SARS-CoV-2 viral dynamics in immunocompromised patients

To the Editor,

While the median duration of SARS-CoV-2 viral RNA detection in nasopharyngeal swabs collected from immunocompetent subjects is approximately 18 days,¹ data for immunocompromised patients are not yet available. Here, we prospectively monitored the dynamic change in SARS-CoV-2 RNA viral loads in serial nasopharyngeal swab, saliva, and respiratory specimens collected from kidney transplant recipients (KTR) hospitalized with a confirmed diagnosis of COVID-19. Nasopharyngeal samples were collected by trained nurses following the CDC recommendations. Sample collection was performed using a single type of collection tube (UTM Viral Transport; COPAN Diagnostics, Murrieta, CA). Serial dilutions of in vitro transcribed RNA (quantity: 10¹¹ copies) derived from the BetaCoV_Wuhan_WIV04_2019 strain (EPI_ISL_402124) were used. An in-house reverse transcriptase polymerase chain reaction (RT-PCR)–based assay targeting two different regions of the RNA-dependent RNA polymerase (RdRp) gene was used for the detection of SARS-CoV-2 in accordance with the WHO technical guidance.² A total of 168 swab samples (median number of specimens per patient: 4; interquartile range: 3–5) were obtained from 31 men and 11 women over a period that spanned from the onset of symptoms up to 60 days afterward, with the exception of patients who died before. Two cases—in whom the diagnosis was made based on chest CT findings—had persistently negative RT-PCR results throughout the entire study period. Table 1 summarizes the general characteristics of the study patients and their clinical course.

TABLE 1.

General characteristics, immunosuppressive treatment, COVID-19 symptoms, and clinical course in the 42 study patients

Characteristics	Value
Men, n (%)	31 (73.8)
Age (years), median (interquartile range)	63.3 (55.8–67.9)
BMI (kg/m2), median (interquartile range)	27 (23.2–33.7)
Cardiovascular disease, n (%)	16 (38)
Respiratory disease, n (%)	15 (35.7)
Diabetes, n (%)	19 (45.2)
Hypertension, n (%)	35 (83.3)
Use of RAAS inhibitors, n (%)	15 (35.7)
Delay since transplantation (years), median (interquartile range)	5.3 (2–13.6)
Maintenance immunosuppression, n (%)
Tacrolimus	23 (54.7)
Ciclosporin	13 (30.9)
MMF/MPA	35 (83.3)
mTOR inhibitors	6 (14.3)
Azathioprine	1 (2.4)
Steroids	24 (57.1)
Clinical symptoms at hospitalization, n (%)
Dyspnea	16 (38)
Cough	26 (61.9)
Fever	37 (88)
Myalgia	23 (54.7)
Headache	9 (21.4)
Diarrhea	26 (61.9)
Anosmia/ageusia	7 (16.7)
Evolution, n (%)
O2 requirement	22 (52.3)
Need for ICU transfer	14 (33.3)
Need for RRT	4 (9.5)
Death	7 (16.7)

Abbreviations: BMI, body mass index; ICU, intensive care unit, RRT: renal replacement therapy; MMF, mycophenolate mofetil; MPA, mycophenolic acid; RAAS, renin–angiotensin–aldosterone system.

The median viral load at diagnosis was 5.12 (interquartile range: 3.8–6.5) log10 copies per reaction, followed by a gradual decline over the subsequent weeks. The temporal profile of viral loads for each patient is presented in Figure 1A, whereas their general dynamics are summarized in Figure 1B. At day 30, 15 patients (43%) were considered to have a viral load >3 log10 copies per reaction, the threshold above which there may be a SARS-CoV-2 transmission risk.³ Thirteen patients had low but detectable viral loads and only eight patients (23%) achieved complete viral clearance. At day 45, 66% of the study patients had negative swabs; however, 12 cases still had detectable viral loads in their specimens. Notably, five patients had still viral loads >3 log10 copies per reaction after day 30 (Figure 1B). The maximum duration of a viral load >3 log10 copies per reaction was not lower than 43 days (possibly until 54 days; Figure 1A). At the time of last follow-up (D60), six of 35 patients (17%) had low but still detectable SARS-CoV-2 loads.

FIGURE 1.

(A) Temporal profile of viral loads in nasopharyngeal swab, saliva, and respiratory specimens obtained from kidney transplant recipients according to the days from the onset of symptoms. Each line represents a patient, whereas one case denotes 1 day (days from the onset of symptoms). The first colored box is the day of the diagnosis. The numbers express viral loads (log10 copies/reaction). To convert viral loads from copies/reaction to copies/mL, add 1.69 log. The gray cases indicate the days either before COVID-19 diagnosis or following patient death. Red cases denote the days until the viral load was measured below 3 log10 copies/reaction, whereas orange cases indicate the days until the viral load became undetectable. Green cases denote days from which viral loads were undetectable until day 60. Patient death; *viral loads measured in tracheal aspiration fluid or BAL; **viral loads measured in saliva (while negative in the nasopharyngeal swab). (B) General dynamics of viral loads reduction in nasopharyngeal swabs from 42 kidney transplant recipients with COVID-19. Days from the onset of symptoms are plotted along the X axis, whereas viral loads (log10 copies/ reaction) are represented along the Y axis. To convert viral loads from copies/reaction to copies/mL, add 1.69 log. Viral loads were high (3.9 log copies/mL) between 0 and 15 days from the onset of symptoms (plain square), intermediate (1.6 log copies/ reaction) between 15 and 30 days (dashed square), and low (<3 log copies/reaction) between 30 and 60 days (dotted square). Thirty-five percent of specimens were tested positive between day 30 and day 60 and 5 patients had still viral load above 3 log copies/reaction after day 30 (circles). The minimum detection limit of the RT-PCR assay for the identification of SARS-CoV-2 was 10 copies/reaction [Color figure can be viewed at wileyonlinelibrary.com]

The present study demonstrates that most KTR harbor high viral loads within the first 15 days from the onset of symptoms. These results are in line with those obtained in the general population⁴ and suggest a high risk of transmissibility. Moreover, we show that almost half of our patients still had sustained viral loads at day 30—with only 23% achieving complete viral clearance at this time point. Finally, immunocompromised KTR may have SARS-CoV-2–positive nasopharyngeal swabs as long as 60 days after the onset of symptoms—a remarkably longer period than that described for the immunocompetent population (20–25 days).^{4 , 5} It should be kept in mind that the detection of viral RNA does not necessarily equate to the presence of a live, infectious virus. Currently, the more widely accepted viral load threshold for virus isolation (and—consequently—the risk of contagion) is approximately 1000000 copies/mL.^{5 , 6} While viral loads were low in the majority of cases, transplant recipients should be considered a vulnerable population^{7 , 8} characterized by a prolonged viral shedding. In this scenario, transmission-based precautions should be enforced longer in KTR than in healthy persons.