Cycle Thresholds Among Solid Organ Transplant Recipients Testing Positive for SARS-CoV-2

Abstract

Background:

The optimal duration of Transmission-Based Precautions among immunocompromised patients with SARS-CoV-2 is unknown.

Methods:

Retrospective review of patients with solid organ transplant with positive SARS-CoV-2 PCR result from nasopharyngeal specimens admitted to the hospital between 3/13/2020 and 5/15/2020.

Results:

Twenty-one percent of solid organ transplant recipients with positive SARS-CoV-2 PCR detected ≥ 20 days after symptom onset (or after first positive test among asymptomatic individuals) had a low cycle threshold (i.e. high viral load). The majority of these patients were asymptomatic or symptomatically improved.

Conclusions:

Solid organ transplant recipients may have prolonged high viral burden of SARS-CoV-2. Further data are needed to understand whether cycle threshold data can help inform strategies for prevention of healthcare-associated transmission of SARS-CoV-2 and for appropriate discontinuation of Transmission-Based Precautions.

Introduction

SARS-CoV-2, the virus that causes COVID-19, continues to pose significant infection prevention and control (IP&C) challenges. Currently, reverse transcription polymerase chain reaction (PCR) testing is used for COVID-19 diagnosis and decision-making for IP&C. While PCR testing is highly sensitive, the presence of viral RNA does not equate with infectivity, and PCR testing does not distinguish viable virus from nonviable virus.^1,2 As of 8/10/2020, the Centers for Disease Control and Prevention recommend a symptom-based strategy using 20 days and symptom improvement to discontinue Transmission-Based Precautions for immunocompromised individuals.³ However, the CDC acknowledged in October 2020 that data in immunocompromised populations are limited and allowed for consideration of a test-based strategy in consultation with infectious diseases experts.⁴ Hence, questions about the duration of infectivity for immunocompromised individuals remain, especially given the well-described phenomenon of prolonged detection of respiratory viruses, including SARS-CoV-2, by PCR assays.^5,6,7

Recent data show that PCR cycle thresholds (Ct) targeting the envelope (E) gene correlate with SARS-CoV-2 infectivity. In respiratory samples obtained from mostly immunocompetent individuals, higher Ct values, i.e., E-gene Ct value > 24, were significantly correlated with loss of infectivity, defined as lack of SARS-CoV-2 growth in cell culture.⁸ Another published report found no positive viral cultures when the E-gene Ct was ≥ 34, although the immune status of patients in this cohort was not reported.⁹ Few reports exist regarding Ct data among immunocompromised individuals with COVID-19. In 1 small cohort, among 5 solid organ transplant (SOT) recipients with serial PCR testing, Ct values <35.0 were detected ≥27 days after symptom onset in 2 patients.¹⁰ In 1 case report, an immunocompromised individual had persistent detection of SARS-CoV-2 with low Ct values more than 140 days after first positive test.¹¹ And a recent series of 20 patients with hematopoietic stem-cell transplantation found prolonged viral shedding.¹² Here we review initial and follow-up SARS-CoV-2 PCR testing and associated Ct values among SOT recipients to help address the knowledge gap for safely discontinuing Transmission-Based Precautions for this population.

Methods

We conducted a retrospective study of patients with kidney, liver, lung, or heart transplant with positive SARS-CoV-2 PCR result from nasopharyngeal (NP) specimens admitted between 3/13/2020 and 5/15/2020. Beginning 4/4/20, all patients were tested for SARS-CoV-2 upon hospital admission per institutional policy. Repeat testing during this period was performed at the discretion of the clinical team; during the study period, a test-based strategy for discontinuation of Transmission-Based Precautions was employed for inpatients. Review of the electronic medical record was performed after 6/15/2020 to allow ≥ 30 days of follow up for each patient. SARS-CoV-2 PCR tests performed on the cobas® 6800 (Roche Molecular Diagnostics, Pleasanton, CA) platform were included, and E-gene Ct values were obtained, when available. Ct < 40 are generally considered positive by manufacturers of the cobas® 6800. Selected clinical characteristics were recorded for patients with E-gene Ct < 34 at ≥ 20 days (“Day 20”) after symptom onset (or after first positive SARS-CoV-2 PCR test for asymptomatic patients). E-gene cutoff of 34 was chosen to reflect the highest published Ct value linked to cultured virus.⁹ The Institutional Review Board of Columbia University Irving Medical Center approved this study with a waiver of informed consent.

Results

60 SOT recipients with a total of 178 SARS-CoV-2 PCR tests were identified. Forty-seven patients had a test collected on or after Day 20 (n=104 tests); 23 patients had a positive test collected on or after Day 20 (n=35 tests). Among those 23 patients, 17 (n=24 tests) had a test with an available E-gene Ct value. Of these, 10 patients (n=14 tests) had E-gene Ct <34. Ct values of the E-gene over time are presented in Figure 1. A flow chart of patients is presented in Figure 2.

Figure 1.

Cycle threshold (Ct) for the E-gene over time.

Day 0 is the day of symptom onset (or the first positive test if the patient was asymptomatic). Negative SARS-CoV-2 PCR tests are shown at the bottom of the figure on line “Not detected”.

Figure 2.

Flowchart of patients.

The 10 patients with Ct < 34 on or after Day 20 are described in Table 1. Mean age was 58.7 years. Transplanted organs included the kidney (n=6), liver (n=1), lung (n=1), and heart (n=2). Regarding severity of illness, 4 of the 10 patients never required supplemental oxygen during their illness, 2 patients required oxygen by nasal cannula (NC), and 4 patients were intubated or required oxygen by nonrebreather mask or high-flow NC. Regarding persistence of symptoms at or beyond Day 20, 3 of the 10 patients had persistent, unimproved symptoms (fever, dyspnea, and/or hypoxia), 6 of the 10 patients had symptom improvement or resolution and no oxygen requirement, and 1 of the 10 patients was first symptomatic at or beyond Day 20 and then had resolution of symptoms while still testing positive. Notably, a 69-year-old heart transplant recipient had a Ct value of 15 at Day 46 while dyspneic and on NC and later had a Ct value of 15 at Day 62 while asymptomatic and on room air.

Table 1.

Characteristics of patients with E-gene cycle threshold < 34 at Day 20 or later.

Patient number	Age	Organ	Day	Cycle threshold	Disposition at time of testing	Maximum oxygen delivery	Oxygen delivery at time of test	Symptoms at time of test
4	36	Kidney	38	31.7	Discharged	None	None	Cough (improved)
			52	27.9	Discharged			Cough (improved)
14	57	Liver	35	23	Discharged	Nasal cannula	None	None
			52	33.5	Readmitted		None	None
21	65	Kidney	29	32	Discharged	None	None	None
27	71	Kidney	56	32.5	Admitted	Mechanical ventilation	None	None
28	74	Lung	46	32.1	Admitted	Hi-flow nasal cannula	Nonrebreather mask	Dyspnea
32	69	Heart	38	21.2	Admitted	Nonrebreather mask	Nasal cannula	Dyspnea
			46	14.8	Admitted		Nasal cannula	Dyspnea
			62	15.1	Admitted		None	None
33	69	Kidney	43	33.0	Admitted	Nasal cannula	None	Fever
47	40	Kidney	39	26.2	Admitted	Mechanical ventilation	Mechanical ventilation	Fever
54	52	Kidney	30	32.2	Discharged	None	None	Dyspnea (improved)
61	54	Heart	28	33.5	Discharged	None	None	Weakness (improved)

Discussion

The COVID-19 pandemic has significantly affected the care of SOT recipients, with fewer transplant surgeries, increases in waitlist deaths, and high mortality among patients admitted to the hospital.^13–15 Limiting healthcare-associated transmission of SARS-CoV-2, in particular among immunocompromised patients, continues to be a high priority. Nevertheless, there are limited data guiding the duration of Transmission-Based Precautions for this population, in particular those based on PCR results. In this brief study, 10/47 (21%) of SOT recipients undergoing SARS-CoV-2 PCR testing at least 20 days after symptom onset or first positive test had a positive result with a E-gene Ct < 34, a value associated with potential viral viability. More importantly, the majority of these patients were asymptomatic or symptomatically improved by that time and would have thus been discontinued from Transmission-Based Precautions as recommended by current CDC guidelines. It is unclear if culturing viable virus late in the clinical course of COVID-19 correlates with infectivity, since current data suggest that transmission occurs in the early symptomatic and presymptomatic stages.¹⁶ However, SOT recipients may be at increased risk of poor outcomes from SARS-CoV-2^{11, 17, 18}, so minimizing the potential for transmission is critical.

Our study has several limitations. We did not use viral culture to confirm that tests with a Ct <34 contained viable virus. Our analysis only included SOT recipients, so results may not be generalizable to other immunocompromised individuals, including bone marrow transplant recipients or patients receiving chemotherapy.

Given shortages of testing supplies and personal protective equipment and the discomfort to patients from repeated NP testing, avoiding PCR-based strategies for discontinuation of Transmission-Based Precautions may be preferable. More data, including prospective studies with set intervals for repeat testing, are needed to clarify the utility of using PCR results with Ct to help determine infectivity and the optimal duration of Transmission-Based Precautions for immunocompromised individuals.

Abbreviations:

Ct

cycle threshold

IP&C

infection prevention and control

NC

nasal cannula

NP

nasopharyngeal

SOT

solid organ transplant

PCR

polymerase chain reaction