The recent emergence of B.1.1.529, the Omicron varian

Boon, Adrianus C M

Case, James Brett

Chong, Zhenlu

Darling, Tamarand L

Diamond, Michael S

et al,

Halfmann, Peter J

Iida, Shun

Iwatsuki-Horimoto, Kiyoko

Joshi, Astha

Kiso, Maki

Maemura, Tadashi

Scheaffer, Suzanne M

Thackray, Larissa B

Whitener, Bradley

Ying, Baoling

English

Digital Commons@Becker

SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamstersIn the format provided by the authors and uneditedNature | www.nature.com/natureSupplementary informationhttps://doi.org/10.1038/s41586-022-04441-6Supplemental Table 1. List of experiments and viruses used by different laboratories Laboratory Animal model Phenotype Virus detection method Days post infection Virus isolates Kawaoka (YK) BALB/c mice Virus titer in Nasal turbinates and Lungs; WBP* Infectious virus titer 2 B.1.351 (hCoV-19/USA/MD-HP01542/2021)  B.1.1.529 (hCoV-19/Japan/NC928-2N/2021)   Syrian Hamster Weight loss; Virus titer in Nasal turbinates and Lungs; WBP; CT scan& Infectious virus titer 3 B.1.617.2 (hCoV-19/USA/WI-UW-5250/2021)  B.1.1.529 (hCoV-19/Japan/NC928-2N/2021)  hACE2-transgenic Syrian Hamster Weight loss; Survival; Virus titer in Nasal turbinates and Lungs Infectious virus titer 3 and 5 HP-095 (SARS-CoV-2/UT-HP095-1N/Human/2020/Tokyo)  B.1.1.529 (hCoV-19/USA/WI-WSLH-221686/2021) Suzuki (TS) Syrian Hamster Histopathology   B.1.617.2 (hCoV-19/USA/WI-UW-5250/2021)  B.1.1.529 (hCoV-19/Japan/NC928-2N/2021) Diamond (MD) K18-hACE2 transgenic mice Weight loss; Virus titer in Lungs RT-qPCR and Infectious virus titer 3 WA1/2020-D614G B.1.1.529 (hCoV-19/USA/WI-WSLH-221686/2021) Boon (AB) Syrian Hamster Weight loss; Virus titer in Nasal wash and Lungs RT-qPCR 4 WA1/2020-D614G B.1.1.529 (hCoV-19/USA/WI-WSLH-221686/2021) Seder (RS) Syrian Hamster Weight loss - - B.1.1.529 (hCoV-19/USA/GA-EHC-2811C/2021) B.1.617.2 (hCoV-19/USA/PHC658/202) Garcia-Sastre (AGS) 129 mice Weight loss; Virus titer in Nasal turbinates and Lungs Infectious virus titer 4 B.1.1.529 (hCoV-19/USA/NY-MSHSPSP-PV44476/2021) B.1.1.529 (hCoV-19/USA/NY-MSHSPSP-PV44488/2021) B.1.351 (hCoV-19/USA/MD-HP01542/2021)  K18-hACE2 transgenic mice Weight loss; Virus titer in Nasal turbinates and Lungs; Cytokine production Infectious virus titer 3 B.1.1.529 (hCoV-19/USA/NY-MSHSPSP-PV44476/2021) B.1.351 (hCoV-19/USA/MD-HP01542/2021) Perlman (SP) C57BL/6 mice Weight loss - - B.1.1.529 (hCoV-19/USA/GA-EHC-2811C/2021) B.1.351 (hCoV19/20H/501Y.V2) B.1.1.7 (hCoV-19/USA/CA_CDC_5574/2020) Suthar (MS) 129 mice Weight loss; Virus titer in Nasal turbinates and Lungs RT-qPCR 3 B.1.1.529 (hCoV-19/USA/GA-EHC-2811C/2021) B.1.351 (hCoV-19/USA/MD-HP01542/2021) Webby (RW) Syrian hamster Weight loss; Virus titer in Nasal wash RT-qPCR 4 B.1.1.529 (hCoV-19/USA/GA-EHC-2811C/2021) USA-WA1/2020  * Whole Body Plethysmography, & Computerized tomography scan     	Supplementary Table 2. Alignment of Key Sequence Changes in B.1.1.529 Omicron Isolates  Gene NT change AA changea 7263803b 7171744b 7507055b 7908052b 7908059b ORF1ab A2832G K856R          ORF1ab 6513_6515 del SL2083I          ORF1ab G8393A A2710T          ORF1ab C10029T T3255I          ORF1ab C10449A P3395H          ORF1ab 11288_11296 del SGF3675 del          ORF1ab C14408T P4715L          ORF1ab A18163G I5967V          ORF1ab C21034T L6924F          S C21762T A67V          S 21765_21770 del HV69 del          S C21846T T95I          S 21987_21995 del G142D          S 21987_21995 del VYY143 del          S 22194_22196 del NL211I          S 22205GAGCCAGAA ins 214EPE ins          S G22578A G339D          S C22674T S371F          S T22679C S373P          S C22686T S375F          S G22813T K417N          S T22882G N440K          S G22898A G446S          S G22992A S477N          S C22995A T478K          S A23013C E484A          S A23040G Q493R          S G23048A G496S          S A23055G Q498R          S A23063T N501Y          S T23075C Y505H          S C23202A T547K          S A23403G D614G          S C23525T H655Y          S T23599G N679K          S C23604A P681H          S C23632T A701V          S C23854A N764K          S G23948T D796Y          S C24130A N856K          S A24424T Q954H          S T24469A N969K          S C24503T L981F          E C26270T T9I          M A26530G D3G          M C26577G Q19E          M G26709A A63T          N C28311T P13L          N 28362_28370 del ERS31 del          N G28881A, G28882A, G28883C RG203KR          	aGreen cells indicate the presence of indicated amino acid substitution in a given isolate; white cells indicate the absence of the substitution in a given isolate. b Isolate identifiers correspond to GISAID sequences Supplemental Table 3: Cytokine and chemokine concentration in SARS-CoV-2-infected K18-hACE2 transgenic mice Cytokine/Chemokine Concentration (mean + SD (pg/mL)) Mock B.1.351 B.1.1.529 + A701V IL-10 2.7 + 0.9 2.0 + 0.0 3.2 + 1.5 IL-1β 1.4 + 0.0 2.3 + 1.0 1.6 + 0.2 IL-2 7.8 + 1.8 4.7 + 2.6 7.1 + 5.5 CXCL10 17.8 + 0.7 155.4 + 4.7 42.8 + 28.1 IL-4 1.4 + 0.0 1.4 + 0.0 1.4 + 0.0 IL-5 2.2 + 0.0 5.4 + 2.3 5.2 + 4.5 IL-6 6.7 + 1.7 452.2 + 357.8 12.5 + 7.5 IL-22 13.0 + 0.0 13.6 + 1.1 14.2 + 2.1 IL-9 38.7 + 15.4 34.3 + 14.6 56.9 + 32.0 IL-13 2.9 + 0.0 2.9 + 0.0 3.2 + 0.6 IL-27 2.8 + 0.2 2.7 + 0.1 2.6 + 0.0 IL-23 19.3 + 6.3 26.8 + 13.3 37.1 + 28.2 IFN-γ 2.2 + 0.0 4.9 + 2.8 2.2 + 0.0 IL-12p70 2.3 + 0.0 2.8 + 0.5 2.3 + 0.0 GM-CSF 3.2 + 0.0 8.0 + 1.4 3.4 + 0.4 CXCL1 20.1 + 1.8 136.8 + 80.6 25.0 + 11.5 CCL5 441.3 + 98.9 453.1 + 226.1 268.5 + 165.9 TNF-α 3.7 + 0.0 14.9 + 12.0 5.1 + 2.0 CCL3 8.2 + 1.2 59.6 + 7.4 10.4 + 4.1 CCL7 34.0 + 26.5 790.0 + 363.8 57.1 + 42.7 CCL2 77.8 + 9.8 535.3 + 343.0 91.9 + 47.4 IL-17A 156.3 + 0.0 156.3 + 0.0 172.4 + 28.0 CXCL2 9.5 + 0.1 27.9 + 3.4 13.8 + 4.5 CCL11 175.6 + 29.6 212.9 + 75.6 387.7 + 306.3 IL-18 78.2 + 34.4 220.2 + 124.1 89.1 + 50.6 CCL4 14.9 + 1.5 34.0 + 15.4 9.9 + 3.9   

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

https://digitalcommons.wustl.edu/cgi/viewcontent.cgi?filename=0&article=12641&context=open_access_pubs&type=additional

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

Abstract

Similar works

Full text

Available Versions

Digital Commons@Becker