Printing Tables and Figures for Manuscript Main Text

The goal of this Markdown is to print the tables and figures directly from the R code and files used for analysis. The purpose of printing directly into the Markdown, which can be drawn into a manuscript easily, is to prevent errors in translating these results into a format acceptable for publication The analysis was produced by the EMIT_Quarantine_Main_Analysis.R script and a couple of additional supporting tables were produced by the EMIT_Quarantine_Text_Analysis.R script.

First I will setup the programming environment and note the session information. Because the output for this step is long and not very useful for immediate use, we will keep the output hidden, however it can be called up if needed.

We will also read in the data required to make the tables and figure included in the main text.

## ─ Session info ──────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 3.5.1 (2018-07-02)
##  os       macOS  10.14.4              
##  system   x86_64, darwin15.6.0        
##  ui       X11                         
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       America/New_York            
##  date     2019-04-06                  
## 
## ─ Packages ──────────────────────────────────────────────────────────────
##  package     * version date       lib source        
##  arsenal     * 1.5.0   2018-11-09 [1] CRAN (R 3.5.0)
##  assertthat    0.2.0   2017-04-11 [1] CRAN (R 3.5.0)
##  backports     1.1.2   2017-12-13 [1] CRAN (R 3.5.0)
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##  broom         0.5.0   2018-07-17 [1] CRAN (R 3.5.0)
##  callr         3.0.0   2018-08-24 [1] CRAN (R 3.5.0)
##  cellranger    1.1.0   2016-07-27 [1] CRAN (R 3.5.0)
##  cli           1.0.1   2018-09-25 [1] CRAN (R 3.5.0)
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##  desc          1.2.0   2018-05-01 [1] CRAN (R 3.5.0)
##  devtools    * 2.0.1   2018-10-26 [1] CRAN (R 3.5.1)
##  digest        0.6.18  2018-10-10 [1] CRAN (R 3.5.0)
##  dplyr       * 0.7.7   2018-10-16 [1] CRAN (R 3.5.0)
##  DT          * 0.4     2018-01-30 [1] CRAN (R 3.5.0)
##  evaluate      0.12    2018-10-09 [1] CRAN (R 3.5.0)
##  forcats     * 0.3.0   2018-02-19 [1] CRAN (R 3.5.0)
##  fs            1.2.6   2018-08-23 [1] CRAN (R 3.5.0)
##  ggplot2     * 3.1.0   2018-10-25 [1] CRAN (R 3.5.0)
##  glue          1.3.0   2018-07-17 [1] CRAN (R 3.5.0)
##  gtable        0.2.0   2016-02-26 [1] CRAN (R 3.5.0)
##  haven         1.1.2   2018-06-27 [1] CRAN (R 3.5.0)
##  hms           0.4.2   2018-03-10 [1] CRAN (R 3.5.0)
##  htmltools     0.3.6   2017-04-28 [1] CRAN (R 3.5.0)
##  htmlwidgets   1.3     2018-09-30 [1] CRAN (R 3.5.0)
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##  jsonlite      1.5     2017-06-01 [1] CRAN (R 3.5.0)
##  kableExtra  * 0.9.0   2018-05-21 [1] CRAN (R 3.5.0)
##  knitr       * 1.20    2018-02-20 [1] CRAN (R 3.5.0)
##  lattice       0.20-38 2018-11-04 [1] CRAN (R 3.5.0)
##  lazyeval      0.2.1   2017-10-29 [1] CRAN (R 3.5.0)
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##  magrittr      1.5     2014-11-22 [1] CRAN (R 3.5.0)
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##  rlang         0.3.0.1 2018-10-25 [1] CRAN (R 3.5.0)
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##  rstudioapi    0.8     2018-10-02 [1] CRAN (R 3.5.0)
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##  sessioninfo   1.1.0   2018-09-25 [1] CRAN (R 3.5.0)
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##  yaml          2.2.0   2018-07-25 [1] CRAN (R 3.5.0)
## 
## [1] /Library/Frameworks/R.framework/Versions/3.5/Resources/library

Table 1: Symptoms and Infection Status of Donors

Printing a formatted Table 1 with Kable

Clinical Illness (% of Infected)
Laboratory Confirmed Infection Criteria (% of Infected)
Quarantine # Infected/Inoculated (%) Symptomatic Febrile ILI PCR Confirmed Infection PCR Confirmed Infection and Seroconversion Seroconversion by HAI : MN : Either
1 15/20 (75) 11 (73) 4 (27) 8 (53) 12 (80) 11 (73) 12 : 14 : 14
2 11/12 (92) 7 (64) 0 (0) 5 (45) 10 (91) 8 (73) 9 : 7 : 9
3 16/20 (80) 14 (88) 2 (12) 12 (75) 14 (88) 12 (75) 14 : 11 : 14
Total 42/52 (81) 32 (76) 6 (14) 25 (60) 36 (86) 31 (74) 35 : 32 : 37

Table 2: Viral Shedding of Infected Donors

Printing a formatted Table 2 with Kable

Coarse Aerosol (>5um)
Fine Aerosol (≤5um)
Quarantine # N Subjects N Samples Coarse Positive Subjects (%) Coarse Positive Samples (%) Mean of Positive Coarse Samples* Fine Positive Subjects (%) Fine Positive Samples (%) Mean of Positive Fine Samples*
1 15 27 1 (7) 1 (4) 2.79e+04 3 (20) 5 (19) 3.32e+04
2 11 30 3 (27) 3 (10) 2.16e+03 3 (27) 4 (13) 1.80e+04
3 16 32 2 (12) 2 (6) 1.73e+03 5 (31) 5 (16) 1.70e+03
Total 42 89 6 (14) 6 (7) 6.31e+03 11 (26) 14 (16) 1.76e+04
The arithmetic mean RNA copy number used data from positive samples only. The geometric means (GM) and geometric standard deviations (GSD) were 2.90E+3 (3.22) and 5.24E+3 (6.62) for positive coarse and positive fine aerosol samples, respectively. Quantitative RT-PCR assays for aerosol samples were run in duplicate and in instances where one replicate was positive and the other was negative (i.e., non-detectable), we imputed for the non-detectable replicate using LOQ(1/sqrt(2)) where LOQ is the limit of quantification computed as the most dilute sample that gave a positive result in all replicates. The LOQ for this assay was 2,000 copies per sample. Such imputed values for non-detectable replicates were used in computing arithmetic mean, GM, and GSD.

Table 3: Symptoms and Infection Status of Recipients

Printing a formatted Table 3 with Kable

Clinical Illness (% of Exposed)
Laboratory Confirmed Infection Criteria (% of Exposed)
Quarantine # Recipient Classification Infected/Exposed (%) Symptomatic Febrile ILI PCR Confirmed Infection PCR Confirmed Infection and Seroconversion Seroconversion by HAI : MN : Either
1 Control (CR) 0/11 (0) 4 (36) 0 (0) 3 (27) 0 (0) 0 (0) 0 : 0 : 0
Intervention (IR) 0/10 (0) 2 (20) 0 (0) 1 (10) 0 (0) 0 (0) 0 : 0 : 0
2 Control (CR) 1/9 (11) 2 (22) 0 (0) 2 (22) 0 (0) 0 (0) 1 : 1 : 1
Intervention (IR) 0/10 (0) 3 (30) 0 (0) 2 (20) 0 (0) 0 (0) 0 : 0 : 0
3 Control (CR) 0/15 (0) 6 (40) 0 (0) 4 (27) 0 (0) 0 (0) 0 : 0 : 0
Intervention (IR) 0/20 (0) 6 (30) 0 (0) 2 (10) 0 (0) 0 (0) 0 : 0 : 0
Total Control (CR) 1/35 (3) 12 (34) 0 (0) 9 (26) 0 (0) 0 (0) 1 : 1 : 1
Intervention (IR) 0/40 (0) 11 (28) 0 (0) 5 (12) 0 (0) 0 (0) 0 : 0 : 0

Two Plots for Figure 3

Bar chart of viral shedding (by qPCR) from NP swabs, coarse aerosol, fine aerosol, both coarse and fine aerosol, either coarse or fine aerosol

Line chart of the arithmetic mean ct values and 1 arithmetic standard deviation above and below bars for NP swabs that were postiive on study days 1-4.

Printing Other Supporting Tables & Figures

There are some additional tables that hold information required for fully describing the results in the paper. These will be produced here. Tables and figures from among this set can be selected for inclusion in manuscript SI.

Supporting Analysis: Donor Status

Donors with Greater than Anticipated Immunity by Quarantine

This table provides output that is used in the footnote for Table 1.

Quarantine # Greater than Anticipated HAI Greater than Anticipated MN Greater than Anticipated HAI and MN Greater than Anticipated HAI or MN Seroconverted Positive by qPCR Seroconverted and Positive by qPCR
1 3 1 0 4 2 2 2
2 1 2 1 2 0 1 0
3 3 2 1 4 2 2 2
Total 7 5 2 10 4 5 4
1 Greater than anticipated immunity by HAI consisted of HAI titer >10 at study baseline (i.e., admission to quarantine), or MN ≥80: indicated by 1 if true and 0 otherwise;
2 4-fold or greater rise in HAI or MN titres between Day -2 (baseline) and Day 28 (followup): indicated by 1 if true and 0 otherwise;
3 ≥2 positive NPS test results by qPCR (if a single sample, two positive aliquots required): indicated by 1 if true and 0 otherwise

Summary by subject ID of donors with greater than anticipated immunity.

Quarantine # Subject ID Greater than Anticipated HAI Greater than Anticipated MN Greater than Anticipated HAI and MN Seroconverted Days qPCR Positive Positive by qPCR
1 102 1 0 0 0 0 0
107 0 1 0 1 6 1
110 1 0 0 1 4 1
119 1 0 0 0 0 0
2 121 0 1 0 0 0 0
124 1 1 1 0 2 1
3 133 1 0 0 1 6 1
134 1 1 1 1 4 1
139 0 1 0 0 0 0
140 1 0 0 0 1 0
Note:
This table provides the information for each of the 10 subject IDs that were aggregated by quarantine in the Summary by Quarantine of Donors with Greater than Anticipated Immunity table.
1 Greater than anticipated immunity by HAI consisted of HAI titer >10 at study baseline (i.e., admission to quarantine), or MN ≥80): indicated by 1 if true and 0 otherwise;
2 4-fold or greater rise in HAI or MN titres between Day -2 (baseline) and Day 28 (followup): indicated by 1 if true and 0 otherwise;
3 ≥2 positive NPS test results by qPCR (if a single sample, two positive aliquots required): indicated by 1 if true and 0 otherwise

Asymptomatic Infected Donors

The number of asymptomatic, infected donors is mentioned in the Results. This table supports those written findings.

Quarantine # Asymptomatic
1 4
2 4
3 2
Total 10
Note:
Asymptomatic was defined as volunteers who did not reach symptomatic status, with symptomatic defined as evidence of any respiratory symptom lasting ≥24 hours during study days 1-6. In Q3, one donor had a single instance of low-grade fever at 37.9 degrees C in the morning of study day 3. This donor exhibited no other symptoms and was included as one of the asymptomatic donors

Infected Donor PCR Positivity by Study Day

Looking at this in tabular form.

Study Day PCR Positive Subjects (%)
1 19 (53)
2 34 (94)
3 35 (97)
4 31 (86)
5 33 (92)
6 24 (67)
Total 176 (81)
Note:
Only the 36 donors who met laboratory case criteria by PCR (i.e., two or more positive NPS test results by qRT-PCR) were included. Percents were computed out of these 36 for each study day (i.e., one nasopharyngeal swab per infected donor per day, for each study day 1-6.

Plot the pooled data from all three quarantines.