Presymptomatic SARS-CoV-2 Infections and Transmission in a Skilled Nursing Facility

Abstract

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can spread rapidly within skilled nursing facilities. After identification of a case of Covid-19 in a skilled nursing facility, we assessed transmission and evaluated the adequacy of symptom-based screening to identify infections in residents.

Methods: We conducted two serial point-prevalence surveys, 1 week apart, in which assenting residents of the facility underwent nasopharyngeal and oropharyngeal testing for SARS-CoV-2, including real-time reverse-transcriptase polymerase chain reaction (rRT-PCR), viral culture, and sequencing. Symptoms that had been present during the preceding 14 days were recorded. Asymptomatic residents who tested positive were reassessed 7 days later. Residents with SARS-CoV-2 infection were categorized as symptomatic with typical symptoms (fever, cough, or shortness of breath), symptomatic with only atypical symptoms, presymptomatic, or asymptomatic.

Results: Twenty-three days after the first positive test result in a resident at this skilled nursing facility, 57 of 89 residents (64%) tested positive for SARS-CoV-2. Among 76 residents who participated in point-prevalence surveys, 48 (63%) tested positive. Of these 48 residents, 27 (56%) were asymptomatic at the time of testing; 24 subsequently developed symptoms (median time to onset, 4 days). Samples from these 24 presymptomatic residents had a median rRT-PCR cycle threshold value of 23.1, and viable virus was recovered from 17 residents. As of April 3, of the 57 residents with SARS-CoV-2 infection, 11 had been hospitalized (3 in the intensive care unit) and 15 had died (mortality, 26%). Of the 34 residents whose specimens were sequenced, 27 (79%) had sequences that fit into two clusters with a difference of one nucleotide.

Conclusions: Rapid and widespread transmission of SARS-CoV-2 was demonstrated in this skilled nursing facility. More than half of residents with positive test results were asymptomatic at the time of testing and most likely contributed to transmission. Infection-control strategies focused solely on symptomatic residents were not sufficient to prevent transmission after SARS-CoV-2 introduction into this facility.

Figure 1. Residents in Facility A on March 3 through Two Point-Prevalence Surveys.

Shown are all 89 residents who lived in skilled nursing facility A from March 3, when the first resident tested positive for SARS-CoV-2. By March 13, the date of the first point-prevalence survey, 82 residents remained in the facility, and 76 were tested. By the second point-prevalence survey, 48 of the 76 residents tested in the point-prevalence surveys had been identified as positive. Overall, 57 residents were positive as of March 26. Cycle threshold values were available for 47 residents who tested positive in the point-prevalence surveys on March 13 and March 19–20.

Figure 2. Cycle Threshold Values and Results of Viral Culture for Residents with Positive SARS-CoV-2 Tests According to Their Symptom Status.

Shown are N1 target cycle threshold values and viral culture results for 47 residents’ first positive test for SARS-CoV-2 stratified by the resident’s symptom status at the time of the test. One positive test was not assessed for culture growth. Typical symptoms include fever, cough, and shortness of breath; atypical symptoms include chills, malaise, increased confusion, rhinorrhea or nasal congestion, myalgia, dizziness, headache, nausea, and diarrhea.

Figure 3. Cycle Threshold Values Relative to First Evidence of Fever, Cough, or Shortness of Breath.

Shown are N1 target cycle threshold values and viral culture results for each resident’s positive tests for SARS-CoV-2 shown by day since the first evidence of fever, cough, or shortness of breath (N=55). Dates of onset of typical symptoms were known for 43 residents; 12 residents with two specimens that were positive for SARS-CoV-2 are also included. One positive test was not assessed for culture growth. The relationship between the first test and the second test for residents who had two positive tests is shown in Figure S2.

Figure 4. Timeline Showing Prevalence, Notable Events, and Implementation of Infection Prevention and Control Measures at Facility A.

Dashed lines indicate the prevalence of Covid-19 based on test results obtained during clinical evaluation of symptomatic residents before a unit-wide or facility-wide point-prevalence survey (PPS); the dotted line indicates the prevalence based on results from a unit-specific point-prevalence survey; and solid lines indicate the prevalence based on results from clinical evaluation and a facility-wide point-prevalence survey. PPE denotes personal protective equipment.