Viral dynamics of SARS-CoV-2 across a spectrum of disease severity in COVID-19.

Dear Editor,

Fang et al. reported in this journal that viral shedding of SARS-CoV-2 in nasal swabs was longer in intensive care unit (ICU) patients compared with non-ICU patients with Coronavirus Disease 2019 (COVID-19). COVID-19 encompasses a heterogeneous spectrum of illness, ranging from asymptomatic and mild infections, to severely ill cases in 4–16%. , Here, we report the findings of a prospective cohort study to determine viral dynamics of SARS-CoV-2 in mild to critical severity of illness, and the temporal viral burden at different body sites.

We included the first eleven laboratory-confirmed COVID-19 patients hospitalized in two hospitals in Hong Kong in February 2020. Disease severity was categorized as previously defined. We collected serial upper (pooled nasopharyngeal and throat swabs, N = 75) and lower respiratory tract samples (sputum and tracheal aspirate, N = 43), peripheral blood plasma (N = 50), urine (N = 43) and stool (N = 43) samples from all participants, and monitored SARS-CoV-2 viral loads in these samples.

One participant had mild, 5 moderate, 3 severe, and 2 critical disease. All patients were discharged; no one died. Their clinical and epidemiological features are shown in Table 1 . Viral loads for each sample are shown in Supplementary Table 1.

Table 1

Epidemiological and clinical characteristics and outcomes of the participants.

Variables1	All	Critical/Severe disease	Moderate/Mild disease
Number	11	5	6
Age, years	58 (42, 70)	65 (62, 70)	51.5 (38, 58)
Male	7 (63.6%)	4 (80.0%)	3 (50.0%)
Comorbidities2	6 (54.5%)	4 (80.0%)	2 (33.3%)
Travel to Wuhan	0 (0%)	0 (0%)	0 (0%)
Travel to other parts of China	2 (18.2%)	1 (20.0%)	1 (16.7%)
Household contact with confirmed case	2 (18.2%)	0 (0%)	2 (33.3%)
Duration of symptoms before admission, days	7 (5, 10)	9 (5, 10)	6.5 (5, 10)
Symptoms at presentation
Fever	8 (72.7%)	3 (60.0%)	5 (83.3%)
Cough	8 (72.7%)	4 (80.0%)	4 (66.7%)
Shortness of breath	3 (27.3%)	3 (60.0%)	0 (0%)
Diarrhea3	2 (18.2%)	2 (40.0%)	0 (0%)
Complications
Viral pneumonitis	10 (90.9%)	5 (100%)	5 (83.3%)
Cardiac ischemia	1 (9.1%)	1 (20.0%)	0 (0%)
Acute kidney injury	1 (9.1%)	1 (20.0%)	0 (0%)
Liver dysfunction	3 (27.3%)	1 (20.0%)	2 (33.3%)
Myositis	1 (9.1%)	0 (0%)	1 (16.7%)
Bacterial sepsis	1 (9.1%)	1 (20.0%)	0 (0%)
Supplemental oxygen	5 (45.5%)	5 (100%)	0 (0%)
Mechanical ventilation	2 (18.2%)	2 (40.0%)	0 (0%)
Intensive care admission	2 (18.2%)	2 (40.0%)	0 (0%)
Antiviral therapy
Lopinavir/ritonavir	11 (100%)	5 (100%)	6 (100%)
Ribavirin	8 (72.7%)	3 (60.0%)	5 (83.3%)
Beta-interferon	5 (45.5%)	2 (40.0%)	3 (50.0%)
Corticosteroid therapy4	1 (9.1%)	1 (20.0%)	0 (0%)
Death	0 (0%)	0 (0%)	0 (0%)

Values are expressed in number (percentage) and median (interquartile range).

Critical/severe disease: Patient A had hypertension, Patient C had coronary artery disease, Patient E had heart block, Patient I had diabetes; moderate/mild disease: Patient H had diabetes, Patient K had hypertension.

Diarrhea developed in 6 other patients during hospitalization, possibly due to use of antiviral agents.

Patient E received intravenous hydrocortisone 150 mg/day from Day 5 to 10 of illness.

Nine participants, including 4 participants with mild-moderate disease, had viral shedding lasting longer than 14 days in the respiratory tract. In four (36%) participants, return to PCR positivity in the respiratory tract was observed after ≥1 negative test, without worsening of symptoms. In patient A, PCR positivity occurred in upper and lower respiratory tract samples after a 7-day “apparent clearance” where 3 upper and 3 lower respiratory samples were negative (Fig. 1 ).

Fig. 1

Viral loads in log copies/mL at each body site are shown for each patient at various time points from onset of illness. The clinical features, including duration of fever, supplemental oxygen, mechanical ventilation, and antiviral therapy, are shown at the bottom.

Viral loads in respiratory tract samples did not correlate with disease severity. However, the timing of peak viral burden differed between participants with different severity. In all five participants with severe/critical and three with moderate disease, viral loads in respiratory tract samples continued to rise and peaked in the second week of illness (range 5.57–9.66 log copies/mL). In the remaining three with mild/moderate disease, viral load peaked in the first week of illness (range 3.25–6.40 log copies/mL) (Fig. 1 and Supplementary Fig.1 ).

Viral burden peaked later, viral load was significantly higher, and duration of viral shedding appeared to be longer in lower than in upper respiratory tract samples (Supplementary Table 2). Three of the five participants with severe/critical disease had both upper and lower respiratory tract samples tested. At the time of respiratory failure requiring supplemental oxygen or mechanical ventilation, two of these participants (patients B and E) had positive RT-PCR in lower respiratory tract samples while upper respiratory tract samples had turned negative for ≥7 days (Fig. 1 and Supplementary Fig. 1).

All eleven participants had at least one stool sample tested positive for SARS-CoV-2. The timing of diarrhea did not correlate with stool PCR positivity. Four participants had longer duration (by 1–4 days) of viral shedding in stool than in respiratory tract. Viral loads in stool were lower than in either upper or lower respiratory tract samples (Supplementary Table 2), but did not differ between mild-moderate and severe-critical diseases.

SARS-CoV-2 was not detected in any of the 43 urine samples. In particular, all 8 urine samples from patient B were negative despite the need for renal replacement therapy for acute kidney injury. His-renal biopsy showed features of acute tubular injury; electron microscopy did not reveal viral particles in proximal tubules.

One patient with moderate and one with critical disease had transient viremia, lasting 1 and 5 days, with peak viral loads 4.00 and 3.65 log copies/mL, respectively.

In this study of patients with COVID-19 across a wide spectrum of severity, we observed that viral shedding in the respiratory tract lasting longer than 14 days was common. Viral load peaked later in the second week of illness in more severe disease. Extrapulmonary detection of RT-PCR positivity other than the gut was uncommon.

We observe two patterns of viral dynamics trajectory in the respiratory tract. In more severe disease, viral load appeared to peak in the second week of illness in both upper and lower respiratory tract. A more heterogeneous pattern was seen in milder disease. Time to dyspnea and intensive care was around 8–10 days after illness onset. Therefore, continued viral replication in the respiratory tract, correlated with this timing of clinical deterioration, as observed in other studies. , This observation implied that antiviral therapy, rather than immunomodulatory agents, might be more effective as treatment for severe disease.

Viral load was significantly higher and peaked later in lower than upper respiratory tract samples. In severe/critical disease, monitoring should be performed using lower respiratory tract samples. Firstly, viral shedding was more prolonged in lower than upper respiratory tract samples, thus serves as better guidance for the duration of infection prevention measures. Secondly, viral loads in lower respiratory tract better reflected the temporal course of clinical progression in severe disease than upper respiratory tract samples. ,

All patients demonstrated stool RT-PCR positivity at some stage of their disease, regardless of gastrointestinal symptoms. While other series had positivity rates of around 50%, , , repeated testing in our study allowed detection of transient positivity lasting 1–2 days. There is widespread presence of ACE2 as cellular receptors and viral particles in epithelial cells along different parts of the gastrointestinal tract. While the clinical role of testing SARS-CoV-2 from stool as monitoring or discharge criteria remains uncertain, stool as an additional specimen to assist diagnosis, particularly in asymptomatic contacts of confirmed patients, is worth exploring.

Our study was limited by the small sample size. Asymptomatic patients were not studied, and the effect of antiviral therapy could not be determined. Viral dynamics at different sites should be further explored in larger populations of COVID-19 patients.

In conclusion, viral shedding in respiratory tract lasting longer than 14 days was common in all spectrum of COVID-19 severity. Clinical deterioration correlated temporally with viral replication in severe disease, especially in the lower respiratory tract, highlighting the importance of effective antiviral therapy. Extrapulmonary detection of SARS-CoV-2 PCR other than the gut was uncommon.