key: cord-0714430-pp46xp16 authors: Lutgring, Joseph D; Tobolowsky, Farrell A; Hatfield, Kelly M; Lehnertz, Nicholas B; Sullivan, Maureen M; Martin, Karen G; Keaton, Amelia; Sexton, D Joseph; Tamin, Azaibi; Harcourt, Jennifer L; Thornburg, Natalie J; Reddy, Sujan C; Jernigan, John A title: Evaluating the Presence of Replication-Competent SARS-CoV-2 from Nursing Home Residents with Persistently Positive RT-PCR Results date: 2021-05-14 journal: Clin Infect Dis DOI: 10.1093/cid/ciab436 sha: feab1502dc2c76fd477906a612e85c75666a109e doc_id: 714430 cord_uid: pp46xp16 Replication-competent virus has not been detected in individuals with mild to moderate COVID-19 more than 10 days after symptom onset. It is unknown whether these findings apply to nursing home residents. Of 273 specimens collected from nursing home residents >10 days from the initial positive test, none were culture positive. M a n u s c r i p t 3 The duration of infectiousness of persons infected with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has important implications for infection control practice including when transmission-based precautions can be discontinued. Individuals can test positive with a nucleic acid amplification test (NAAT) for weeks after the onset of coronavirus disease 2019 (COVID-19) symptoms [1] [2] [3] . However, replication-competent virus has not been detected in individuals with mild to moderate COVID-19 more than 10 days after symptom onset [1, 2, 4, 5] . There are instances of the detection of replicationcompetent virus between 10-20 days in individuals with severe COVID-19 [6] . There are also reports of severely immunocompromised individuals (e.g., hematopoietic stem-cell transplant recipients) with detectable replication-competent virus beyond 20 days [7] . The Centers for Disease Control and Prevention (CDC) interim guidance on the discontinuation of transmission-based precautions recommends a symptom-and time-based strategy with specific recommendations and considerations based on illness severity and whether the patient is severely immunocompromised [8] . The studies supporting this recommendation have not focused on nursing home residents [1, 2, 5, 6] . Nursing home residents have been significantly impacted by the COVID-19 pandemic and outbreaks with high case fatality rates have been reported [4] . The nursing home resident population is unique for several reasons. Residents experience immunosenescence due to their age, frequently have multiple medical comorbidities, and are often frail. Symptom ascertainment is often unreliable due to dementia or other contributing factors [4, 9] . In addition, SARS-CoV-2 can spread rapidly amongst nursing home residents who often have roommates at high risk for severe disease. Therefore, appropriate initiation and discontinuation of transmission-based precautions in this population are critical. More data A c c e p t e d M a n u s c r i p t 4 are needed to assess whether the duration of infectiousness with SARS-CoV-2 differs in nursing home residents. In this investigation, we sought to assess whether replicationcompetent virus could be detected in nursing home residents with persistently positive realtime reverse transcription-polymerase chain reaction (RT-PCR) test results. We obtained upper respiratory specimens from nursing home residents in two ways. First, CDC collected specimens by recruiting nursing homes that had experienced prior COVID-19 outbreaks. Six nursing homes from four states participated in this targeted sample. Each facility provided a line list of residents that had previously tested positive, and CDC collected nasopharyngeal swab specimens from these individuals at various time points from their initial positive result. Additional data collected included patient age, sex, and date of initial positive NAAT result. All specimens underwent testing for SARS-CoV-2 at CDC using the CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panel (CDC) [10] . Virus culture was attempted for all RT-PCR positive specimens with an N1 (nucleocapsid) target cycle threshold (Ct) value <34. The viral culture procedure was described previously [11] . A second group of specimens were collected by the Minnesota Department of Health (DOH). Our findings support the current CDC interim guidance for the discontinuation of transmission-based precautions and disposition of patients with COVID-19 in healthcare settings which indicates a preference for a strategy based on symptoms and time, and that, just as for the general population, a test-based strategy is not necessary for most nursing home residents [8] . Also, our data support the recommendation that retesting asymptomatic individuals in the 90 days after illness onset is unlikely to yield useful information (i.e., any positive RT-PCR test likely represents persistent shedding of viral RNA rather than a new infection) [12] . There are several limitations to our study. We did not collect symptom or severity information about the initial illness or data on the presence of resident comorbidities. Thus, we could not measure time from symptom onset to the study specimen collection, we were not able to classify residents as having mild, moderate, or severe COVID-19, and it is not known whether any residents had severe immunocompromising conditions. However, symptom data can be difficult to ascertain in nursing home residents [4, 9] . Furthermore, many nursing home residents are undergoing screening testing and thus SARS-CoV-2 is being detected when residents are either asymptomatic or presymptomatic. Thus, we think our findings will likely be applicable to the nursing home resident population more broadly. Another limitation is the use of virus culture as a surrogate for infectiousness. In this study, we recovered virus only from specimens with an N1 Ct <23, whereas in other studies, virus has been recovered from specimens with an N1 Ct of up to 34 [4] . Many factors can contribute to whether virus can be recovered in culture, and therefore it is difficult to determine why virus was not recovered from any particular specimen. We believe that any positive culture indicates the presence of replication-competent virus, and thus likely A c c e p t e d M a n u s c r i p t 8 infectiousness, although we acknowledge a negative culture does not rule out infectiousness (i.e., loss of viability due to transport, storage, or other factors). In summary, we tested 361 specimens from nursing home residents, and 273 of these specimens were collected 11 to 63 days after the initial positive specimen. Similarly, to what others have found, persistently positive RT-PCR results beyond 10 days were common [1] [2] [3] . However, we found no replication-competent virus amongst any of the specimens beyond 10 days of the initial positive test. Predicting infectious SARS-CoV-2 from diagnostic samples Chuang VWM, Peiris M. SARS-CoV-2 Virus Culture and Subgenomic RNA for Respiratory Specimens from Patients with Mild Coronavirus Disease Dynamic profile of RT-PCR findings from 301 COVID-19 patients in Wuhan, China: A descriptive study Public Health-Seattle and King County, CDC COVID-19 Investigation Team. Presymptomatic SARS-CoV-2 Infections and Transmission in a Skilled Nursing Facility Virological assessment of hospitalized patients with COVID-2019 Duration and key determinants of infectious virus shedding in hospitalized patients with coronavirus disease-2019 (COVID-19) Shedding of Viable SARS-CoV-2 after Immunosuppressive Therapy for Cancer Prevention: Discontinuation of Transmission-Based Precautions and Disposition of Patients with SARS-CoV-2 Infection in Healthcare Settings Asymptomatic and Presymptomatic SARS-CoV-2 Infections in Residents of a Long-Term Care Skilled Nursing Facility -King County Centers for Disease Control and Prevention: CDC's Diagnostic Test for COVID-19 Only and Supplies Severe Acute Respiratory Syndrome Coronavirus 2 from Patient with Coronavirus Disease, United States Centers for Disease Control and Prevention: Interim Guidance on Duration of Isolation and Precautions for Adults with COVID-19 A c c e p t e d M a n u s c r i p t A c c e p t e d M a n u s c r i p t