By Stan Deresinski, MD, FACP, FIDSA

Clinical Professor of Medicine, Stanford University

Dr. Deresinski reports no financial relationships relevant to this field of study.

SYNOPSIS: Significantly immunocompromised patients with COVID-19 may shed cultivatable virus for as long as two months or more after symptom onset.

SOURCES: Aydillo T, Gonzalez-Reiche AS, Aslam S, et al. Shedding of viable SARS-CoV-2 after immunosuppressive therapy for cancer. N Engl J Med 2020; Dec 1. doi: 10.1056/NEJMc2031670. [Online ahead of print].

Choi B, Choudhary MC, Regan J, et al. Persistence and evolution of SARS-CoV-2 in an immunocompromised host. N Engl J Med 2020;383:2291-2293.

Aydillo and colleagues evaluated the duration of shedding of viable (replication-competent) SARS-CoV-2 in 20 immunocompromised patients with COVID-19. Two had lymphoma and the remaining 18 had either received hematopoietic stem cell transplants or chimeric antigen receptor T-cell (CAR-T) therapy. Fifteen patients were receiving active therapy, and COVID-19 was judged to be severe in 11 patients.

Testing of serially obtained nasopharyngeal and sputum samples was able to detect viral ribonucleic acid (RNA) for as long as 78 days (interquartile range, 24 to 64 days) after the onset of symptoms. Detection of viable virus was accomplished by culture on Vero cells and was identified in nasopharyngeal samples of 10 of 14 patients for whom nasopharyngeal samples on the first day of testing were available. Follow-up cultures were positive in five patients, remaining so for eight, 17, 25, 26, and 61 days after their symptom onset. Whole-genome sequencing demonstrated that each of the five patients was infected with a distinct viral strain and that the subsequently recovered virus isolates were essentially identical to the original isolate in each.

Separately, Choi and colleagues reported recovery of SARS-CoV-2 in culture from a single patient at day 75. They also found evidence that the virus had undergone evolution during its sojourn in the patient.


The fact that that SARS-CoV-2 RNA shedding may last for weeks after the onset of symptoms has led to prolonged patient isolation in many cases. However, it has become clear that viral RNA may continue to be detected long after viable virus can no longer be detected. Studies involving small numbers of patients have concluded that virus can no longer be recovered in tissue culture eight to 10 days after symptom onset. These findings undoubtedly contributed to the current Centers for Disease Control and Prevention (CDC) recommendation that transmission-based precautions may be discontinued:1

  • 10 days since symptoms first appeared; AND
  • absence of fever (in absence of antipyretics) for 24 hours; AND
  • other symptoms are improving (although anosmia and ageusia may persist for weeks to months).

The studies indicating apparent absence of replication of competent virus by approximately 10 days after symptom onset did not, however, include patients with significant immunocompromise. Nonetheless, the CDC does take the potential for more prolonged shedding of viable virus into account:

“A limited number of persons with severe illness may produce replication-competent virus beyond 10 days that may warrant extending duration of isolation and precautions for up to 20 days after symptom onset; consider consultation with infection control experts.” Elsewhere, the CDC states, “People who are severely ill with COVID-19 might need to stay home longer than 10 days and up to 20 days after symptoms first appeared. Persons who are severely immunocompromised may require testing to determine when they can be around others.” They define an immunocompromised state as one resulting from having received “… bone marrow, or organ transplant; HIV; use of corticosteroids; or use of other immune weakening medicines.” They also state that a “test-based strategy,” using polymerase chain reaction (PCR) or antigen detection, could be used, with consultative input from infection control experts, in decisions regarding the discontinuation of “isolation or precautions.”

However, using the standard PCR will lead to unnecessarily prolonged isolation in many patients because of its long period of positivity despite the absence of viable virus. On the other hand, some immunocompromised patients may shed cultivatable virus for as long as two months, as demonstrated by Aydillo and colleagues. Laboratory culture of SARS-CoV-2, a biohazardous endeavor, is an impractical approach to the problem, but others have been proposed.

Like all coronaviruses, SARS-CoV-2 is a single-strand positive-sense RNA virus used to generate a complementary minus-sense strand intermediate. In addition, positive-sense subgenomic RNAs necessary for viral replication are generated. Although the detection of subgenomic RNA has been reported to indicate the presence of replication competent virus, a very recent study has contradicted this finding and indicated that they are protected from destruction by cellular nucleases by inclusion in double-membraned vesicle.2

Another approach (currently in use at Stanford) is the detection of negative sense SARS-CoV-2 RNA as an indication of replication competence. Although the data are not all in, testing for this moiety by PCR may prove to be a useful way to make decisions about infectivity, particularly in immunocompromised patients.


  1. Centers for Disease Control and Prevention. Coronavirus Disease 2019 (COVID-19). When you can be around others after you have had or likely had COVID-19. Updated Dec. 1, 2020.
  2. Alexandersen S, Chamings A, Bhatta TR. SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication. Nat Commun 2020;11:6059.