SIV RNA levels in genital tract tissues at 11 weeks post infection.

b<p>log10 vRNA copies per ug tissue RNA.</p

Highlighter plots of SGA derived env sequences from macaque 36199.

<p>(A) Highlighter plot of SIV <i>env</i> nucleotide sequences from blood plasma (red), epididymis (purple), axillary lymph node (green), prostate (yellow), seminal vesicle (blue) and testis (orange) in male macaque 36199. Sequences from blood plasma and seminal plasma are from 5, 8, 9, and 11 weeks post-infection. Sequences from epididymis, axillary lymph node, prostate, and testis were taken 11 weeks post-infection with SIVmac251. Individual nucleotide polymorphisms are indicated by green (adenine), red (thymine), yellow (guanine), or blue (cytosine) ticks and are in comparison to master sequence 4BP05_01. Gaps are indicated in gray. (B) Highlighter plot of SIV <i>env</i> amino acid sequences from tissues.</p

Highlighter plots of SGA derived <i>env</i> sequences from macaque 36338.

<p>(A) Highlighter plot of SIV <i>env</i> nucleotide sequences from blood plasma (red), epididymis (purple), axillary lymph node (green), prostate (yellow), seminal vesicle (blue) and testis (orange) in male macaque 36338, 11 weeks post infection with SIVmac251. Individual nucleotide polymorphisms are indicated by green (adenine), red (thymine), yellow (guanine), or blue (cytosine) ticks and are in comparison to master sequence 1BP11_01. Gaps are indicated in gray. (B) Highlighter plot of SIV env amino acid sequences from tissues.</p

Neighbor joining tree of SGA derived <i>env</i> sequences from macaque 36199.

<p>Midpoint rooted Neighbor-joining tree of the <i>env</i> sequences from SIVmac251 infected animal 36199, 11 weeks post-infection. Bar represents 0.001 nucleotide substitutions per site.</p

SIV RNA levels in blood plasma, seminal plasma and semen cells.

a<p>log10 vRNA copies per ml blood plasma and seminal plasma.</p>b<p>log10 vRNA copies per ug cellular RNA.</p

Neighbor Joining tree of SGA derived <i>env</i> sequences from macaque 36338.

<p>Midpoint rooted Neighbor-joining trees of the <i>env</i> sequences from SIVmac251 infected animal 36338 at 11 weeks post infection. Bar represents 0.001 nucleotide substitutions per site.</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

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

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

Animal demographics.

(DOCX)</p