Methods

Initial Response to the Outbreak and Follow-Up
The ship had been at sea for 13 days when three crew members presented to the medical department with symptoms suggestive of coronavirus disease 2019 (Covid-19). All three underwent testing by real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) and were found to be positive for SARS-CoV-2. Over the next 24 hours, additional symptomatic crew members and approximately 400 close contacts were identified by contact tracing. Four days after the first positive test result was reported, the ship reached Naval Base Guam. Crew members with confirmed cases of Covid-19 were placed in isolation on Naval Base Guam or in the base hospital. Persons with one or more negative Covid-19 tests and no symptoms were quarantined in hotels off base or on Naval Base Guam. In addition, essential personnel who were uninfected stayed aboard the ship in port.
All members of the crew underwent screening for signs and symptoms of Covid-19 and testing by rRT-PCR. Those who tested positive for SARS-CoV-2 were placed in isolation and received twice-daily symptom, temperature, and pulse oximetry checks. Those who tested negative were placed in quarantine. Ultimately, 4079 SARS-CoV-2–negative crew members who did not have symptoms were quarantined in 11 hotels in Guam. All were placed in single-occupancy rooms.
A surveillance model was implemented that relied on in-person health screenings. These screenings were supplemented by self-reporting with the use of a symptom checker developed by Defense Digital Service. Health screenings and symptom-checker data were collated and analyzed each morning by 9 a.m. and again in the evening by 9 p.m. Crew members who had progressive symptoms or were deemed to have conditions potentially placing them at higher risk for poorer outcomes were followed up with additional screening. Any crew members who were determined by on-site medical providers to need closer observation or treatment were transported to Naval Hospital Guam for care. In addition to Covid-19–related health surveillance, crew members received primary care, pharmacy, and psychiatric services to ensure a complete scope of medical coverage.
On completion of prespecified periods of isolation or quarantine, all personnel were required to undergo repeat rRT-PCR testing. To be eligible for exit testing, a crew member had to remain in isolation or quarantine for a minimum of 14 days. Those in isolation were also required to be symptom-free for 3 days before exit testing. Any crew member in quarantine in whom symptoms developed was tested and moved to isolation for at least 14 additional days. All crew members were followed up for a minimum of 10 weeks, regardless of their Covid-19 status.

Laboratory Testing
Nasopharyngeal swab specimens were obtained from all members of the crew with the use of viral transport medium swab kits. The presence of SARS-CoV-2 infection was determined by rRT-PCR testing with the Thermo Fisher ABI 7500 or the Bio-Rad CFX96 Touch Real-Time PCR Detection System. Samples were processed with either the Qiagen QIAamp Viral RNA Mini Kit or the Roche MagNA Pure 96 instrument for automated nucleic acid extraction, and testing was performed with the Seegene Allplex 2019-nCOV assay test kit or the Centers for Disease Control and Prevention (CDC) emergency-use-authorization assay.1 These assays included the detection of two targets in the nucleocapsid gene, N1 and N2. Surveillance testing for influenza-like illness was conducted with the Biofire Respiratory 2 Panel.

Collection of Outbreak Data
The Navy and Marine Corps Public Health Center was tasked with providing public health support for the outbreak investigation and conducting data analysis in alignment with its core public health mission. Data were collected as part of a coordinated public health outbreak investigation conducted by the Navy to bring the outbreak under control, ensure the well-being of the crew, assess the spread and effects of SARS-CoV-2, and implement measures to return the crew to work safely. Under Navy public health support criteria, the intent of the outbreak investigation was to mitigate spread, inform decision making, gather information for use in other outbreaks, and decrease the effect on the health of the crew. This project was deemed to be nonresearch with respect to the use of human subject information and was exempt from review by the institutional review board as an emergency public health outbreak investigation.
A roster of Electronic Data Interchange Personal Identifiers for the shipboard population was matched to Defense Manpower Data Center personnel rosters from February 2020 to identify demographic information for each crew member and to confirm personal identifiers. Civilian personnel and anyone with an Electronic Data Interchange Personal Identifier that did not match with Defense Manpower Data Center were excluded from analysis. The Defense Enrollment Eligibility Reporting System was used to identify race and ethnic group for all crew members. Ages of crew members at time of the outbreak were calculated from the date of birth to March 3, 2020.
Medical surveillance data collected by the ship medical department, Naval Hospital Guam, and the joint medical task force were collated with the roster to create a data set that included dates of symptom onset, daily clinical signs and symptoms, and test results. Data from the Defense Digital Service MySymptoms symptom-tracker application were also collated into the final data set. For the purpose of this analysis, fever is defined as subjective fever reported by the crew member or a measured temperature of 100.0°F or higher. All other symptoms were reported by the crew members. Data on health-related factors were obtained from a number of existing clinical Military Health System data sources, including the Armed Forces Health Longitudinal Technology Application and Military Health System Genesis.
A confirmed case of Covid-19 was defined as one in which a nasopharyngeal swab specimen was positive for SARS-CoV-2 by rRT-PCR. A suspected case of Covid-19 was defined as one that met Council of State and Territorial Epidemiologists clinical criteria for Covid-19 without a positive test result. Confirmed cases were further classified as symptomatic (with symptom onset before the first positive laboratory test), presymptomatic (with the first positive laboratory test before subsequent symptom onset), and asymptomatic (positive laboratory test but clinical criteria never met). Patients with confirmed or suspected infection were classified as having been hospitalized for Covid-19 if the admission diagnosis suggested a Covid-19–related illness.

Statistical Analysis
Data collation and analysis were performed with the use of SAS software, version 9.4 (SAS Institute). Baseline characteristics among crew members who were infected and those who were not infected were compared and univariate odds ratios with 95% confidence intervals were calculated with OpenEpi (www.openepi.com). For denominators of less than 20, odds ratios were not calculated. All reported odds ratios are not adjusted for multiple comparisons.