generalized linear model with pearson's chi-square  (CH Instruments)

Journal: Nature Communications

Article Title: Immunization with V987H-stabilized Spike glycoprotein protects K18-hACE2 mice and golden Syrian hamsters upon SARS-CoV-2 infection

doi: 10.1038/s41467-024-46714-w

Figure Lengend Snippet: SARS-CoV-2 viral load was analyzed in oropharyngeal swabs, and samples from nasal turbinate, lung, and brain of K18-hACE2 mice upon challenge. Virus distribution and tissue damage were analyzed by histopathology. Four mice per timepoint were analyzed, with two exceptions: 1) day 0: S-V987H = 2, RBD = 3, and Infected control = 3; and 2) days 6–7: Infected control = 8 a Levels of SARS-CoV-2 gRNA (expressed as logarithmic of copies/mL) in oropharyngeal swabs, nasal turbinate, lung, and brain during infection. Dot line indicates limit of detection (100 copies/mL). Differences between animals were analyzed using two-sided Peto & Peto left-censored k sample test, correcting by FDR. b Titer of infectious virions (IVs) in oropharyngeal swabs, nasal turbinate, lung, and brain during infection. Results are shown as Log10 of Median Tissue Culture Infectious Dose per mL (TCID50/mL). Differences between groups were analyzed as indicated in ( a ) . c Detection of SARS-CoV-2 nucleocapsid protein in brain, lung, and nasal turbinate by immunohistochemistry. Staining score: (0) no, (1) low, (2) moderate, and (3) high amount of viral antigen. d Histopathological analysis of nasal turbinate, lung and brain by hematoxylin and eosin staining. Lesion score: (0) no, (1) mild, (2) moderate, and (3) severe lesion. Differences between groups were analyzed using two-sided Asymptotic Generalized Pearson Chi-Squared test with FDR correction. * p < 0.05, ** p < 0.01. P values proximal to statistical significance are shown as numbers. Mean plus standard error of the mean (SEM) are shown. Data represented in Fig. 3 correspond to one experiment. Source data are provided as a Source Data Fig. 3.

Article Snippet: Histopathology analysis was carried out using two-tailed Asymptotic Generalized Pearson Chi-Squared test with FDR correction.

Techniques: Virus, Histopathology, Infection, Control, Immunohistochemistry, Staining

Journal: Nature Communications

Article Title: Immunization with V987H-stabilized Spike glycoprotein protects K18-hACE2 mice and golden Syrian hamsters upon SARS-CoV-2 infection

doi: 10.1038/s41467-024-46714-w

Figure Lengend Snippet: SARS-CoV-2 viral load was analyzed in oropharyngeal swabs, and samples from nasal turbinate and lung of infected GSHs. Virus distribution and tissue damage was analyzed by histopathology. S-2P, S-V987H and infected control n = 4 per group and timepoint. Uninfected control n = 4 on day 7. a Levels of SARS-CoV-2 gRNA, expressed as Log10 copies/mL, in oropharyngeal swabs, nasal turbinate and lung during infection. Dot line indicates limit of detection (100 copies/mL). Differences between groups were analyzed using two-sided Peto & Peto left-censored k sample test with FDR correction. b Titer of infectious virions determined in samples from nasal turbinate, oropharyngeal swab, and lung. Data are shown as Log10 of Median Tissue Culture Inhibition Dose per mL (TCID50/mL). Mean plus standard error of the mean (SEM) are shown. c Detection of SARS-CoV-2 nucleocapsid protein in lung and nasal turbinate by immunohistochemistry. Staining score: (0) no, (1) low, (2) moderate, and (3) high amount of viral antigen. d Histopathologic analysis of nasal turbinate and lung by hematoxylin and eosin staining. Lesion score: (0) no, (1) mild, (2) moderate, and (3) severe lesion. Differences between groups were analyzed by the two-sided Asymptotic Generalized Pearson Chi-Squared test corrected using FDR. Mean plus standard errors of the means (SEM) are shown. * p < 0.05, ** p < 0.01, *** p < 0.001. Data represented in Fig. 5 correspond to one experiment. Source data are provided as a Source Data Fig. 5.

Article Snippet: Histopathology analysis was carried out using two-tailed Asymptotic Generalized Pearson Chi-Squared test with FDR correction.

Techniques: Infection, Virus, Histopathology, Control, Inhibition, Immunohistochemistry, Staining

Journal: Nature Communications

Article Title: Immunization with V987H-stabilized Spike glycoprotein protects K18-hACE2 mice and golden Syrian hamsters upon SARS-CoV-2 infection

doi: 10.1038/s41467-024-46714-w

Figure Lengend Snippet: SARS-CoV-2 viral load was analyzed in oropharyngeal swabs, and samples from nasal turbinate, lung and brain of infected K18-hACE2 mice. Virus distribution and tissue damage was analyzed by immunohistochemistry and histopathology. S-2P group: n = 6 on days 3 and 6; n = 8 on day 14, n = 1 clinical endpoints. S-V987H: n = 6 on days 3 and 6, n = 9 on day 14. Infected control: n = 6 on day 3, n = 2 on day 6, and n = 8 on clinical endpoints. Uninfected control: n = 10 on day 14. a Levels of SARS-CoV-2 gRNA (expressed as log10 of copies/mL) in oropharyngeal swabs, nasal turbinate, lung, and brain during infection. Dot line indicates limit of positivity (100 copies/mL). Differences between groups were analyzed using two-sided Peto & Peto left-censored k sample test with FDR correction. b Titer of infectious virions determined in samples from nasal turbinate, oropharyngeal swab, lung and brain. Data are shown as Log10 of Median Tissue Culture Inhibition Dose per mL (TCID50/mL). Data were analyzed as indicated in ( a ). c Detection of SARS-CoV-2 nucleocapsid protein in brain, lung, and nasal turbinate by immunohistochemistry. Staining score: (0) no, (1) low, (2) moderate, and (3) high amount of viral antigen. d Histopathological analysis of brain, lung, and nasal turbinate by hematoxylin and eosin staining. Lesion score: (0) no, (1) mild, (2) moderate, and (3) severe lesion. Differences between groups were analyzed using two-sided Asymptotic Generalized Pearson Chi-Squared test with FDR correction. Mean plus standard error of the mean (SEM) is shown in ( a, b, c , and d ). * p < 0.05, ** p < 0.01. Data represented in Fig. 7 correspond to one experiment. Source data are provided as a Source Data Fig. 7.

Article Snippet: Histopathology analysis was carried out using two-tailed Asymptotic Generalized Pearson Chi-Squared test with FDR correction.

Techniques: Infection, Virus, Immunohistochemistry, Histopathology, Control, Inhibition, Staining

Journal: Nature Communications

Article Title: Immunization with V987H-stabilized Spike glycoprotein protects K18-hACE2 mice and golden Syrian hamsters upon SARS-CoV-2 infection

doi: 10.1038/s41467-024-46714-w

Figure Lengend Snippet: K18-hACE2 mice were immunized twice with S-V987H or S-2P, adjuvanted with AddaVax. Then, mice were challenged with the SARS-CoV-2 Omicron BQ1.1 VoC. The humoral response, weight changes and survival of mice were evaluated after immunization and/or viral challenge. Tissue damage and viral loads were also analyzed. a Overview of vaccine strategy and infection timeline. Blood drops indicate collection of biological samples. b Kinetics of anti-RBD antibodies in serum samples expressed as arbitrary units (arb. units). Red triangles: S-2P group ( n = 18). Blue squares: S-V987H group ( n = 18). White circles: unvaccinated-challenged mice ( n = 18) (Infected control). Gray circles: uninfected and unvaccinated mice ( n = 6) (Uninfected control). Groups in each time point were analyzed using two-sided Conover-Iman test with multiple comparison correction by FDR. Differences among animals within a particular group along time were analyzed using two-sided Friedman test with FDR correction. c Percentage of weight variation in SARS-CoV-2 B.1.351 infected K18-hACE2 mice over time. Statistical analysis was performed against the unvaccinated and challenged group using two-sided Kruskal-Wallis test with FDR correction. S-2P, S-V987H, and unvaccinated-challenged mice: n = 18 on days 0–3, n = 12 on days 4–6, n = 6 on days 7–14. Uninfected and unvaccinated mice: n = 6 on days 0-14. d Levels of SARS-CoV-2 gRNA (expressed as logarithmic of copies/mL) in oropharyngeal swabs, nasal turbinate, lung, and brain during infection. Dot line indicates limit of positivity (100 copies/mL). Differences between groups were analyzed using two-sided Peto & Peto left-censored k sample test with FDR correction. e Histopathological analysis of lung and brain by hematoxylin and eosin staining. Lesion score: (0) no, (1) mild, (2) moderate, and (3) severe lesion. f Detection of SARS-CoV-2 nucleocapsid protein in lung and brain by immunohistochemistry. Staining score: (0) no, (1) low, (2) moderate, and (3) high amount of viral antigen. Differences between groups in ( e ) and ( f ) were analyzed using two-sided Asymptotic Generalized Pearson Chi-Squared test with FDR correction. Statistically significant differences are indicated as follows: * p < 0.05, ** p < 0.01, *** p < 0.001. Mean plus standard errors of the means (SEM) are shown. Samples distribution in ( d , e and f ) is as described in ( b ). Data represented in Fig. 8 correspond to one experiment. Source data are provided as a Source Data Fig. 8.

Article Snippet: Histopathology analysis was carried out using two-tailed Asymptotic Generalized Pearson Chi-Squared test with FDR correction.

Techniques: Infection, Control, Comparison, Staining, Immunohistochemistry