Detection of SARS-CoV-2 RNA in 12 types of specimen of hospitalized COVID-19 patients
SARS-CoV-2 virus may attack different tissues and organs of human being. In order to understand the distribution of SARS-CoV-2 RNA in different specimens, we collected the specimens available from the upper respiratory tract (nasopharynx and oropharynx) and lower respiratory tract (sputum and alveolar lavage fluid), digestive system (intestinal tract and anus), urinary system (urine), blood system (peripheral blood), conjunctiva (conjunctival secretion), the nervous system (cerebrospinal fluid, CSF), peritoneal dialysis fluid (PDF), corneal secretion and sweat glands (sweat) for each hospitalized patients with COVID-19 (Fig. 1).
We performed SARS-CoV-2 RNA detection with the 12 types of specimens from 1,008 hospitalized patients with COVID-19 (Table 1). The double positive for both ORF1ab gene and N gene were 64.15% in nasopharyngeal swab, 46.67% in BALF, 25.64% in oropharynx swab, 15.97% in sputum, 12.21% in stool, 8.89% in urine, 8.16% in anal swab, 7.50% in blood and 1.49% in corneal secretion (Fig. 2). The single positive for either ORF1ab gene or N gene were 20.00% in BALF, 12.57% in sputum, 7.40% in urine, 6.91% in nasopharyngeal swab, 5.13% in oropharynx swab, 5.00% in blood and 3.05% in stool (Fig. 2). No SARS-CoV-2 RNA was detected in PDF and CSF specimens.
Table 1
SARS-CoV-2 RNA in different specimens from COVID-19 patients
Types of sample | Sample number | ORF1ab and N genes both positive | Only ORF1ab gene positive | Only N gene positive | ORF1ab and N genes both negative |
No. | rate (%) | No. | rate (%) | No. | rate (%) | No. | rate (%) |
nasopharyngeal swab | 463 | 297 | 64.15 | 28 | 6.05 | 4 | 0.86 | 134 | 28.94 |
oropharyngeal swab | 39 | 10 | 25.64 | 0 | 0.00 | 2 | 5.13 | 27 | 69.23 |
sputum | 382 | 61 | 15.97 | 37 | 9.69 | 11 | 2.88 | 273 | 71.47 |
BALF | 15 | 7 | 46.67 | 3 | 20.00 | 0 | 0.00 | 5 | 33.33 |
stool | 262 | 32 | 12.21 | 7 | 2.67 | 1 | 0.38 | 230 | 87.79 |
anal swab | 98 | 8 | 8.16 | 2 | 2.04 | 1 | 1.02 | 87 | 88.78 |
urine | 135 | 12 | 8.89 | 6 | 4.44 | 4 | 2.96 | 113 | 83.70 |
PDF | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 100 |
blood | 40 | 3 | 7.50 | 1 | 2.50 | 1 | 2.50 | 35 | 87.50 |
sweat | 12 | 0 | 0 | 0 | 0 | 0 | 0 | 12 | 100 |
CSF | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 100 |
corneal secretion | 67 | 1 | 1.49 | 1 | 1.49 | 0 | 0 | 65 | 97.02 |
BALF, Broncho alveolar lavage fluid; PDF, peritoneal dialysis fluid; CSF, cerebrospinal fluid |
Detection of SARS-CoV-2 RNA in 7 types of specimen from discharged patients with COVID-19
In order to explain the cause about so-called recovered positive, we further analyzed 7 types of specimens of nasopharyngeal swab, oropharyngeal swab, sputum, stool, anal swab, urine and peripheral blood in 20 discharged patients with COVID-19 in their quarantine time up to 14 days. The average of the quarantine time was 8.1 ± 3.4 days, ranging from 4 to 14 days (Table 2). All the 6 patients showed positive viral RNA for at least one gene in nasopharyngeal swab, 2 patients had both ORF1ab and N gene positive, another 3 patients only showed ORF1ab positive and 2 patient showed N gene positive. The double positive of both ORF1ab and N gene RNA were found in 5 cases at least in one specimen simultaneously, while 2 of which in sputum, 1 of which in nasopharynx swab, 1 of which in anal swab and 1 of which in the 3 specimens (nasopharynx swab, oropharynx swab and sputum) simultaneously. No positive SARS-CoV-2 RNA was detected in the specimens of stool, urine and blood of the 20 discharge patients (Table 2).
Table 2
SARS-CoV-2 RNA positive in different specimens from the discharged COVID-19 patients in isolation period
Patients | Gene | nasopharyngeal swab | oropharyngeal swab | sputum | stool | anal swab | urine | blood |
number | isolated days |
P3 | 6 | ORF1ab | + | - | - | - | - | - | - |
N | + | - | - | - | - | - | - |
P6 | 8 | ORF1ab | + | - | + | - | - | - | - |
N | - | - | + | - | - | - | - |
P7 | 9 | ORF1ab | + | - | + | - | - | - | - |
N | - | - | + | - | - | - | - |
P8 | 4 | ORF1ab | + | - | - | - | - | - | - |
N | - | + | - | - | - | - | - |
P12 | 8 | ORF1ab | - | - | - | - | + | | - |
N | + | - | - | - | + | - | - |
P15 | 4 | ORF1ab | + | + | + | - | - | - | - |
N | + | + | + | - | - | - | - |
+, positive; -, negative |
During the quarantine time of these 20 patients, the positive rate of SARS-CoV-2 was 30% (6/20) in nasopharyngeal swab, 10% (2/20) in oropharyngeal swab, 15% (3/20) in sputum, and 5% (1/20) in anal swab, respectively. The double positive of both ORF1ab and N gene RNA were found in 25% (5/20) cases at least in one specimen simultaneously (Fig. 3).