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.

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##  ui       X11                         
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       America/New_York            
##  date     2019-04-06                  
## 
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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
1	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
2	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
3	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
Total	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
2	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.

Infected Donor PCR Positivity by Study Day, by Quarantine

Looking at PCR positive donor data over the 6 study days, as before, but this time stratified by the 3 Q to see if the Q were similar.

Study Day	Q1 PCR Positive Samples (%)	Q2 PCR Positive Samples (%)	Q3 PCR Positive Samples (%)	All Q PCR Positive Samples (%)
1	3 (25)	4 (40)	12 (86)	19 (53)
2	10 (83)	10 (100)	14 (100)	34 (94)
3	12 (100)	10 (100)	13 (93)	35 (97)
4	11 (92)	8 (80)	12 (86)	31 (86)
5	12 (100)	9 (90)	12 (86)	33 (92)
6	9 (75)	6 (60)	9 (64)	24 (67)
Total	57 (79)	47 (78)	72 (86)	176 (81)
Note:
Only the 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 the number of total samples collected from positive donors for each study day (i.e., one nasopharyngeal swab per infected donor per day, for each study day 1-6. These totals are 12, 10, 14, and 36 for Q1, Q2, Q3, and all Q together, respectively.

Plot the data by each quarantine, and pooled data on the same plot.

Nasopharyngeal Swab CT Values Over Study Days 1-6

What was the CT value trend for positive nasopharyngeal swabs and did each Q follow a similar trend over the 6 study days?

Donor Positivity by Serology and PCR

Looking at the risk of become positive, among donors inoculated, and among donors infected, by: HAI or MN, and PCR; HAI and MN, and PCR; HAI or MN, but not PCR; HAI and MN, but not PCR.

		Positive by PCR		Not Positive by PCR
Quarantine #	Infected/Inoculated (%)	Seroconversion by HAI or MN, plus PCR Positive (% of Infected) (% of Inoculated)	Seroconversion by HAI and MN, plus PCR Positive (% of Infected) (% of Inoculated)	Seroconversion by HAI or MN, but not PCR Positive (% of Infected) (% of Inoculated)	Seroconversion by HAI and MN, but not PCR Positive (% of Infected) (% of Inoculated)
1	15/20 (75)	11 (73) (55)	9 (60) (45)	3 (20) (15)	3 (20) (15)
2	11/12 (92)	8 (73) (67)	6 (55) (50)	1 (9) (8)	1 (9) (8)
3	16/20 (80)	12 (75) (60)	10 (62) (50)	2 (12) (10)	1 (6) (5)
Total	42/52 (81)	31 (74) (60)	25 (60) (48)	6 (14) (12)	5 (12) (10)
Note:
Seroconversion: 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; PCR Positivity: ≥2 positive NPS test results by qPCR (if a single sample, two positive aliquots required): indicated by 1 if true and 0 otherwise

If we want to do the same analysis but only include the risk of seroconversion among the infected donors (not intention to treat analysis), then we can produce a new table.

		Positive by PCR		Not Positive by PCR
Quarantine #	Infected/Inoculated (%)	Seroconversion by HAI or MN, plus PCR Positive (% of Infected)	Seroconversion by HAI and MN, plus PCR Positive (% of Infected)	Seroconversion by HAI or MN, but not PCR Positive (% of Infected)	Seroconversion by HAI and MN, but not PCR Positive (% of Infected)
1	15/20 (75)	11 (73)	9 (60)	3 (20)	3 (20)
2	11/12 (92)	8 (73)	6 (55)	1 (9)	1 (9)
3	16/20 (80)	12 (75)	10 (62)	2 (12)	1 (6)
Total	42/52 (81)	31 (74)	25 (60)	6 (14)	5 (12)
Note:
Seroconversion: 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; PCR Positivity: ≥2 positive NPS test results by qPCR (if a single sample, two positive aliquots required): indicated by 1 if true and 0 otherwise

Table 1 Main Text with Stringent Symptom and ILI Criteria

If we apply a more stringent criteria to the symptom classification where symptoms that appear before study day 1 are not included in the criteria for symptoms or ILI, then we get a slightly different count for the symptomatic category, but not for the ILI.

Printing a new Table 1 with the stringent criteria applied.

		Laboratory Confirmed Infection & 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)	10 (67)	4 (27)	8 (53)	12 (80)	11 (73)	12 : 14 : 14
2	11/12 (92)	6 (55)	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)	30 (71)	6 (14)	25 (60)	36 (86)	31 (74)	35 : 32 : 37

If we wanted to compare just the original Table 1 with this new, more stringent version, by the only variables of interest (sympomatic, febrile, and ILI), we could produce a new comparison table.

## Joining, by = "Quarantine #"

	Original Table 1 Values		Stringent Criteria Values
Quarantine #	Table1 Symptomatic	Table1 ILI	Stringent Symptomatic	Stringent ILI
1	11 (73)	8 (53)	10 (67)	8 (53)
2	7 (64)	5 (45)	6 (55)	5 (45)
3	14 (88)	12 (75)	14 (88)	12 (75)
Total	32 (76)	25 (60)	30 (71)	25 (60)

It’s easy to see here that the more stringent criteria produces very similar values compared with the original Table 1. The minor difference is that the symptomatic group by stringent criteria is 2 less compared with the original Table 1.

Supporting Analysis: Infected Donor Viral Shedding

Printing the number of person-day G2 samples by quarantine.

Quarantine #	G2 Person-Day Samples
1	36
2	34
3	40
Total	110

Now examining within each of these quarantines, to see how many subjects gave how many G2 samples.

Quarantine #	1 Day	2 Days	3 Days	4 Days
1	4	16	0	0
2	0	5	4	3
3	0	20	0	0
Total	4	41	4	3

Printing the number of volunteers who gave G2 samples over the 4 study days of exhaled breath collection (study days 1-4).

Study Day	Volunteers Who Gave a G2 Sample
1	25
2	31
3	30
4	24
Total	110

Geometric Mean and Geometric Standard Deviation of Positive Fine and Coarse Samples

This information was included in the footnote of Table 2.

Fine Aerosol Shedding (Among Infected Donors in the Quarantine Trial)

Fine_Positive_Samples_GeomMean	Fine_Positive_Samples_GSD	Fine_Positive_Samples_Max	Fine_Positive_Samples_n
5.239559e+03	4.616176	8.023674e+04	14

Coarse Aerosol Shedding (Among Infected Donors in the Quarantine Trial)

Coarse_Positive_Samples_Geom_Mean	Coarse_Positive_Samples_GSD	Coarse_Positive_Samples_Max	Coarse_Positive_Samples_n
2.903816e+03	3.217316	2.789903e+04	6

For Comparison: The Geometric Mean and Geometric Standard Deviation of Fine and Coarse Samples from UMD Population

Fine Aerosol Shedding (Among Influenza Cases in EMIT UMD Population – 2012-13 flu season among UMD campus community)

Fine_Positive_Samples_Geom_Mean	Fine_Positive_Samples_GSD	Fine_Positive_Samples_Max	Fine_Positive_Samples_n
3.978051e+04	13.39223	4.374907e+07	167

Coarse Aerosol Shedding (Among Influenza Cases in EMIT UMD Population – 2012-13 flu season among UMD campus community)

Coarse_Positive_Samples_Geom_Mean	Coarse_Positive_Samples_GSD	Coarse_Positive_Samples_Max	Coarse_Positive_Samples_n
1.430876e+04	11.8416	4.283182e+08	88

Boxplots of Fine and Coarse Aerosol Shedding

There were 14 positive fine and 6 poisitive coarse samples. Previously we plotted these without using log base 10 ont he y-axis and had issues, so we are going to plot these boxplots using log10 on the y-axis.

Supporting Analysis: Recipient Status

Table 3 Footnote: Greater than Anticipated Immunity Upon Entry to Quarantine

Greater than anticipated immunity for Intervention Receipients (IR).

Quarantine #	Greater than Anticipated HAI	Greater than Anticipated MN	Greater than Anticipated HAI and MN	Seroconverted
1	1	2	0	0
3	0	2	0	0

Greater than anticipated immunity for Control Receipients (CR).

Quarantine #	Greater than Anticipated HAI	Greater than Anticipated MN	Greater than Anticipated HAI and MN	Seroconverted
1	1	2	0	0
3	1	2	0	0

Table 3 Footnote: Greater than Anticipated Immunity Upon Entry to Quarantine

If we apply a more stringent criteria to the symptom classification where symptoms that appear before study day 1 are not included in the criteria for symptomatic and ILI, then we gets slightly different counts.

Printing a new Table 3 with the stringent criteria applied.

			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)	3 (27)	0 (0)	3 (27)	0 (0)	0 (0)	0 : 0 : 0
1	Intervention (IR)	0/10 (0)	2 (20)	0 (0)	1 (10)	0 (0)	0 (0)	0 : 0 : 0
2	Control (CR)	1/9 (11)	1 (11)	0 (0)	1 (11)	0 (0)	0 (0)	1 : 1 : 1
2	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
3	Intervention (IR)	0/20 (0)	6 (30)	0 (0)	2 (10)	0 (0)	0 (0)	0 : 0 : 0
Total	Control (CR)	1/35 (3)	10 (29)	0 (0)	8 (23)	0 (0)	0 (0)	1 : 1 : 1
Total	Intervention (IR)	0/40 (0)	11 (28)	0 (0)	5 (12)	0 (0)	0 (0)	0 : 0 : 0

If we wanted to compare just the original Table 3 with this new, more stringent version, by the only variables of interest (sympomatic and ILI), we could produce a new comparison table.

		Original Table 3 Values		Stringent Criteria Values
Quarantine #	Recipient Classification	Table3 Symptomatic	Table3 ILI	Stringent Symptomatic	Stringent ILI
1	Control (CR)	4 (36)	3 (27)	3 (27)	3 (27)
1	Intervention (IR)	2 (20)	1 (10)	2 (20)	1 (10)
2	Control (CR)	2 (22)	2 (22)	1 (11)	1 (11)
2	Intervention (IR)	3 (30)	2 (20)	3 (30)	2 (20)
3	Control (CR)	6 (40)	4 (27)	6 (40)	4 (27)
3	Intervention (IR)	6 (30)	2 (10)	6 (30)	2 (10)
Total	Control (CR)	12 (34)	9 (26)	10 (29)	8 (23)
Total	Intervention (IR)	11 (28)	5 (12)	11 (28)	5 (12)

It’s easy to see here that the more stringent criteria produces very similar values compared with the original Table 3. The minor difference is that the CR symptomatic group by stringent criteria is 2 less, and the CR ILI group by stringent criteria is 1 less.

Serology for the CR that Seroconverted and the 2 CRs with 1 Day of PCR Positivity

MN Serology for the 3 CR with Some Evidence of Infection

Subject ID	Quarantine Number	Draw Date	MN Visit	MN Titer to A/WI/67/2005
233	2	2013-04-05	Screening	5
	2	2013-04-15	Q baseline	10
	2	2013-05-16	F/up	320
236	2	2013-03-28	Screening	40
	2	2013-04-15	Q baseline	40
	2	2013-05-18	F/up	57
242	2	2013-03-21	Screening	40
	2	2013-04-15	Q baseline	40
	2	2013-05-13	F/up	20
^* Volunteer 233 was positive by both MN and HAI. Volunteers 236 and 242 did not seroconvert by either MN or HAI, however they each had a single day of PCR positivity, thus we wanted to explore their serology scores regardless.

HAI Serology for the 3 CR with Some Evidence of Infection

Subject ID	Quarantine Number	HAI 2 Days Before Entry to Q	HAI 2 Days Before Entry to Q (Recoded Nondetect)	HAI Day 28
233	2	NDA	5	40
236	2	NDA	5	NDA
242	2	NDA	5	NDA
^* Volunteer 233 was positive by both MN and HAI. Volunteers 236 and 242 did not seroconvert by either MN or HAI, however they each had a single day of PCR positivity, thus we wanted to explore their serology scores. NDA: No detectable antibody.

PCR ct values for the NP swabs of Recipients with only one day of detectable InfA RNA

Subject ID	Randomized Group	Quarantine Number	Study Day	Date	Ct Value
236	CR	2	6	2013-04-24	28.99
242	CR	2	2	2013-04-20	36.55
^* Volunteers 236 and 242 did not seroconvert by either MN or HAI, however they each had a single day of PCR positivity. CR: Control Recipient

Symptoms for the CR that Seroconverted and the 2 CRs with 1 Day of PCR Positivity

Perhaps the easiest way to describe this is through a line plot. Volunteer 233 had some symptoms but volunteers 236 and 242 did not have any symptoms at all. Thus the line plot will plot the symptoms from 233 only.

The total respiratory score, presented here is a sum of the total “respiratory”" symptom scores for each day of symptoms surveillance. “Respiratory” symptoms include: runny nose, stuffy nose, sneezing, sore throat, cough, and shortness of breath.

Note: We took a mean symptom score for the combined respiratory symptom scores (runnyNose, stuffyNose, sneezing, soreThroat, cough, SOB), by score instance (there were mostly 3 instances of symptoms scoring per day). Then took the mean by study day to get a single mean, total respiratory symtpom score for study days -3 through 10.

Applying Killingley et al, 2012 qRT-PCR infection criteria to Main Q study

Table 1: Donor Status Using Proof of Concept Study (Killingley et al, 2012) Infection Criteria

		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)	13 (87)	12 (80)	12 : 14 : 14
2	11/12 (92)	7 (64)	0 (0)	5 (45)	11 (100)	9 (82)	9 : 7 : 9
3	18/20 (90)	16 (89)	2 (11)	14 (78)	17 (94)	13 (72)	14 : 11 : 14
Total	44/52 (85)	34 (77)	6 (14)	27 (61)	41 (93)	34 (77)	35 : 32 : 37

Table 3: Recipient Status Using Proof of Concept Study (Killingley et al, 2012) Infection Criteria

			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
1	Intervention (IR)	0/10 (0)	2 (20)	0 (0)	1 (10)	0 (0)	0 (0)	0 : 0 : 0
2	Control (CR)	3/9 (33)	2 (22)	0 (0)	2 (22)	2 (22)	0 (0)	1 : 1 : 1
2	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
3	Intervention (IR)	0/20 (0)	6 (30)	0 (0)	2 (10)	0 (0)	0 (0)	0 : 0 : 0
Total	Control (CR)	3/35 (9)	12 (34)	0 (0)	9 (26)	2 (6)	0 (0)	1 : 1 : 1
Total	Intervention (IR)	0/40 (0)	11 (28)	0 (0)	5 (12)	0 (0)	0 (0)	0 : 0 : 0

Group Comparisons with Respect to SAR Outcomes

## Making some comparisons between the Proof of Concept study (PoC) and the Main Q study

# Comparing PoC with PoC criteria versus Main Q with Main Q criteria:
fisher.test(matrix(c(3, 12-3, 1, 75-1), ncol = 2))

## 
##  Fisher's Exact Test for Count Data
## 
## data:  matrix(c(3, 12 - 3, 1, 75 - 1), ncol = 2)
## p-value = 0.007635
## alternative hypothesis: true odds ratio is not equal to 1
## 95 percent confidence interval:
##     1.654114 1298.609426
## sample estimates:
## odds ratio 
##   22.94739

# Comparing PoC with PoC criteria versus Main Q CR with Main Q criteria:
fisher.test(matrix(c(3, 12-3, 1, 35-1), ncol = 2))

## 
##  Fisher's Exact Test for Count Data
## 
## data:  matrix(c(3, 12 - 3, 1, 35 - 1), ncol = 2)
## p-value = 0.04595
## alternative hypothesis: true odds ratio is not equal to 1
## 95 percent confidence interval:
##    0.7514072 609.1667276
## sample estimates:
## odds ratio 
##    10.5893

# But the correct comparison (applying the more stringent Main Q criteria to both studies) between Main Q overall and PoC would be:
fisher.test(matrix(c(1, 12-1, 1, 75-1), ncol = 2))

## 
##  Fisher's Exact Test for Count Data
## 
## data:  matrix(c(1, 12 - 1, 1, 75 - 1), ncol = 2)
## p-value = 0.2582
## alternative hypothesis: true odds ratio is not equal to 1
## 95 percent confidence interval:
##    0.07860667 532.30389339
## sample estimates:
## odds ratio 
##   6.484249

# Correct comparison (stringent Main Q criteria applied to both studies) between Main Q CR and PoC:
fisher.test(matrix(c(1, 12-1, 1, 35-1), ncol = 2))

## 
##  Fisher's Exact Test for Count Data
## 
## data:  matrix(c(1, 12 - 1, 1, 35 - 1), ncol = 2)
## p-value = 0.4496
## alternative hypothesis: true odds ratio is not equal to 1
## 95 percent confidence interval:
##    0.03611969 249.05125239
## sample estimates:
## odds ratio 
##     3.0025

# Correct comparison (stringent Main Q criteria applied to both studies) between Main Q IR and PoC:
fisher.test(matrix(c(1, 12-1, 0, 40-0), ncol = 2))

## 
##  Fisher's Exact Test for Count Data
## 
## data:  matrix(c(1, 12 - 1, 0, 40 - 0), ncol = 2)
## p-value = 0.2308
## alternative hypothesis: true odds ratio is not equal to 1
## 95 percent confidence interval:
##  0.08546999        Inf
## sample estimates:
## odds ratio 
##        Inf

# Correct comparison (stringent Main Q criteria) of Main Q CR to Main Q IR:
fisher.test(matrix(c(1, 35-1, 0, 40-0), ncol = 2))

## 
##  Fisher's Exact Test for Count Data
## 
## data:  matrix(c(1, 35 - 1, 0, 40 - 0), ncol = 2)
## p-value = 0.4667
## alternative hypothesis: true odds ratio is not equal to 1
## 95 percent confidence interval:
##  0.02930372        Inf
## sample estimates:
## odds ratio 
##        Inf

# Correct comparison (with less stringent PoC criteria) of Main Q CR to Main Q IR
fisher.test(matrix(c(3, 35-3, 0, 40-0), ncol = 2))

## 
##  Fisher's Exact Test for Count Data
## 
## data:  matrix(c(3, 35 - 3, 0, 40 - 0), ncol = 2)
## p-value = 0.09693
## alternative hypothesis: true odds ratio is not equal to 1
## 95 percent confidence interval:
##  0.481905      Inf
## sample estimates:
## odds ratio 
##        Inf

## Additional computations using PoC criteria to compare between both studies:

# Comparing PoC with IR
fisher.test(matrix(c(3, 12-3, 0, 40-0), ncol = 2))

## 
##  Fisher's Exact Test for Count Data
## 
## data:  matrix(c(3, 12 - 3, 0, 40 - 0), ncol = 2)
## p-value = 0.009955
## alternative hypothesis: true odds ratio is not equal to 1
## 95 percent confidence interval:
##  1.521788      Inf
## sample estimates:
## odds ratio 
##        Inf

# Comparing PoC with CR
fisher.test(matrix(c(3, 12-3, 3, 35-3), ncol = 2))

## 
##  Fisher's Exact Test for Count Data
## 
## data:  matrix(c(3, 12 - 3, 3, 35 - 3), ncol = 2)
## p-value = 0.1642
## alternative hypothesis: true odds ratio is not equal to 1
## 95 percent confidence interval:
##   0.3927752 30.4494160
## sample estimates:
## odds ratio 
##   3.440052

# Comparing PoC with overall Main Q
fisher.test(matrix(c(3, 12-3, 3, 75-3), ncol = 2))

## 
##  Fisher's Exact Test for Count Data
## 
## data:  matrix(c(3, 12 - 3, 3, 75 - 3), ncol = 2)
## p-value = 0.03226
## alternative hypothesis: true odds ratio is not equal to 1
## 95 percent confidence interval:
##   0.8949201 66.7448743
## sample estimates:
## odds ratio 
##    7.67835

## Using the Main Q criteria for infection status in both studies: 
## We got 1/75 (overall, and 1/35 for CR group, and 0/40 for IR group) but we were expecting at least .16 (double the infecteds and recipients, double the time)
# Comparing the theoretical ~16% expected versus the 1/75 actual (overall study)
n_successes = 1
n = 75
p = 0.16
binom.test(n_successes, n, p)$p.value

## [1] 5.228346e-05

# Comparing the theoretical ~16% expected versus the 1/35 actual (CR group only)
n_successes = 1
n = 35
p = 0.16
binom.test(n_successes, n, p)$p.value

## [1] 0.03460563

## Using the POC criteria for infection status in both studies:
## We got 3/75 (overall, and 3/35 for the CR group, and 0/40 for IR group) and we were expecting at least .5 (double the infecteds and recipients, double the time)
# Comparing the theoretical ~50% expected versus the 1/75 actual (overall study)
n_successes = 3
n = 75
p = 0.50
binom.test(n_successes, n, p)$p.value

## [1] 3.725674e-18

# Comparing the theoretical ~50% expected versus the 1/35 actual (CR group only)
n_successes = 3
n = 35
p = 0.50
binom.test(n_successes, n, p)$p.value

## [1] 4.176982e-07

Baseline Characteristics Table

	CR (N=35)	D (N=52)	IR (N=40)
Gender
f	12 (34.3%)	15 (28.8%)	13 (32.5%)
m	23 (65.7%)	37 (71.2%)	27 (67.5%)
Age
Median (Q1, Q3)	27 (25, 36)	30 (25, 38)	28 (24, 34)

Quarantine Main Paper Tables 1-3, Figure 3, and Other Supporting Tables and Figures

Jacob Bueno de Mesquita

04/6/2019

Printing Tables and Figures for Manuscript Main Text

Table 1: Symptoms and Infection Status of Donors

Table 2: Viral Shedding of Infected Donors

Table 3: Symptoms and Infection Status of Recipients

Two Plots for Figure 3

Printing Other Supporting Tables & Figures

Supporting Analysis: Donor Status

Donors with Greater than Anticipated Immunity by Quarantine

Asymptomatic Infected Donors

Infected Donor PCR Positivity by Study Day

Infected Donor PCR Positivity by Study Day, by Quarantine

Nasopharyngeal Swab CT Values Over Study Days 1-6

Donor Positivity by Serology and PCR

Table 1 Main Text with Stringent Symptom and ILI Criteria

Supporting Analysis: Infected Donor Viral Shedding

Geometric Mean and Geometric Standard Deviation of Positive Fine and Coarse Samples

For Comparison: The Geometric Mean and Geometric Standard Deviation of Fine and Coarse Samples from UMD Population

Boxplots of Fine and Coarse Aerosol Shedding

Supporting Analysis: Recipient Status

Table 3 Footnote: Greater than Anticipated Immunity Upon Entry to Quarantine

Table 3 Footnote: Greater than Anticipated Immunity Upon Entry to Quarantine

Serology for the CR that Seroconverted and the 2 CRs with 1 Day of PCR Positivity

MN Serology for the 3 CR with Some Evidence of Infection

HAI Serology for the 3 CR with Some Evidence of Infection

PCR ct values for the NP swabs of Recipients with only one day of detectable InfA RNA

Symptoms for the CR that Seroconverted and the 2 CRs with 1 Day of PCR Positivity

Applying Killingley et al, 2012 qRT-PCR infection criteria to Main Q study

Table 1: Donor Status Using Proof of Concept Study (Killingley et al, 2012) Infection Criteria

Table 3: Recipient Status Using Proof of Concept Study (Killingley et al, 2012) Infection Criteria

Group Comparisons with Respect to SAR Outcomes

Baseline Characteristics Table