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1 doi: /nature12391 Table 1. Binding of A(H7N9) viruses to individual glycan structures. # Structure a Anhui1 Shanghai1 1 Neu5Acα nb nb 2 Neu5Acα ++ nb 3 Neu5Acβ nb nb 4 Neu5Acα2-3(6-O-Su)Galβ1-4GlcNAcβ nb nb 5 Neu5Acα2-3Galβ1-3[6OSO3]GalNAcα nb nb 6 Neu5Acα2-3Galβ1-4[6OSO3]GlcNAcβ Neu5Acα2-3Galβ1-4(Fucα1-3)[6OSO3]GlcNAcβ-propyl-NH Neu5Acα2-3Galβ1-3[6OSO3]GlcNAc-propyl-NH Neu5Acα2-3Galβ1-3(Neu5Acα2-3Galβ1-4)GlcNAcβ Neu5Acα2-3Galβ1-3(Neu5Acα2-3Galβ1-4GlcNAcβ1-6)GalNAcα Neu5Acα2-3Galβ1-4GlcNAcβ1-2Manα1-3(Neu5Acα2-3Galβ1-4GlcNAcβ1-2Manα1-6)Manβ1-4GlcNAcβ1-4GlcNAcβ Neu5Acα(2-3)-Galβ(1-4)-GlcNAcβ(1-3)-Galβ(1-4)-GlcNAcβ(1-2)-Manα(1-3)- [Neu5Acα(2-3)-Galβ(1-4)-GlcNAcβ(1-3)-Galβ(1-4)-GlcNAcβ(1-2)-Manα(1-6)]-Manβ(1-4)-GlcNAcβ(1-4)-GlcNAcβ Neu5Acα2-3Galβ nb Neu5Acα2-3Galβ1-3GalNAcα Neu5Acα2-3Galβ1-3GlcNAcβ Neu5Acα2-3Galβ1-3GlcNAcβ Neu5Acα2-3Galβ1-4Glcβ + nb 18 Neu5Acα2-3Galβ1-4Glcβ nb Neu5Acα2-3Galβ1-4GlcNAcβ nb nb 20 Neu5Acα2-3Galβ1-4GlcNAcβ nb Neu5Acα2-3GalNAcβ1-4GlcNAcβ nb + 22 Neu5Acα2-3Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ + nb 23 Neu5Aca2-3Galβ1-3GlcNAcβ1-3Galβ1-4GlcNAcβ nb Neu5Acα2-3Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ ++ nb 25 Neu5Acα2-3Galβ1-4GlcNAcβ1-3Galβ1-3GlcNAcβ Neu5Acα2-3Galβ1-3GalNAcα nb Galβ1-3(Neu5Acα2-3Galβ1-4(Fucα1-3)GlcNAcβ1-6)GalNAcα Neu5Acα2-3Galβ1-3(Fucα1-4)GlcNAcβ nb Neu5Acα2-3Galβ1-4(Fucα1-3)GlcNAcβ nb Neu5Acα2-3Galβ1-4(Fucα1-3)GlcNAcβ Neu5Acα2-3Galβ1-4(Fucα1-3)GlcNAcβ1-3Galβ Neu5Acα2-3Galβ1-3[Fucα1-4]GlcNAcβ1-3Galβ1-4[Fucα1-3]GlcNAcβ Neu5Acα2-3Galβ1-3[Fucα1-3]GlcNAcβ1-3Galβ1-4[Fucα1-3]GlcNAcβ Neu5Acα2-3Galβ1-4(Fucα1-3)GlcNAcβ1-3Galβ1-4(Fucα1-3)GlcNAcβ1-3Galβ1-4(Fucα1-3)GlcNAcβ Neu5Acα2-3(GalNAcβ1-4)Galβ1-4GlcNAcβ nb nb 36 Neu5Acα2-3(GalNAcβ1-4)Galβ1-4GlcNAcβ Neu5Acα2-3(GalNAcβ1-4)Galβ1-4Glcβ nb nb 38 Galβ1-3GalNAcβ1-4(Neu5Acα2-3)Galβ1-4Glcβ nb nb 39 Fucα1-2Galβ1-3GalNAcβ1-4(Neu5Acα2-3)Galβ1-4Glcβ nb nb 40 Fucα1-2Galβ1-3GalNAcβ1-4(Neu5Acα2-3)Galβ1-4Glcβ nb nb 41 Neu5Acα2-6Galβ1-4[6OSO3]GlcNAcβ + nb 1
2 42 Neu5Acα2-6Galβ1-4GlcNAcβ1-2Manα1-3(Galβ1-4GlcNAcβ1-2Manα1-6)Manβ1-4GlcNAcβ1-4GlcNAcβ nb nb 43 Neu5Acα2-6Galβ1-4GlcNAcβ1-2Manα1-3(Neu5Acα2-6Galβ1-4GlcNAcβ1-2Manα1-6)Manβ1-4GlcNAcβ1-4GlcNAcβ ++ nb 44 Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ1-2Manα1-3[Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ1-2Manα1-6]Manβ1-4GlcNAcβ1-4GlcNAcβ +++ nb 45 Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ1-2Manα1-3[Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ1-2Manα1-6]- Manβ1-4GlcNAcβ1-4GlcNAcβ Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ1-3[Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ1-6]GalNAca ++ nb 47 Neu5Acα2-6Galβ1-4GlcNAcβ1-3[Neu5Acα2-6Galβ1-4GlcNAcβ1-6]GalNAca ++ nb 48 Neu5Acα2-6GalNAcα Neu5Acα2-6Galβ nb nb 50 Neu5Acα2-6Galβ1-4Glcβ nb nb 51 Neu5Acα2-6Galβ1-4Glcβ + nb 52 Neu5Acα2-6Galβ1-4GlcNAcβ nb nb 53 Neu5Acα2-6Galβ1-4GlcNAcβ nb nb 54 Neu5Acα2-6GalNAcβ1-4GlcNAcβ + nb 55 Neu5Acα2-6Galβ1-4GlcNAcβ1-3GalNAcα nb nb 56 Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ + nb 57 Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ1-3GalNAcα nb nb 58 Neu5Aca2-6Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ ++ nb 59 Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4(Fucα1-3)GlcNAcβ1-3Galβ1-4(Fucα1-3)GlcNAcβ + nb 60 Galβ1-3(Neu5Acα2-6)GlcNAcβ1-4Galβ1-4Glcβ-Sp Neu5Acα2-6[Galβ1-3]GalNAca nb nb 62 Neu5Acα2-6Galβ1-4GlcNAcβ1-6[Galβ1-3]GalNAca Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ1-6[Galβ1-3]GalNAca + nb 64 Neu5Acα2-3Galβ1-4GlcNAcβ1-2Manα1-3(Neu5Acα2-6Galβ1-4GlcNAcβ1-2Manα1-6)Manβ1-4GlcNAcβ1-4GlcNAcβ + nb 65 Neu5Acα2-6Galβ1-4GlcNAcβ1-2Manα1-3(Neu5Acα2-3Galβ1-4GlcNAcβ1-2Manα1-6)Manβ1-4GlcNAcβ1-4GlcNAcβ Neu5Acα2-3Galβ1-3(Neu5Acα2-6)GalNAcα Neu5Acα2-3(Neu5Acα2-6)GalNAcα + nb 68 Neu5Gcα + nb 69 Neu5Gcα2-3Galβ1-3(Fucα1-4)GlcNAcβ nb nb 70 Neu5Gcα2-3Galβ1-3GlcNAcβ nb + 71 Neu5Gcα2-3Galβ1-4(Fucα1-3)GlcNAcβ nb Neu5Gcα2-3Galβ1-4GlcNAcβ nb Neu5Gcα2-6GalNAcα nb nb 74 Neu5Gcα2-6Galβ1-4GlcNAcβ nb nb 75 Neu5Acα2-8Neu5Acα nb nb 76 Neu5Acα2-8Neu5Acα2-8Neu5Acα nb nb 77 Neu5Acα2-8Neu5Acα2-3(GalNAcβ1-4)Galβ1-4Glcβ nb nb 78 Neu5Acα2-8Neu5Acα2-3Galβ1-4Glcβ nb nb 79 Neu5Acα2-8Neu5Acα2-8Neu5Acα2-3(GalNAcβ1-4)Galβ1-4Glcβ + nb 80 Neu5Acα2-8Neu5Acα2-8Neu5Acα2-3Galβ1-4Glcβ + nb 81 Neu5Acα2-8Neu5Acβ-Sp17 + nb 82 Neu5Acα2-8Neu5Acα2-8Neu5Acβ nb nb 83 Neu5Acβ2-6GalNAcα nb nb 3 2
3 84 Neu5Acβ2-6Galβ1-4GlcNAcβ Neu5Gcβ2-6Galβ1-4GlcNAc nb nb 86 Galβ1-3(Neu5Acβ2-6)GalNAcα nb nb 87 [9NAc]Neu5Acα nb nb 88 [9NAc]Neu5Acα2-6Galβ1-4GlcNAcβ nb nb 89 Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ1-3Galβ1-4GlcNAcβ nb nb 90 Galβ1-3GlcNAcβ1-3Galβ1-3GlcNAcβ + nb 91 Galβ1-4GlcNAcβ1-2Manα1-3[Galβ1-4GlcNAcβ1-2Manα1-6]Manβ1-4GlcNAcβ1-4GlcNAcβ nb nb 92 GalNAcα1-3(Fucα1-2)Galβ1-3GlcNAcβ nb nb 93 GalNAcα1-3(Fucα1-2)Galβ1-4GlcNAcβ nb nb 94 Galα1-3(Fucα1-2)Galβ1-3GlcNAcβ + nb 95 Galα1-3(Fucα1-2)Galβ1-4(Fucα1-3)GlcNAcβ ++ nb 96 Galβ1-3GalNAcα nb nb a Glycan microarray differences between Anhui1 and Shanghai1. The color coding in the left hand column reflects the same coloring scheme used in Figure 1. Significant binding of samples to glycans were qualitatively estimated based on relative strength of the signal for the data shown in the figure; fluorescence intensity strong (+++), medium (++), weak (+), no binding (nb). Different categories of glycans on the array are color-coded in column 1 as follows: No color, sialic acid; blue, α2-3 sialosides; red, α2-6 sialosides, violet, mixed α2-3/α2-6 biantennaries; green, N-glycolylneuraminic acid-containing glycans; brown, α2-8 linked sialosides; pink, β2-6 linked and 9-O-acetylated sialic acids; grey, asialo glycans. 3
4 Table 2. Complete blood counts of H7N9 and H3N2 influenza virus-infected ferrets. Blood count ± SD (K/µl) b Cell type a Day p.i. Texas/50 Anhui/1 Shanghai/1 WBC ± ± ± ± ± ± ± ± ± 2.9 LY ± 1.0 (63.9%) 4.33 ± 1.3 (64.5%) 6.43 ± 3.2 (71.0%) ± 0.8 (51.0%) 3.12 ± 1.1 (41.4%) 3.67 ± 2.1 (53.4%) ± 2.5 (52.5%) 3.85 ± 1.3 (43.1%) 5.26 ± 2.3 (56.9%) NE ± 0.9 (27.9%) 1.75 ± 0.6 (26.0%) 1.68 ± 0.7 (19.8%) ± 1.4 (31.2%) 3.21 ± 1.2 (42.9%) 1.84 ± 0.8 (28.6%) ± 0.4 (35.5%) 3.40 ± 1.3 (38.4%) 2.13 ± 0.8 (25.3%) MO ± 0.2 (6.53%) 0.56 ± 0.3 (8.22%) 0.66 ± 0.2 (7.93%) ± 0.2 (8.28%) 0.87 ± 0.5 (12.9%) 1.11 ± 0.6 (16.8%) ± 0.1 (10.1%) 1.54 ± 0.7 (16.7%) 1.48 ± 0.6 (16.6%) EO ± 0.1 (1.49%) 0.11 ± 0.1 (1.69%) 0.12 ± 0.1 (1.03%) ± 0.1 (2.2%) 0.17 ± 0.2 (2.12%) 0.07 ± 0.1 (1.04%) ± 0.1 (1.94%) 0.13 ± 0.1 (1.55%) 0.02 ± 0.1 (1.0%) BA ± 0.1 (0.16%) 0.01 ± 0.1 (0.20%) 0.03 ± 0.1 (0.29%) ± 0.1 (0.08%) 0.06 ± 0.1 (0.56%) 0.01 ± 0.1 (0.22%) ± 0.1 (0.10%) 0.01 ± 0.1 (0.18%) 0.01 ± 0.1 (0.22%) PLT ± ± ± ± ± ± ± ± ± 83 a WBC, total white blood cells; LY, total lymphocytes; NE, total neutrophils; MO, total monocytes; EO, total eosinophils; BA, total basophils; PLT, total platelets. b Values are mean total count for each cell type ± standard deviation of 6-11 ferrets; the percentage of each cell subset among all circulating white blood cells is denoted in parentheses where appropriate. 4
5 Table 3. Replication of H7 influenza viruses following ocular inoculation in mice. Virus titer a Tissue Day p.i. Shv/Egypt/07 Anhui/1 Shanghai/1 Eye (1/3) < (1/3) Nose 3 < ± 1.0 (2/3) 3.2 ± 0.2 (2/3) Lung 3 <10 <10 <10 Eye 6 <10 < ± 0.1 (2/3) Nose ± 1.5 (2/3) 3.2 ± ± 0.7 (2/3) Lung 6 <10 < (1/3) a Mean virus titers in mice inoculated with 10 6 PFU/5µl of virus following corneal scarification. Virus titers are expressed as the mean log 10 PFU ± standard deviation among mice with positive virus detection (data are representative of all mice examined, unless denoted in parentheses, in which the number of mice with positive virus detection/total number of mice in the group are indicated). The limit of virus detection was 10 PFU. 5
6 Figure 1. Morbidity following H7N9 virus infection in ferrets. Ferrets were intranasally inoculated with 10 6 PFU of Anhui/1 or Shanghai/1 (A) virus, and monitored daily for morbidity (as measured by weight loss) and mortality (filled circles). Any ferret which exhibited severe lethargy or lost >25% initial body weight was euthanized (denoted by *). A naïve ferret was placed in the same cage as each inoculated ferret 24 hours p.i. (DC transmission, filled squares) or in an adjacent cage with perforated side-walls (RD transmission, open squares) and were monitored daily for morbidity and mortality (B). Results from individual ferrets with positive virus isolation from nasal washes are presented. 6
7 Figure 2. Detection of H7N9 and H3N2 viruses in ferret tissues. Three ferrets were intranasally inoculated with 10 6 PFU of Anhui/1 (H7N9), Shanghai/1 (H7N9), or Texas/50 (H3N2) virus. Tissues were collected 3 days p.i. for determination of virus titer. NT, nasal turbinates; Tr, trachea; Bn OB, olfactory bulb; Bn Ant, anterior brain; Bn Pos, posterior brain; Bd, blood; Sp, spleen; Kd, kidney; Int, intestine (pooled ducdenum, jejuno-ileal loop, and descending colon); Lv, liver; Eye, pooled right and left eyes; Conj, pooled right and left conjunctiva. Mean virus titers of positive samples only are presented as log 10 PFU/g plus standard deviation for all tissues except NT, Bd, Eye, Conj which are expressed as PFU/ml. Anhui/1 brain, liver, and conjunctivitis titers are reflective of 1/3 positive ferrets; Shanghai/1 brain titers are reflective of 2/3 positive ferrets; Texas/50 nasal turbinate titers are reflective of 2/3 positive ferrets. The limit of detection was 10 PFU. 7
8 Figure 3. Comparison of H7N9 and H3N2 virus recovery in conjunctival wash and rectal swab samples in ferrets. Ferrets were inoculated with 10 6 PFU of Texas/50 (H3N2, n=6) (A), Anhui/1 (H7N9, n=11) (B) or Shanghai/1 (H7N9, n=8) (C) virus. Viral titers were measured in conjunctival washes (CW) or rectal swabs (RS) collected on indicated days p.i. Results from individual ferrets are expressed as log 10 PFU/ml. The limit of virus detection was 10 PFU. 8
9 Figure 4. Transmissibility of H7N9 and H3N2 viruses in the ferret model. Groups of ferrets (6 to 10) were intranasally inoculated with 10 6 PFU of Texas/50 (A), Anhui/1 (B) virus, or Shanghai/1 (C) virus, respectively. Nasal washes were collected from each ferret on indicated days p.i. (Left). A naïve ferret was placed in the same cage as each inoculated ferret 24 hours p.i. (DC transmission) or in an adjacent cage with perforated side-walls (RD transmission) and nasal washes were collected from each contact ferret on indicated days p.c. (Right). Results from individual ferrets are presented. The limit of virus detection was 10 PFU. 9
10 Figure 5. Disease outcome and replication following H7N9 and H9N2 virus infection in mice. Groups of five mice were intranasally inoculated with 10 6 PFU of Anhui/1 (H7N9), Shanghai/1 (H7N9), shv/egypt/07 (H7N9), or ck/vn/11 (H9N2) virus and monitored daily for morbidity (as measured by weight loss), (A) and mortality (B). Any mouse which lost >25% initial body weight was euthanized. Lungs (C) and noses (D) were collected days 3 and 6 p.i. from three mice per group for determination of viral titer. Titers are expressed as mean log 10 PFU/ml plus standard deviation. The limit of detection was 10 PFU. *, p<0.05 by one-way ANOVA with a Bonferroni post-test. 10
11 Figure 6. Cytokine and chemokine production in influenza virus infected mouse lungs. Groups of three mice were intranasally inoculated with influenza virus, and lungs were removed at the indicated days p.i. and frozen at -70 C until processed. Clarified cell lysates from lungs homogenized in 1ml cold PBS were analyzed with the BioPlex Mouse Cytokine 23-Plex panel (BioRad). The constitutive cytokine levels present in the lung were determined by harvesting lungs of mice inoculated with PBS as a mock control. The mean cytokine levels plus standard deviation are shown. Baseline levels in mock: IL-6 and IFNγ, undetectable; IL-10, 65.7pg; MCP- 1, 987.8pg; MIP-1α, 98.9pg; MIP-1β, 472pg. 11
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