocyte–macrophage CSF; IFNγ, interferon-γ. Source data
Fig. 2
Fig. 2. B.1.1.529 is less pathogenic in wild-type and hACE2-transgenic Syrian hamsters.
a, Weight change in uninfected age-matched hamsters (n = 3) or in hamsters inoculated with B.1.1.529 or B.1.617.2 (n = 4). Mean ± s.e.m. b, Weight change in uninfected age-matched hamsters (n = 9) or in hamsters inoculated with B.1.1.529 (n = 10) or WA1/2020 D614G (n = 6). Mean ± s.e.m. (red, *P = 0.0293; red, **P = 0.0046 and 0.0014; black, **P = 0.0021; black, ***P = 0.0001). c, Weight change in hamsters inoculated with 103, 104, 105 or 106 PFU of B.1.1.529 or 103 PFU of B.1.617.2 (n = 4). Mean ± s.e.m. Comparison between B.1.617.2 and B.1.1.529 (103 PFU): *P = 0.0476, **P = 0.0041, 0.0041, 0.0047 and 0.0019, respectively. d, Weight change in hamsters inoculated with B.1.1.529 (n = 5) or WA1/2020 (n = 9). Mean ± s.e.m. (****P < 0.0001). e, Viral RNA level in hamsters inoculated with WA1/2020 D614G or B.1.1.529 (n = 15) (*P = 0.015, ***P < 0.0003). f, Infectious virus titre in hamsters inoculated with B.1.617.2 or B.1.1.529 (n = 4) (*P = 0.0286; NS, not significant). g, Nasal wash viral RNA level in hamsters inoculated with WA1/2020 (n = 8) or B.1.1.529 (n = 3). TCID50, median tissue culture infectious dose. h, Pulmonary function analysis by whole-body plethysmography. Mean ± s.e.m. (Penh and Rpef, comparison between B.1.617.2 and B.1.1.529: *P = 0.0263 (3 dpi), *P = 0.0186 (5 dpi), ***P = 0.0005 (7 dpi), ****P < 0.0001) (n = 4). i, Micro-CT images of the lungs of mock-infected (n = 3) or B.1.617.2- (n = 4) and B.1.1.529-infected (n = 4) hamsters at 7 dpi. Multifocal nodules (black arrows), ground-glass opacity (white arrowheads) and pneumomediastinum (white asterisk) are indicated. j, CT score for uninfected hamsters (n = 3) or those inoculated with B.1.617.2 or B.1.1.529 (n = 4) (****P < 0.0001). k, Weight change in hACE2 hamsters inoculated with HP-095 D614G or B.1.1.529 (n = 4). Error bars indicate s.e.m. l, Survival of hACE2 hamsters after inoculation with HP-095 D614G or B.1.1.529 (n = 4) (*P = 0.029). m, Infectious virus titre of hACE2 hamsters inoculated with HP-095 D614G or B.1.1.529; n = 3 (3 dpi), n = 4 (5 dpi) (*P = 0.0286). The results are from one (a, c, d, fm) or two to three independent (b, e) experiments. Dotted lines represent the limit of detection. Statistical analysis (bd, h: two-way ANOVA with multiple comparisons test; e, j: two-tailed t-test, f, m: two-tailed Mann–Whitney test, l: log-rank test) was performed on datasets with four or more data points. See Supplementary Table 1 for more information. Source data
Fig. 3
Fig. 3. Pathological findings in the lungs of SARS-CoV-2-infected Syrian hamsters.
Hamsters were inoculated with 103 PFU of B.1.617.2 or B.1.1.529 and euthanized at 3 and 6 dpi (n = 4). a, Macroscopic images of the lungs obtained at 6 dpi. Yellow arrows indicate haemorrhage. b, Lung sections from animals infected with B.1.617.2 or B.1.1.529. Scale bars, 200 µm. Focal alveolar haemorrhage in B.1.617.2-infected animals at 6 dpi is outlined and shown at higher magnification in the inset (scale bar, 100 µm). Black arrow indicates focal inflammation. c, Histopathological score of pneumonia based on the percentage of alveolitis in a given section using the following scoring: 0, no pathological change; 1, affected area (≤10%); 2, affected area (<50%, >10%); 3, affected area (≥50%); an additional point was added when pulmonary edema and/or alveolar haemorrhage was observed. Data are median score (n = 4; *P = 0.0286; two-tailed Mann–Whitney test). d, RNA in situ hybridization for SARS-CoV-2 viral RNA. Representative images for the alveoli and bronchi of hamsters infected with B.1.617.2 or B.1.1.529 (n = 4) virus at 3 or 6 dpi are shown. Scale bars, 20 µm. See Supplementary Table 1 for more information. Source data

Update of

  • The SARS-CoV-2 B.1.1.529 Omicron virus causes attenuated infection and disease in mice and hamsters.
    Diamond M, Halfmann P, Maemura T, Iwatsuki-Horimoto K, Iida S, Kiso M, Scheaffer S, Darling T, Joshi A, Loeber S, Foster S, Ying B, Whitener B, Floyd K, Ujie M, Nakajima N, Ito M, Wright R, Uraki R, Li R, Sakai Y, Liu Y, Larson D, Osorio J, Hernandez-Ortiz J, Čiuoderis K, Florek K, Patel M, Bateman A, Odle A, Wong LY, Wang Z, Edara VV, Chong Z, Thackray L, Ueki H, Yamayoshi S, Imai M, Perlman S, Webby R, Seder R, Suthar M, Garcia-Sastre A, Schotsaert M, Suzuki T, Boon A, Kawaoka Y, Douek D, Moliva J, Sullivan N, Gagne M, Ransier A, Case J, Jeevan T, Franks J, Fabrizio T, DeBeauchamp J, Kercher L, Seiler P, Singh G, Warang P, Gonzalez-Reiche AS, Sordillo E, van Bakel H, Simon V. Diamond M, et al. Res Sq [Preprint]. 2021 Dec 29:rs.3.rs-1211792. doi: 10.21203/rs.3.rs-1211792/v1. Res Sq. 2021. Update in: Nature. 2022 Mar;603(7902):687-692. doi: 10.1038/s41586-022-04441-6. PMID: 34981044 Free PMC article. Updated. Preprint.

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