Kinetics of SARS-CoV-2 Shedding in Nursing Home Residents and Staff

Abstract

Background: Nursing homes (NHs) were disproportionately affected by the COVID-19 pandemic. However, little is known regarding the kinetics of SARS-CoV-2 shedding in NH residents and staff, which could inform treatment and infection prevention.

Methods: We enrolled NH residents and staff in eight US states from April to November 2023 and analyzed the kinetics of SARS-CoV-2 using serial antigen and molecular (RT-PCR) tests, whole genome sequencing, and viral culture (VC). Symptoms, vaccination, and treatment were collected via interviews and chart review. Viral load trajectories were modeled with gamma distribution functional forms. Antigen and VC test positivity over time were assessed using a Chi-squared test.

Results: Of the 587 enrolled participants, 86 tested positive and 73 underwent testing for ≥ 10 days; most residents (78%) and staff (87%) had ≥ 3 COVID-19 vaccine doses. The modeled SARS-CoV-2 proliferation period (period prior to reaching peak viral load) had ended for 48% (14/29) of residents and 56% (9/16) of staff when they took the initial RT-PCR test. Both antigen and VC showed higher positivity rates early in the course of disease (Days 0-5 vs. Days ≥ 6) (antigen: p < 0·001, VC: p < 0·001). VC positivity was 15% after Day 5 (14/96); two participants were VC positive after Day 10.

Conclusions: Peak viral load occurs early in the disease, suggesting asymptomatic and presymptomatic transmission may be a significant driver of transmission. Only two participants had a positive VC after Day 10, supporting current isolation and return to work recommendations.

Keywords: COVID‐19; SARS‐CoV‐2; kinetics; nursing home; shedding.

FIGURE 1 |

Consort diagram, April–November 2023. This diagram describes enrolled participants, cases, cases with 10 or more days of follow-up, and unenrolled cases who were identified through routine health surveillance.

FIGURE 2 |

Kaplan–Meier analysis of the time to first negative for both antigen and RT-PCR test results among residents and staff, April– November 2023. Differences in the survival curves between residents and staff were significant for RT-PCR (p = 0.007) but not antigen (p = 0.425) by the log rank test. There are 10 fewer participants (one staff and nine residents) for the RT-PCR curve because five participants never tested RT-PCR positive and five participants did not have the required 10 days follow-up after initial RT-PCR positive.

FIGURE 3 |

Percentage of antigen tests results that were positive for a RT-PCR Ct value range-day pair, April–November 2023. The black text is the number of antigen tests that occurred on a given day that corresponded to a RT-PCR Ct value in the given range. Dark red denotes that all antigen results were positive and purple denotes all antigen tests were negative. Early infection and at low Ct values a majority of antigen test are positive. Later in the infection and at higher Ct values a majority of antigen tests are negative. There is a small subset of antigen tests that were positive when the RT-PCR test results were negative. These results belong to three participants, one tested antigen positive and RT-PCR negative on Days 0, 1, 2, 3, 6, 7, 10, and 13 while the other two each tested antigen positive and RT-PCR negative once on Days 4 and 6.

FIGURE 4 |

Concordance between viral culture and antigen results by (A) Ct value and (B) time, April–November 2023. Dark red denotes both antigen and viral culture results are positive while purple denotes that both antigen and viral culture results are negative. Most viral culture positives occur when Ct < 24. The two viral culture positives after day 10 were participants who experienced rebound.