In this longitudinal study, we demonstrate that the maximum duration of nasopharyngeal (25 days) and fecal (42 days) SARS-CoV-2 RNA shedding is longer than the recommended (at least 24 hours with no fever, and at least 10 days from initial symptom onset) quarantine duration [13].
Nearly, one third of our hospitalized COVID-19 patients had positive nasopharyngeal RT-PCR at the time of discharge and about one tenth of them had virus persistence in nasopharynx longer than 14 days from the first positive test. Maximum duration of nasopharyngeal shedding was 25 days from admission. These findings are compatible with some studies that revealed, some patients continued to be upper respiratory tract RT-PCR positive after discharge from hospital, for the next few days [18, 19]. We did not identify any determinants of viral persistence, but a study in china demonstrated that the prolonged presence of the virus in upper respiratory tract was associated with disease severity [20].While, another study in Portugal revealed the viral RNA persistence not associated with disease severity and stronger immune response are the determinants of virus RNA clearance [21].
Positive blood SARS-CoV-2 RNA RT-PCR was detected in about one third of our patient, but most of them turned to negative at the time of discharge. The studies on detecting SARS-CoV-2 RNA in blood were limited, but a study in china revealed that the SARS-CoV-2 RNA detected in the blood of 6 out of 57 Chinese patients and all 6 positive bloods RT-PCR had a severe clinical picture [22]. The higher positive rate of blood RT-PCR in our study was probably due to the disease severity in our patients and hospital-based design.
Our findings revealed that the positive urine SARS-CoV-2 RNA RT-PCR was less common (7 out of 100 patients) in our study population and all of them turned to negative at the time of discharge. Our result was in accordance with studies in Turkey and China that demonstrated nearly 5–7% of COVID-19 patient had positive urine RT-PCR [23, 24].
Positive stool SARS-CoV-2 RNA RT-PCR was detected in only 6 out of 100 patients in our study, but the duration of time for a positive stool RT-PCR test to turn negative was longer than nasopharynx, urine and blood RT-PCR tests, with a maximum duration of fecal shedding of 42 days. Therefore, fecal positive hospitalized patients with positive stool RT-PCR, represent the need for precautions and protective equipment for interventional procedures involving the gastrointestinal tract in a hospital environment., Similarly, a study in china demonstrates that an asymptomatic case was positive in the stool RT-PCR for a period as long as 42 days and also, reported that in almost two third of patients, the clearance of fecal shedding takes a longer time than the nasopharyngeal sample [19].
Although, our findings demonstrate that the maximum duration of nasopharyngeal and fecal SARS-CoV-2 RNA shedding is longer than the recommended quarantine duration by the CDC 13, however, it is unclear whether individuals with persistent positive RNA PCR represent an infectious risk. Future studies are needed to determine whether PCR positivity is due to infective virus or non- infective nucleic acid fragments. Therefore, until such studies are concluded, prolonged isolation duration at least 25 days may be recommended, and aggressive contact tracing might also be considered. Also, patients are advised to take strict hygiene measures, especially those with gastrointestinal symptoms for about one month, in order to prevent potential fecal-oral transmission.
The strengths of the current study are the long term follow up and detecting virus RNA in respiratory and extra-respiratory sites. However, the hospital-based design is the limitation of our study, leading to more severe patient enrollment that limits the generalizability of findings. Another limitation of our study was that the day of symptom onset was not available, and all calculations and analyses were based on first nasopharyngeal RT-PCR test at admission time thus, the duration of viral shedding was underestimated. Another limitation of current study was that the, virus isolation and tests of specimens’ infectivity were not conducted and CT value of RT-PCR was not available.