sj-docx-1-cad-10.1177_00111287221126075 – Supplemental material for Examining Avoidance, Victimization Risk, and Perceptions of Community Safety in Latinx Communities

Supplemental material, sj-docx-1-cad-10.1177_00111287221126075 for Examining Avoidance, Victimization Risk, and Perceptions of Community Safety in Latinx Communities by Alexis Yohros, Isabel Geisler, Sarah Lockwood, Emelyn Miller, Candence Wills, Amy Farrell and Carlos Cuevas in Crime & Delinquency</p

Summary of radiological scoring.

All thorax radiographs were scored blinded by a veterinary radiologist, with scores of 0 to 3 assigned to each of the 7 lung lobes. For each time point, the total score of all lung lobes was tabulated. Thus, the maximum score per time point is 21. (DOCX)</p

Multivariable correlation analysis.

(A). Spearman r correlation matrix in heatmap format. For this analysis, lung pathology scores are the interstitial cellularity scores (from Fig 7). Lung ISH are the in situ hybridization data of Fig 6. Peak NT50 represents the peak neutralizing antibody titers up to day 5 (i.e., prior to possible de novo antibody responses). VITROS anti-spike total Ig represents the peak value for each animal (i.e., day 2; Fig 2). Nasal, oropharyngeal and BAL sgRNA values are based on AUC of the data in S7 Fig. Clinical scores (sedated and cage-side) are the tabulated scores of each animal over the 7-day observation period (Fig 3C and 3F). (B) Correlation between neutralizing antibody peak NT50 values and lung pathology scores (Spearman r = -0.87; p < 0.0005). The labels next to each symbol indicate the individual animal.</p

Lack of effect of convalescent plasma on sgRNA kinetics in nasal and oropharyngeal swabs and BAL of SARS-CoV-2 infected macaques.

A weighted average analysis was performed on the sgRNA data from nasal and oropharyngeal swabs and BAL (S7 Fig.) to calculate the relative decline of viral RNA (relative to cellular mRNA in the sample) from day 1 to day 7. For each animal, the AUC of relative sgRNA per cellular mRNA over time was tabulated using day 1 as baseline value, and then divided by 6 days to get the weighted average in the decline of sgRNA over the 6-day time period. Lines indicate mean values. On panel C, animal CCP-2 was excluded, as it had no detectable viral RNA in the BAL sample, which precluded this analysis. Statistical analysis revealed no effects between the control and CCP groups (panel A, p = 0.29; panel B: p = 0.30; panel C, p = 0.88; unpaired t-test). (TIFF)</p

Quantitation of SARS-CoV-2 RNA-positive cells in lung sections.

In situ hybridization (RNAScope) was used to detect viral RNA in lung sections. (A) For each animal, the number of positive cells was counted in approximately 20 fields of right caudal lung lobe. Lines indicate median values. There were no differences between both study groups (p = 0.89, Mann Whitney test). (B) Example of lung section of animal CCP-2, with the arrows indicating RNA-positive cells.</p

Time course of additional cytokines and chemokines in plasma of SARS-CoV-2 inoculated animals.

Cytokines and chemokines presented in this panel were ones that did not show consistent changes among animals. The legend is the same as that of S4 Fig. (TIFF)</p

Multivariable correlation analysis on CCP-treated animals.

Multivariate analysis was performed on the 8 CCP-treated animals only. (A). Spearman r correlation matrix in heatmap format. For this analysis, the markers used are the same ones as in Fig 8. (B) Correlation between neutralizing antibody peak NT50 values and clinical scores based on cage-side observations (Spearman r = -0.77; p = 0.04). (TIFF)</p

Clinical measurements collected at time of sedation.

Red and black arrows indicate time of virus inoculation and monoclonal antibody administration on days 0 and 1, respectively. (A) Body weight remained stable. (B) Rectal temperature; horizontal line indicates the cut-off of 103° F, above which ketoprofen treatment was administered. (C) Respiratory rate; the horizontal line indicates a cut-off value of 55 (per minute) as upper normal range. (D) Oxygen saturation measured by pulse oximetry; the horizontal line indicates 95% as the lower end cut-off of the normal range. Total clinical scores, including the markers not graphed above, are presented in Fig 3. (TIFF)</p

Animal demographics.

(DOCX)</p

Innate and adaptive immune responses following infection.

(A) Representative gating strategy for innate immune cells in whole blood. Fluorochromes used: CD66:APC, CD20/CD3/Dead: APC-Cy7, Ki67:AF488, CD14:AF700, CD123:BV421, CD16:BV605, HLA-DR:BV786, CD11c:PE-Cy7. Kinetics of circulating neutrophils, proinflammatory monocytes, mDCs, and pDCs measured at 0,1,3,5, and 7 days post SARS-CoV-2 infection. (B) Representative T cell gating strategy from whole blood. Fluorochromes used: CD25: APC, CD20/Dead: APC-Cy7, Ki67:AF488, CD3:AF700, CD95:BUV737, CD8:BUV805, CD4:BV650, CD69:BV711, CD28:PECF594, PD-1:PE-Cy7. Kinetics of circulating naïve, central memory, effector memory populations, and Ki67+PD-1+ memory cells of CD4 T cell. Kinetics of circulating naïve, central memory, effector memory, and CD69+ effector memory CD8 T cells. Significance was calculated using one tailed paired t test comparing pooled convalescent plasma and normal plasma animals against Day 0 *p = 0.05, **p = 0.01, ***p = 0.001. Statistical analysis yielded no significant different between convalescent and normal plasma groups. (PDF)</p