On June 2, 2020, this report was posted as an MMWR Early Release on the MMWR website (https://www.cdc.gov/mmwr).The coronavirus disease 2019 (COVID-19) pandemic has resulted in substantial morbidity and mortality since it was first described in December 2019 (1). Based on epidemiologic data showing spread in congregate settings (2-4), national, state, and local governments instituted significant restrictions on large gatherings to prevent transmission of disease in early March 2020. This and other nonpharmaceutical interventions (NPIs) have shown initial success in slowing the pandemic across the country (5). This report examines the first 7 weeks (March 1-April 18) of implementation of NPIs in Basic Military Training (BMT) at a U.S. Air Force base. In a population of 10,579 trainees, COVID-19 incidence was limited to five cases (47 per 100,000 persons), three of which were in persons who were contacts of the first patient. Transmission of symptomatic COVID-19 was successfully limited using strategies of quarantine, social distancing, early screening of trainees, rapid isolation of persons with suspected cases, and monitored reentry into training for trainees with positive test results after resolution of symptoms.BMT is the first step in the accession of airmen into the USAF. Approximately 40,000 new airmen are trained each year at Joint Base San Antonio-Lackland (JBSA) in Texas with an average of approximately 800 trainees arriving per week. Approximately 75% of incoming trainees are male, and most are in their late teens or early 20s. These trainees are prescreened for underlying medical conditions and are generally in good overall health. Training involves classroom lectures, small group activities, and field exercises. Each training cohort (flight) consists of 50 persons who live in communal, open-bay quarters and perform all daily and training activities as a group. For accountability and safety purposes, trainees are never alone, performing every activity with at least one fellow trainee. In recent decades, outbreaks of respiratory illnesses caused by pathogens such as adenovirus serotype B14 in 2007 have occurred during BMT, resulting in head-to-toe bunk arrangements, regular cleaning of shared equipment, and active syndromic surveillance for respiratory illness (6).

IMPORTANCE Owing to concerns of coronavirus disease 2019 (COVID-19) outbreaks, many congregant settings are forced to close when cases are detected because there are few data on the risk of different markers of transmission within groups. OBJECTIVE To determine whether symptoms and laboratory results on the first day of COVID-19 diagnosis are associated with development of a case cluster in a congregant setting. DESIGN, SETTING, AND PARTICIPANTS This cohort study of trainees with COVID-19 from May 11 through August 24, 2020, was conducted at Joint Base San Antonio-Lackland, the primary site of entry for enlistment in the US Air Force. Symptoms and duration, known contacts, and cycle threshold for trainees diagnosed by reverse transcription-polymerase chain reaction were collected. A cycle threshold value represents the number of nucleic acid amplification cycles that occur before a specimen containing the target material generates a signal greater than the predetermined threshold that defines positivity. Cohorts with 5 or more individuals with COVID-19 infection were defined as clusters. Participants included 10 613 trainees divided into 263 parallel cohorts of 30 to 50 people arriving weekly for 7 weeks of training. EXPOSURES All trainees were quarantined for 14 days on arrival. Testing was performed on arrival, on day 14, and anytime during training when indicated. Protective measures included universal masking, physical distancing, and rapid isolation of trainees with COVID-19. MAIN OUTCOMES AND MEASURES Association between days of symptoms, specific symptoms, number of symptoms, or cycle threshold values of individuals diagnosed with COVID-19 via reverse transcription-polymerase chain reaction and subsequent transmission within cohorts. RESULTS In this cohort study of 10 613 US Air Force basic trainees in 263 cohorts, 403 trainees (3%) received a diagnosis of COVID-19 in 129 cohorts (49%). Among trainees with COVID-19 infection, 318 (79%) were men, and the median (interquartile range [IQR]) age was 20 (19-23) years; 204 (51%) were symptomatic, and 199 (49%) were asymptomatic. Median (IQR) cycle threshold values were lower in symptomatic trainees compared with asymptomatic trainees (21.2 [18.4-27.60] vs 34.8 [29.3-37.4]; P < .001). Cohorts with clusters of individuals with COVID-19 infection were predominantly men (204 cohorts [89%] vs 114 cohorts [64%]; P < .001), had more symptomatic trainees (146 cohorts [64%] vs 53 cohorts [30%]; P < .001), and had more median (IQR) symptoms per patient (3 [2-5] vs 1 [1-2]; P < .001) compared with cohorts without clusters. Within cohorts, subsequent development of clusters of 5 or more individuals with COVID-19 infection compared with those that did not develop clusters was associated with cohorts that had more symptomatic trainees (31 of 58 trainees [53%] vs 43 of 151 trainees [28%]; P = .001) and lower median (IQR) cycle threshold values (22.3 [18.4-27.3] vs 35.3 [26.5-37.8]; P < .001).

Genomic surveillance empowers agile responses to SARS-CoV-2 by enabling scientists and public health analysts to issue recommendations aimed at slowing transmission, prioritizing contact tracing, and building a robust genomic sequencing surveillance strategy. Since the start of the pandemic, real time RT-PCR diagnostic testing from upper respiratory specimens, such as nasopharyngeal (NP) swabs, has been the standard. Moreover, respiratory samples in viral transport media are the ideal specimen for SARS-CoV-2 whole-genome sequencing (WGS). In early 2021, many clinicians transitioned to antigen-based SARS-CoV-2 detection tests, which use anterior nasal swabs for SARS-CoV-2 antigen detection. Despite this shift in testing methods, the need for whole-genome sequence surveillance remains. Thus, we developed a workflow for whole-genome sequencing with antigen test-derived swabs as an input rather than nasopharyngeal swabs. In this study, we use excess clinical specimens processed using the BinaxNOW™ COVID-19 Ag Card. We demonstrate that whole-genome sequencing from antigen tests is feasible and yields similar results from RT-PCR-based assays utilizing a swab in viral transport media.

Background. Transesophageal echocardiography (TEE) is used for the evaluation of the presence of left atrial appendage (LAA) thrombus prior to pulmonary vein isolation (PVI), while coronary computed tomography angiography (CCTA) is used for anatomic mapping during PVI. Methods. We compared the diagnostic performance of single phase CCTA to TEE in excluding the presence of LAA thrombus in patients undergoing PVI in 172 subjects performed during index hospitalization. Results. The mean age was 51 ± 13 years, a median CHADS2 score of 1 [IQR25,75 0,1, range 0–3] and a mean periprocedural INR of 2.1 ± 0.6. The prevalence of an LAA filling defect on single phase CCTA was 9.3% (6/183) and on TEE was 1.2% (2/183). Sensitivity, specificity, positive predictive value, and negative predictive value were 100% (95% CI, 19.8–100%), 91.8% (95% CI, 94–99%), 12.5% (95% CI, 60–76%), and 91.8% (95% CI, 97–100%) for the detection of LAA filling defect, respectively. Conclusion. Given the utility of a preprocedural single phase CCTA for the performance of PVI, the absence of a filling defect negates the need for a subsequent TEE as an adjunct for exclusion of LAA thrombus.