Infectious SARS-CoV-2 Virus in Symptomatic COVID-19 Outpatients: Host, Disease, and Viral Correlates

Abstract

Background: While SARS-CoV-2 infectious virus isolation in outpatients with COVID-19 has been associated with viral RNA levels and symptom duration, little is known about the host, disease and viral determinants of infectious virus detection.

Methods: COVID-19 adult outpatients were enrolled within 7 days of symptom onset. Clinical symptoms were recorded via patient diary. Nasopharyngeal swabs were collected to quantitate SARS-CoV-2 RNA by reverse transcriptase polymerase chain reaction and for infectious virus isolation in Vero E6-cells. SARS-CoV-2 antibodies were measured in serum using a validated ELISA assay.

Results: Among 204 participants with mild-to-moderate symptomatic COVID19, the median nasopharyngeal viral RNA was 6.5 (IQR 4.7-7.6 log₁₀ copies/mL), and 26% had detectable SARS-CoV-2 antibodies (IgA, IgM, IgG, and/or total Ig) at baseline. Infectious virus was recovered in 7% of participants with SARS-CoV-2 antibodies compared to 58% of participants without antibodies (probability ratio (PR)=0.12, 95% CI: 0.04, 0.36; p=0.00016). Infectious virus isolation was also associated with higher levels of viral RNA (mean RNA difference +2.6 log₁₀, 95% CI: 2.2, 3.0; p<0.0001) and fewer days since symptom onset (PR=0.79, 95% CI: 0.71, 0.88 per day; p<0.0001).

Conclusions: The presence of SARS-CoV-2 antibodies is strongly associated with clearance of infectious virus isolation. Seropositivity and viral RNA levels are likely more reliable markers of infectious virus clearance than subjective measure of COVID-19 symptom duration. Virus-targeted treatment and prevention strategies should be administered as early as possible and ideally before seroconversion.

Clinicaltrialsgov identifier: NCT04405570.

Keywords: COVID-19; SARS-CoV-2; infectious virus; outpatient; serostatus.

Figure 1.. SARS-CoV-2 viral RNA levels in nasopharyngeal swab by infectious virus status

Nasopharyngeal viral RNA levels measured via qRT-PCR are displayed by infectious virus status, with culture negative in grey (n = 95) and culture positive (n = 78) in red; each dot represents a participant. Solid lines on the boxplots display the median and 25th-75th percentile (mean = blue dashed line) and the whiskers extend to the extrema (no more than 1.5 times the IQR from the box). LLoQ = lower limit of quantification; SD = standard deviation.

Figure 2.. SARS-CoV-2 viral RNA, time since symptom onset, and infectious virus by SARS-CoV-2 specific antibody serostatus

Panel A shows seropositive participants. Panel B shows seronegative participants. Seropositive is defined as having SARS-CoV-2 specific total Ig, IgG, IgM, or IgA antibodies. Nasopharyngeal viral RNA levels (log₁₀ copies/mL) are shown on the y-axis and days since symptom onset on the x-axis, with infectious virus culture positive participants in red circles, and culture negative participants in grey squares. The overall viral RNA median (Q1, Q3) and LLoQ are indicated by dashed horizontal lines. Ig = immunoglobulin; LLoQ = lower limit of quantification; Q1 = 25^th percentile; Q3 = 75^th percentile.

Figure 3.. Host factor associations with infectious SARS-CoV-2 virus isolation

Bivariate unadjusted analyses are shown. *Prevalence ratios for the probability of infectious virus isolation were estimated for each dichotomous characteristic and a prevalence ratio per unit change was estimated for each continuous characteristic with corresponding 95% confidence intervals. Each continuous characteristic was fit as linear in the log-prevalence of infectious virus isolation. PR = prevalence ratio.