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SARS-CoV-2 Detected in Multiple Sample Types

NEW YORK – The SARS-CoV-2 virus can be detected to varying degrees in lung wash, biopsy, nasal, sputum, feces, and blood samples from infected individuals, but not in urine, according to new research from investigators at China's National Institute for Viral Disease Control and Prevention, Beijing Ditan Hospital, and the Qingdao Municipal Center for Disease Control and Prevention.

In a letter published online in the Journal of the American Medical Association on Wednesday, the researchers outlined efforts to understand which clinical specimens can harbor the SARS-CoV-2 virus, which causes the coronavirus disease COVID-19.

The team collected 1,070 samples from 205 individuals diagnosed with COVID-19, using RNA extraction and real-time reverse transcriptase PCR (RT-qPCR), to search for sequences stemming from SARS-CoV-2. In particular, samples were deemed SARS-Cov-2-positive if RNA from the virus could be detected with 40 or fewer RT-qPCR cycles.

"The cycle threshold values of [RT-qPCR] were used as indicators of the copy number of SARS-CoV-2 RNA in specimens," the authors explained, "with lower cycle threshold values corresponding to higher viral copy numbers."

Using this approach, the researchers detected SARS-CoV-2 RNA in 72 of 104 sputum samples, five of eight nasal swab samples, and 126 of 398 pharyngeal swab samples. While the virus was not found in any of the 72 urine samples tested, it did turn up in 29 percent of the 153 fecal samples assessed, prompting follow-up culturing and electron microscopy analyses on four fecal samples to search for live viruses.

"Importantly," they reported, "the live virus was detected in feces, implying that SARS-CoV-2 may be transmitted by the fecal route."

The most pronounced rates of positivity came from the so-called bronchoalveolar lavage samples, collected by washing and retrieving fluid samples from part of a patient's lung through the mouth or nose. Of the 15 samples collected in that manner, 14 (or 93 percent) were positive for the coronavirus. In contrast, just six of 13 (46 percent) biopsy samples obtained using a fibrobronchoscope brush tested positive for SARS-CoV-2 by RT-qPCR.

The virus was also found only infrequently in the blood in the researchers' analyses. They detected SARS-CoV-2 in just 1 percent of the 307 blood samples tested, totaling three positive blood samples in all — results that they suspect were due to systemic infection in these patients.

The patients included in the study ranged in age from just 5 years old to 67, the authors noted, and were treated at three hospitals in Beijing, Hubei province, and Shandong province between early January and mid-February of this year.

"Blood, sputum, feces, urine, and nasal samples were collected throughout the illness," the authors explained. "Bronchoalveolar lavage fluid and fibrobronchoscope brush biopsy were samples from patients with severe illness or undergoing mechanical ventilation."

Some 19 percent of the patients in that group developed severe illness, while the majority of those diagnosed with the condition experienced now well-documented symptoms such as a fever, fatigue, and a dry cough.

The authors cautioned that the current results do not provide insights into potential ties between different types of positive clinical samples and patient symptoms or disease severity, since they did not have access to in-depth clinical data for all of the patients included in the study.

From their current findings, they concluded that "[f]urther investigation of patients with detailed temporal and symptom data and consecutively collected specimens from different sites is warranted."