key: cord-0832686-b0z447kl
authors: Surie, Diya; Huang, Jennifer Y; Brown, Allison C; Gable, Paige; Biedron, Caitlin; Gilbert, Sarah; Garner, Kelley; Bollinger, Susan; Gulley, Trent; Haney, Tafarra; Lyons, Amanda K; Beshearse, Elizabeth; Gregory, Christopher J; Sabour, Sarah; Clemmons, Nakia S; James, Allison E; Tamin, Azaibi; Reese, Natashia; Perry-Dow, K Allison; Brown, Robin; Harcourt, Jennifer L; Campbell, Davina; Houston, Hollis; Chakravorty, Rohan; Paulick, Ashley; Whitaker, Brett; Murdoch, Jordan; Spicer, Lori; Stumpf, Megan M; Mills, Lisa; Coughlin, Melissa M; Higdem, Pamela; Rasheed, Mohammad Ata Ur; Lonsway, David; Bhatnagar, Amelia; Kothari, Atul; Anderson, Karen; Thornburg, Natalie J; Breaker, Erin; Adamczyk, Michelle; McAllister, Gillian A; Halpin, Alison L; Seely, Kathryn A; Patil, Naveen; McDonald, L Clifford; Kutty, Preeta K
title: Infectious period of SARS-CoV-2 in 17 nursing home residents — Arkansas, June–August 2020
date: 2021-01-30
journal: Open Forum Infect Dis
DOI: 10.1093/ofid/ofab048
sha: 6e3f6931c7a9ef75c4d6d92d44c8393752831ae0
doc_id: 832686
cord_uid: b0z447kl

BACKGROUND: To estimate the infectious period of SARS-CoV-2 in older adults with underlying conditions, we assessed duration of COVID-19 symptoms, reverse-transcription polymerase chain reaction (RT-PCR) positivity, and culture positivity among nursing home residents. METHODS: We enrolled residents within 15 days of their first positive SARS-CoV-2 test (diagnosis) at an Arkansas facility from July 7–15, 2020 and followed them for 42 days. Every 3 days for 21 days and then weekly, we assessed COVID-19 symptoms, collected specimens (oropharyngeal, anterior nares, and saliva), and reviewed medical charts. Blood for serology was collected on days 0, 6, 12, 21, and 42. Infectivity was defined by positive culture. Duration of culture positivity was compared to duration of COVID-19 symptoms and RT-PCR positivity. Data were summarized using measures of central tendency, frequencies and proportions. RESULTS: We enrolled 17/39 (44%) eligible residents. Median participant age was 82 years (range: 58–97 years). All had ≥3 underlying conditions. Median duration of RT-PCR positivity was 22 days (interquartile range [IQR]: 8–31 days) from diagnosis; median duration of symptoms was 42 days (IQR: 28–49 days). Of nine (53%) participants with any culture-positive specimens, 1 (11%) severely immunocompromised participant remained culture-positive 19 days from diagnosis; 8/9 (89%) were culture-positive ≤8 days from diagnosis. Seroconversion occurred in 12/12 (100%) surviving participants with ≥1 blood specimen; all participants were culture-negative before seroconversion. CONCLUSION: Duration of infectivity was considerably shorter than duration of symptoms and RT-PCR positivity. Severe immunocompromise may prolong SARS-CoV-2 infectivity. Seroconversion indicated non-infectivity in this cohort.

As of August 30, 2020, nursing home residents comprised an estimated 3% of all coronavirus disease 2019 cases in the United States, but they represented over a quarter of all COVID-19 deaths [1, 2] . The disproportionate burden of deaths among nursing home residents suggests unique virus-host dynamics in this population, likely due to their older age and underlying conditions [3, 4] . While the infectious period of SARS-CoV-2 has been described in other populations, it is important to understand the natural history and correlates of SARS-CoV-2 infectivity among nursing home residents, to inform infection prevention and control guidance for this population.

The successful isolation of SARS-CoV-2 in cell culture from a clinical specimen is often used as a proxy for infectiousness as it suggests a person is shedding replication-competent virus, which has the potential for transmission. Although the duration of shedding replication-competent virus in mild-to-moderately ill persons has been shown to be less than 10 days from symptom onset, this period has not been assessed prospectively for nursing home residents [5] [6] [7] . In one cross-sectional study of nursing home residents with laboratory-confirmed COVID-19, replication-competent virus was isolated ≤9 days from symptom onset [8] . However, there is evidence that shedding of replication-competent virus can continue for as long as 20 days from symptom onset in hospitalized patients with severe illness or immunocompromise [9] , both of which might also occur commonly in nursing home residents. Without more informed estimates of the infectious period in nursing home residents, the safe movement of residents within nursing homes and between acute and longterm care facilities remains a challenge. Therefore, we aimed to describe the duration SARS-CoV-2 infectivity in specimens from nursing home residents obtained over time. We also examined COVID-19 symptoms, reverse-transcription polymerase chain reaction (RT-PCR) positivity and serologic status as potential correlates of ongoing infectivity.

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We prospectively followed residents with SARS-CoV-2 infection confirmed by RT-PCR during a nursing home outbreak in rural Arkansas. As part of state-supported facility-wide testing for early detection of SARS-CoV-2 infection among nursing homes residents and healthcare personnel (HCP), residents with SARS-CoV-2 infection were identified by RT-PCR through serial point-prevalence surveys (PPS) conducted at the facility from June 9, 2020 through July 15, 2020 (Figure 1) . To describe the natural history of SARS-CoV-2 infectivity in participants who were both close to and farther out from their first RT-PCRpositive result (or diagnosis), we enrolled residents within 15 days of this result (Figure 1 ).

Each participant was followed for a period of 42 days from enrollment. For the first 21 days, participants were visited every three days; for the next 21 days, participants were visited weekly (Figure 2 ).

Symptom assessment, medical chart review, and specimen collection were repeated at each visit according to the project timeline (Figure 2 ). Before enrollment, the following symptoms were assessed twice daily by facility HCP: shortness of breath, cough, malaise, muscle pain, dizziness, diarrhea, vomiting, sore throat, and headache. At enrollment and each subsequent visit, participants were interviewed by project staff about COVID-19 symptoms at the time of interview using the Centers for Disease Control and Prevention (CDC) standard list of symptoms, to which chest and abdominal pain were added [10]. Medical charts were reviewed to abstract information on underlying conditions, medications, vital signs (temperature and oxygen saturation), laboratory test results within the previous 30 days, and any hospitalization records from the previous 30 days. At each visit, collection of respiratory specimens (i.e. oropharyngeal and anterior nares) and saliva specimens was attempted A c c e p t e d M a n u s c r i p t ( Figure 2) . Collection of blood for serology was attempted at enrollment and at visit days 6, 12, 21, and 42 ( Figure 2 ). Patients hospitalized during the assessment period were not interviewed and did not have specimens collected during their hospitalization; however, upon return to the nursing home, participants could choose to continue participating in the assessment.

Definitions SARS-CoV-2 infectivity was defined as isolation of replication-competent virus from a specimen in cell culture. Date of diagnosis was the date of participants' first PCR-positive test. Symptom data collected by the facility and CDC staff were used to determine the earliest date of symptom onset for participants. Although collection of oropharyngeal, anterior nares, and saliva specimens was attempted at each visit, RT-PCR results for each specimen type at each visit were not always available due to challenges with specimen collection, transport, or processing. Thus, we used any positive RT-PCR result among all specimens obtained from a participant on the same day to determine a composite RT-PCR result for each visit. Seroconversion was defined as a signal threshold >1 at the 1:100 dilution. Severe illness, based on adaptation from CDC guidance, was defined as a decrease from baseline of >3% in oxygen saturation (SpO2) regardless of whether the participant was on room air or supplemental oxygen [11] .

All specimens from participants' first RT-PCR-positive test before enrollment were collected during routine PPS conducted at the facility and tested at laboratories external to CDC.

Residual specimen from the first RT-PCR-positive test for each participant was requested from these external laboratories and, if available, re-tested at the CDC to determine if specimen quality would support performing culture. For specimens taken at enrollment and A c c e p t e d M a n u s c r i p t subsequently, oropharyngeal and anterior nares specimens were collected using synthetic swabs (BD NS Regular Flocked Swab, Franklin Lakes, NJ) and preserved in 3 mL of viral transport media. Saliva was collected in OMNIGene®·ORAL kits (DNA Genotek™, Ottawa, Ontario, Canada). Blood was collected in K2 EDTA tubes (BD Vacutainer Plastic Blood Collection Tubes: Hemogard Closure; Franklin Lakes, NJ). All specimens were kept at a temperature of 2-8 o C during transport. Respiratory specimens and saliva were tested using the CDC 2019-Novel Coronavirus RT-PCR Diagnostic Panel [12] .

All oropharyngeal or anterior nares specimens with a positive RT-PCR result were stored at -70 o C and submitted for viral culture within four weeks of RT-PCR testing. RT-PCR-positive saliva specimens could not be cultured because the transport media inactivated the virus [13] . Serum samples were analyzed using a validated pan immunoglobulin (Ig) enzyme-linked immunosorbent assay (ELISA) against the prefusion-stabilized extracellular domain of the SARS-CoV-2 spike protein to detect anti-SARS-CoV-2 antibodies for IgM, IgA, and IgG [14] . A specimen was considered reactive if the signal-to-threshold ratio at a serum dilution of 1:100 with background correction was greater than 1.0.

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We used a convenience sample of residents with RT-PCR-confirmed SARS-CoV-2 infection.

Residents were eligible for inclusion if they were within 15 days of their COVID-19

diagnosis. Residents were excluded if they had died, were hospitalized at the time of enrollment, did not have capacity to make independent decisions, or had their initial RT-PCR-positive test >15 days before enrollment. Data were summarized by measures of central tendency, frequencies and proportions using SAS software version 9.4 (SAS Institute, Cary, North Carolina, USA).

Participation in this activity was voluntary, and all participants were informed about procedures, risks, benefits, and provided written consent. This activity was reviewed by CDC and was determined to be non-human subjects research as part of public health response, consistent with applicable federal law and CDC policy 1 .

Of 90 residents at the facility with SARS-CoV-2 infection confirmed by RT-PCR, 39 (43%) were eligible for enrollment and 17/39 (44%) were enrolled (Figure 3 ). Median age of participants was 82 years (range: 58-97 days) and a majority (10, 59%) were female ( Table   1 ). All participants had ≥3 underlying conditions, most commonly: cardiovascular disease (16, 94%), diabetes (7, 41%), and non-asthmatic chronic lung disease (7, 41%) ( Table 1) . Of M a n u s c r i p t (18%) deaths; two of these were thought by the primary care physician to be COVID-19related.

At their first RT-PCR-positive test, 11 (65%) participants had not reported any COVID-19

symptoms, but all eventually became symptomatic (Figure 4A) . The most frequently reported symptoms at onset were cough (8, 47%), dyspnea (5, 29%), fatigue (5, 29%) and myalgias (5, 29%) ( Table 1) . Symptoms were reported for as long as 53 days, with a median duration of 42 days (interquartile range [IQR]: 28-49 days). The median duration of respiratory symptoms was 44 days (IQR: 28-50 days), which was longer than the median duration of non-respiratory symptoms at 36 days (IQR: 24-50 days). The most frequently reported symptoms at the end of the symptomatic (or study) period were fatigue (10, 59%), cough (9, 53%), rhinorrhea (8, 47%), dyspnea (8, 47%) and headache (6, 35%). Symptoms were distributed across the assessment period without any obvious clustering closer to diagnosis and with 8 (47%) participants reporting symptoms intermittently (Figure 4A) . [5] [6] [7] , although severe immunocompromise remains an important consideration to determine the duration of transmission-based precautions [15] .

The median duration of RT-PCR positivity since symptom onset in this cohort was 20 days. This is slightly longer than the mean duration of 17 days from symptom onset found in a meta-analysis of 43 studies that examined viral RNA detection by RT-PCR in upper respiratory tract specimens [7] . In the meta-analysis, older age correlated with longer durations of viral RNA detection, which might explain the longer duration seen in our older cohort [7] . Despite prolonged RT-PCR positivity in this cohort, the period of infectivity for most participants was shorter and consistent with other reports [7] [8] [9] . A cross-sectional study of 48 nursing home residents with confirmed COVID-19 did not isolate culturable virus beyond 9 days from symptom onset, although none of the residents in the study had any severely immunocompromising conditions [8] . By contrast, in a study of 129 hospitalized patients who had severe and critical COVID-19 and were severely immunocompromised, replication-competent virus was isolated up to 20 days, although the probability decreased to <5% after 15 days [9] . Such findings, including evidence of prolonged infectivity in a participant in our cohort with cancer, support the need to continue transmission-based precautions for extended periods in persons who are severely immunocompromised [15] .

It is important to note that the isolation of replication-competent virus only indicates the potential for onward transmission. At the time of writing, no late-linked transmissions (after a patient has had symptoms for about a week) have been documented, despite isolation of A c c e p t e d M a n u s c r i p t culturable virus beyond a week from symptom onset [16] . However, data from a household transmission study in the United States found that household contacts of immunocompromised patients with COVID-19 had increased risk for infection, suggesting that immunocompromised individuals may be more likely to transmit the virus [17] . A plausible explanation for an increased ability to transmit the virus includes prolonged shedding of replication-competent virus.

We were unable to isolate replication-competent virus from specimens with an N1 Ct value above 29. Previous studies that have examined the relationship between Ct values and recovery of culturable virus have not been able to isolate replication-competent virus above Ct values of 24 or 34 [8, 18, 19] . While our Ct value finding adds to the understanding of Ct values as correlates of the presence of culturable virus, the molecular assays used in these studies were not quantitative, and Ct value does not indicate a direct quantity of virus. Ct values vary across PCR assays and, even when the same PCR assay is used, different Ct values can be obtained by different institutions [18] [19] [20] .

Only about a third of our cohort reported symptoms prior to their first RT-PCR-positive test.

After symptom onset, more than half of participants continued to report respiratory symptoms for >44 days (or non-respiratory symptoms for >36 days), far longer than the ≤8-day period of infectivity observed in this cohort, suggesting that symptoms do not correlate well with infectivity in older adults. Prolonged symptoms in this older cohort might be expected, given that even young, non-hospitalized adults with no or few underlying conditions have been shown to experience prolonged symptoms after SARS-CoV-2 infection [21]. This assessment has several limitations. First, we used viral culture as a proxy for infectiousness. While successful virus isolation implies infectiousness, the inability to culture virus cannot be assumed to mean that an individual is not infectious. Several factors A c c e p t e d M a n u s c r i p t may affect detection of replication-competent virus in cell culture, including viral load, limit of detection, and type of cell line [5, 22] .

Second, determining symptom onset for COVID-19 in nursing home residents is challenging.

Patients often had difficulty distinguishing acute from chronic symptoms, especially for nonspecific symptoms like fatigue and myalgia. Furthermore, because data collected before enrollment used the facility's symptom assessment tool, which did not include all symptoms tracked during our assessment, it is possible early symptoms could have been missed, which could have affected length-of-time measurements that were based on symptom onset.

Third, because we did not collect daily blood samples, detection of seroconversion in this cohort is likely delayed. Thus, although seroconversion only occurred after culture negativity in this cohort, data from larger cohorts with daily blood collections that are also tested for neutralization titers are needed to determine the utility of seroconversion as a diagnostic correlate of non-infectivity.

Fourth, the low participation rate could have biased our sample towards residents who are healthier than those who were already hospitalized or had died prior to enrollment. Lastly, our small sample size of 17 residents, comprising entirely of non-Hispanic whites from a single facility, limits the generalizability of these results. Despite these limitations, our findings are consistent with other assessments of SARS-CoV-2 infectivity [5] [6] [7] [8] [9] 18 ]. A c c e p t e d M a n u s c r i p t anterior nares, and saliva specimens at each visit. Due to challenges with specimen collection, transport, and processing, a RT-PCR result for each specimen type was not always available for each visit. (3) Seroconversion was determined by a signal threshold >1 at the 1:100 dilution. 

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COVID-19)

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The authors are grateful to all residents and staff at the nursing home for their participation and support of this assessment during an especially challenging time. We also thank the staff at Arkansas State Public Health Laboratory and CDC COVID Surge Testing Laboratories for their support.

This assessment has been supported by the United States Centers for Disease Control and Prevention (CDC).

Disclaimer: The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention.

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