SARS-CoV-2 infectious virus, viral RNA in nasopharyngeal swabs, and serostatus of symptomatic COVID-19 outpatients in the United States

Abstract Background SARS-CoV-2 infectious virus isolation in the upper airway of COVID-19 patients is associated with higher levels of viral RNA. However, comprehensive evaluation of the relationships between host and disease factors and infectious, replication competent virus is needed. Methods Symptomatic COVID-19 outpatients were enrolled from the United States. 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. Findings Among 204 participants within one week of reported symptom onset (median=5, IQR 4-5 days), median age was 40 (min-max: 18-82 years), median nasopharyngeal viral RNA was 6.5 (IQR 4.7-7.6 log10 copies/mL), and 26% had detectable SARS-CoV-2 antibodies at baseline. Infectious virus was recovered in 7% of participants with 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 Interpretation The presence of SARS-CoV-2 antibodies is strongly associated with clearance of infectious virus isolation. Seropositivity and viral RNA are likely more reliable markers of infectious virus suppression than subjective measure of COVID-19 symptoms. Virus-targeted treatment and prevention strategies should be administered as early as possible and ideally before seroconversion. Funding Ridgeback Biotherapeutics, LP and NIH ClinicalTrials.gov Identifier NCT04405570 Research in Context Evidence before this study A deeper understanding of the viral and host factors associated with infectious virus detection is essential to accurately identify and quarantine contagious individuals. Several studies have reported associations between SARS-CoV-2 virus isolation and viral RNA levels or time from symptom onset. However, little is known about which host factors (i.e. demographics, comorbidities, SARS-CoV-2 seropositivity, symptomatology etc.) are associated with infectious virus detection. A search of PubMed on 12 April 2021 using keywords “COVID-19” or “SARS-CoV-2” and “infectious virus isolation” yielded 14 publications that evaluated virus isolation from respiratory samples of SARS-CoV-2 infected individuals. Five of these studies were case reports or case series that included up to 5 individuals. Seven studies included cohorts of both outpatients and hospitalized individuals and found strong associations between virus isolation and time from symptom onset and viral RNA level. Of these seven, only two studies evaluated the association between SARS-CoV-2-specific antibodies and virus isolation, but were limited by the late timing of collection (>10 days after symptom onset) or the small number of participants included. The remaining two articles compared virus isolation with antigen and molecular based diagnostics and reviewed prior literature respectively. Collectively, these studies suggest that infectious virus isolation from nasopharyngeal swab samples is possible up to 10 days from symptom onset in individuals with mild disease and for longer in those with severe illness or an underlying immune deficiency. No study has systematically evaluated host, disease, and viral factors associated with infectious virus isolation in the same cohort. Added value of this study To better understand the host, disease, and viral factors associated with virus isolation in ambulatory individuals with COVID-19, we analyzed demographic, symptom, virologic, and SARS-CoV-2-specific antibody data at baseline entry to outpatient care from 204 individuals enrolled in a randomized placebo-controlled study of a novel oral therapeutic. Host characteristics were self-reported and viral RNA quantitation, virus isolation, and SARS-2 specific antibody testing (IgG, IgM, IgA and total Ig) were performed at central laboratories. This represents the largest evaluation of virus isolation from symptomatic outpatients with COVID-19 reported to date, and affords an important opportunity to understand which host, virus, and disease factors are associated with the presence and clearance of infectious virus in the nasopharynx. Consistent with prior studies, we found that isolation of replication competent SARS-CoV-2 in vitro strongly correlated with both higher nasal viral qRT-PCR RNA levels and shorter time since symptom onset. Importantly, we also found that SARS-CoV-2 antibodies are strongly associated with the clearance of infectious virus, with virus isolation in 7% of seropositive individuals compared to 58% of seronegative individuals. Implications of all the available evidence Our findings provide a comprehensive analysis of key virus, host, and disease factors associated with infectious virus isolation and suggest that antibody detection appears to be a more reliable marker of infectious virus clearance than patient-reported symptom duration.