COMMAND INVESTIGATION CONCERNING CHAIN OF COMMAND ACTIONS WITH REGARD TO COVID-19 ONBOARD USS THEODORE ROOSEVELT (CVN 71)

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APPENDIX F: ANALYSIS OF USS THEODORE ROOSEVELT (CVN 71)

BINNACLE LIST

Introduction

Concerns about crew members displaying symptoms prior to the confirmed cases of
Novel Coronavirus 19 (COVID-19) aboard USS Theodore Roosevelt (CVN 71) (TR) led
to an analysis of the ship’s sick call logs, specifically studying the symptoms potentially
indicating early undetected COVID-19 infections, as well as an examination of trends of
respiratory disease. Using International Classification of Diseases 9 (ICD-9) codes, and
the Navy and Marine Corps Public Health Center (NMCPHC) criteria for disease
outbreaks, a trend of increasing acute upper respiratory infections was observed
between March 9th and March 23rd, which may represent early cases of COVID-19. A
parallel epidemiological study, staffed and funded by NMCPHC, is currently being
conducted in the wake of the coronavirus outbreak on the TR. Using more
comprehensive data-sets, and with the visibility provided by Centers for Disease Control
and Prevention (CDC) serology testing on the first 400 TR patients, their preliminary
findings are consistent with those of the command investigation team.

Background Information

Though COVID-19 information is rapidly evolving, well-established symptoms of fever,
non-productive cough, and shortness of breath were among the initial screening criteria
based on data from the initial outbreak location in Wuhan, China. Additionally, travel to
high risk areas (initially China and Korea) or exposure to a person diagnosed with
COVID-19 were both given equal weight in the screening process. On April 27, 2020,
the World Health Organization (WHO) added anosmia and alterations to the sense of
taste to the list of symptoms indicating possible COVID-19 disease.1 CDC guidance as
of May 1 3, 2020 lists the following symptoms for screening for COVID-1 9:2

Cough

Shortness of breath or difficulty breathing

Fever

Chills

Muscle pain

Sore throat

New loss of taste or smell

1 https://www.washingtonpost.com/health/2020/04/27/six-new-coronavirus-symptoms/

2 https://www.cdc.gov/coronavirus/2019-ncov/symptoms-testing/symptoms.html

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In contrast, as of May 15, 2020 Up-to Date (a well-trusted resource for clinical practice)
ranks the prevalence of the following symptoms as the hallmarks of COVID-19:3

Fever - 99 percent

Fatigue - 70 percent

Dry Cough - 59 percent

Anorexia - 40 percent

Myalgia (body aches) - 35 percent

Dyspnea -31 percent

Sputum production - 27 percent

The differences between these lists illustrates the challenges in screening for this
disease based solely on clinical presentation. A wide array of symptoms has been
described, especially in the early stages of COVID-19 disease. Anecdotal evidence for
loss of smell and taste was present in several surveys from Italy on COVID-19 survivors
and these symptoms ranged from 34-64 percent depending on the study.4 Another
European study puts loss of smell and loss of taste as an early symptom at 85 percent
and 88 percent of COVID-19 cases respectively.5

In an interview with the TR Physician Assistant on May 9th, it was mentioned that two to
three days prior to the first patients testing positive for coronavirus on the TR, the
Carrier Air Wing Eleven (CVW-1 1 ) Flight Surgeon had inquired about several members
who reported a decrease in taste or smell (anosmia). Subsequent to this report, the
sick call log was examined as a part of the investigation. Of note, no reports of anosmia
were discovered from the sick call data retrieved. Further analysis looking at the
outbreak of illness affecting the respiratory tract was conducted.

Binnacle List Analysis by Command Investigation Team

Sick call logs from January 2, 2020 until April 7, 2020 were transcribed from PDF files to
Excel. A total of 385 entries were retrieved and evaluated. Of these, 33 ICD-9 codes
were blank, 43 exhibited influenza-like illness (ILI) symptoms, 78 respiratory issues, and
78 diarrhea. Due to only three data points in April (the last week examined), rates were
based on 14 weeks. Acute Upper Respiratory Infection (AURI) and ILI-type symptoms
mimic those of COVID-19 and were chosen as potential indicators of outbreak on the
ship. Due to a known outbreak of norovirus aboard TR in February, diarrheal illness
was also examined to provide a convenient contrast. The ILI-type symptoms occurred

3 https://www.uptodate.com/contents/coronavirus-disease-2019-covid-19-epidemiology-virology-clinical-features-diagnosis-and-
prevention?search=coronavirus-disease-2019-covid-

&source=search_result&selectedTitle=8~150&usage_type=default&display_rank=8

4 https://www.uptodate.com/contents/coronavirus-disease-2019-covid-19-epidemiology-virology-clinical-features-diagnosis-and-
prevention?search=coronavirus-disease-2019-covid-

&source=search_result&selectedTitle=8~150&usage_type=default&display_rank=8

5 https://www.entnet.org/sites/default/files/uploads/lechien_et_al._-_covid19_-_eur_arch_otorhinolaryngol_.pdf

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at a 3.1 -patients per week average, while acute upper respiratory infection and diarrhea
occurred at a rate of 5.6-patients per week.

Significant increases in ILI and AURI symptoms were noted from the week beginning
January 19th until February 16th. Cases of ILI-type symptoms peaked during the week
of January 19th, at 18 cases, and respiratory symptoms peaked during the week of
January 26th with 17 cases; both exceeding the outbreak threshold for aircraft carriers
(CVNs) of 15 cases or 0.3 percent. As this corresponds to the timeframe reported by
the ship of an outbreak of norovirus, cases of diarrhea peaked during the week of
February 9th at 28 cases. Beginning on the week of March 8th, AURI cases again rose,
but did not reach 15 cases before March 22nd. The increase in reported respiratory
symptoms and diarrhea (March 8th to March 22nd) corresponds with the transit period
from Vietnam to Guam. Flowever, the numbers reported do not meet the threshold for
outbreak declaration in accordance with the Navy and Marine Corps Public Health
Center (NMCPHC) Guidance for Underway Evaluation and Management of Suspected
Persons under Investigation (PUI) for 201 9 Novel Coronavirus (COVID-19) for CVNs.
The Binnacle Log data after March 22nd is unreliable due to parallel reporting methods
for COVID-19, which were initiated on or around March 23rd by the ship’s Medical
Department.

A linear regression analysis was conducted on these three symptoms. Little correlation
was discovered between diarrhea and respiratory issues and diarrhea and ILI. For this
reason, multi-linear regression was not conducted. Correlation was found between the
cases of ILI and respiratory issues, but only 41 percent of the variation could be
explained by the model.

A secondary analysis of the combined rate for AURI and ILI was conducted. As
previously stated, COVID-19 symptoms vary widely and span from mild, cold-like
symptoms to pneumonia and respiratory failure. For this reason, combined ILI and AURI
symptoms were considered an accurate proxy for this spectrum of disease. Reports of
ILI and respiratory illness were compared to total numbers on the ship. This revealed
that there was a peak of respiratory illness by February 22nd, prior to VN. There was
another peak in AURI by March 22nd after Vietnam which did not reach outbreak levels.
This potentially represents an early rise in COVID-19 symptoms prior to the first positive
tests. Even with careful surveillance, if the data is accurate, the trend would not have
triggered concern for an outbreak of respiratory illness as the rate failed to exceed the
guidance baseline of 0.3 percent of ship’s crew.6

6 Guidance for Underway Evaluation and Management of Suspected Persons Under Investigation for 2019 Novel Coronavirus, April,
2020 Navy and Marine Corps Public Health Center

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Row Labels Sum of ILI/PNEU

Sum of RESPIRATORY

Sum of DIARRHEA

1

0

0

0

2

0

0

0

3

0

4

0

4

18

10

4

5

7

17

6

6

11

11

15

7

5

8

28

8

2

2

12

9

0

6

6

10

1

0

0

11

0

5

1

12

0

6

5

13

0

7

0

14

0

1

1

15

0

1

0

Grand Total

44

78

78

Table 1 : Binnacle List Analysis

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Week of

ILI

RESP ILL

DIARRHEA

2-Jan

0.00%

0.00%

0.00%

5-Jan

0.00%

0.00%

0.00%

12-Jan

0.00%

0.08%

0.00%

19-Jan

0.36%

0.20%

0.08%

26-Jan

0.14%

0.34%

0.12%

2-Feb

0.22%

0.22%

0.30%

9-Feb

0.10%

0.16%

0.56%

16-Feb

0.04%

0.04%

0.24%

23-Feb

0.00%

0.12%

0.12%

1-Mar

0.02%

0.00%

0.00%

8-Mar

0.00%

0.10%

0.02%

15-Mar

0.00%

0.12%

0.10%

22-Mar

0.00%

0.14%

0.00%

29-Mar

0.00%

0.02%

0.02%

5-Apr

0.00%

0.02%

0.00%

Table 2: Cl Binnacle List Analysis

Binnacle List Analysis Graph 1

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RESPIRATORY VS ILI

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y = 0.6992
R2 = 0

x - 0.7023

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4 1

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Binnacle List Analysis Graph 2

NMCPHC Epidemiologic Analysis?

As stated previously, evaluation of an outbreak based on a spectrum of common signs
and symptoms risks the possibility of over- or understating the prevalence of cases.
Preliminary data from the NMCPHC epidemiological analysis of the first 400 TR cases,
isolation logs from Guam, and backed by serology testing through the CDC provides a
more detailed examination of the coronavirus outbreak on the ship, likely origins of the
outbreak, and provides an epidemiologic curve as support. Of particular interest is that
both the findings from the NMCPHC epidemiological analysis and the Command
Investigation TR Binnacle List Analysis reveal an early rise in COVID-19 symptoms prior
to the first positive test result on TR.

The NMCPHC epidemiologic curve provides a temporal illustration of coronavirus
transmission, and allows sub-analysis of populations within the crew. (NMCPHC Epi-
data study Graph 1)

Key preliminary findings of the NMCPHC epi-data study are as follows:

- COVID-19 illness appears to have occurred on the ship prior to the first Carrier
Onboard Delivery (COD) arrival after the Da Nang port visit, and the growth in cases by

7 NMCPHC “USS Theodore Roosevelt Outbreak Investigation: Epidemiologic Analysis Update #2” 13 May 2020

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March 30th is not consistent with the limited potential introduction of the disease via
COD. This is illustrated in Graph 2 which is an overlay of the COD arrivals with the
epidemiologic curve. (NMCPHC Epi-data study Graph 2)

- Sub-analysis of populations (males and females, and work space) indicates
simultaneous exposure of a group potentially at a mass gathering consistent with the
Vietnam port visit. (NMCPHC Epi-data study Graph 3)

- TR Reactor Department, and two embarked squadrons (HSM-75 and VFA-154)
had early cases, but there was a lag of several incubation periods prior to the next case
indicating transmitters may be asymptomatic or display very mild disease. (NMCPHC
Epi-data study Graph 4)

- Careful use of the correct personal protective equipment (PPE) and hygiene
protocols prevents spread of COVID-19 within the medical department. The medical
department had one symptomatic case despite presumably high contact rates while
caring for ill patients.

- Follow-on analysis looking at rates instead of case counts will be conducted in
order to attempt to identify trends with respect to age, and rank.

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Summary

Though conducted in parallel, the TR Binnacle List Analysis and the NMCPHC USS
Theodore Roosevelt (CVN 71) Outbreak Investigation: Epidemiologic Analysis came to
the following similar conclusions:

- There is no indication that coronavirus came aboard the ship via COD

- There are indications that there were early cases of COVID-1 9 shortly after the
Vietnam port visit

- The ILI outbreak prior to the Vietnam port visit died out spontaneously and does
not appear to have been COVID-1 9

In the TR Binnacle List Analysis attempts to identify and interview the Sailors who cited
experiencing loss of taste or smell as a primary symptom were unsuccessful based on
information available in the sick call logs. It is likely that a Sailor reporting to sick call for
early COVID-1 9 disease and the medical personnel caring for them would not focus on
these symptoms given these symptoms were not known to be early indicators of
COVID-1 9 at the time. If a Sailor later remembered those symptoms, recall bias makes
it difficult to discern the accuracy of their remarks due to the prominence of these
symptoms in the media.8

If several Sailors had displayed anosmia two to three days prior to the first positive
COVID-1 9 test, it would provide support for the illness coming aboard after the port visit
in Vietnam. We did not find evidence to support that, but an increase in AURI
symptoms after Vietnam, up to March 22nd may be an early indication of the COVID-1 9
outbreak in personnel who had early or mild symptoms.

The NMCPHC study’s findings support our findings in regards to coronavirus occurring
onboard soon after visiting Vietnam. Additional study by their team focusing on disease
rates will continue to inform on patterns of coronavirus spread among crewmembers
and be of high value in prevention of this disease aboard naval vessels.

8 https://www.nytimes.com/2020/03/22/health/coronavirus-symptoms-smell-taste.html

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COVID-19 Case Counts Over Time, Symptomatic Cases,
USS Theodore Roosevelt

Date of Symptom Onset

NMCPHC Epi-data Study Graph I9

9 NMCPHC “ATTACHMENT #1 to: USS Theodore Roosevelt Outbreak Investigation for Epidemiologic Analysis Update #2” 13 May
2020, from “USS Theodore Roosevelt Outbreak Investigation: Epidemiologic Analysis Update #2” 13 May 2020

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35

30

a 25

20

O 15

10

ILI and COVID-19 Case Counts Over Time

First positive
test result;
outbreak
identified

24 people arrive
on COD

4 people arrive
on COD each
day, 12 total

Port visit
Vietnam

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Ship arrives
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ILI cases

Date of Clinical Presentation or Symptom Onset

ILI + COVID cases

COVID only cases

NMCPHC Epi-data study Graph 2W

10 NMCPHC “ATTACHMENT #1 to: USS Theodore Roosevelt Outbreak Investigation for Epidemiologic Analysis Update #2” 13
May 2020, from “USS Theodore Roosevelt Outbreak Investigation: Epidemiologic Analysis Update #2” 13 May 2020

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COVID-19 Case Counts Over Time By Gender,
Symptomatic Cases, USS Theodore Roosevelt

Date of Symptom Onset

NMCPHC Epi-data study Graph 31

1 1 NMCPHC “ATTACHMENT #1 to: USS Theodore Roosevelt Outbreak Investigation for Epidemiologic Analysis Update #2” 13
May 2020, from “USS Theodore Roosevelt Outbreak Investigation: Epidemiologic Analysis Update #2” 13 May 2020

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COVID-19 Case Counts Over Time By Select Workcenter,
Symptomatic Cases, USS Theodore Roosevelt

Date of Symptom Onset

NMCPHC Epi-data study Graph 412

12 NMCPHC “ATTACHMENT #1 to: USS Theodore Roosevelt Outbreak Investigation for Epidemiologic Analysis Update #2” 13
May 2020, from “USS Theodore Roosevelt Outbreak Investigation: Epidemiologic Analysis Update #2” 13 May 2020

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