SARS-CoV-2 RNA and Nucleocapsid Antigen Are Blood Biomarkers Associated With Severe Disease Outcomes That Improve in Response to Remdesivir

Abstract

Background: Although antivirals remain important for the treatment COVID-19, methods to assess treatment efficacy are lacking. Here, we investigated the impact of remdesivir on viral dynamics and their contribution to understanding antiviral efficacy in the multicenter Adaptive COVID-19 Treatment Trial 1, which randomized patients to remdesivir or placebo.

Methods: Longitudinal specimens collected during hospitalization from a substudy of 642 patients with COVID-19 were measured for viral RNA (upper respiratory tract and plasma), viral nucleocapsid antigen (serum), and host immunologic markers. Associations with clinical outcomes and response to therapy were assessed.

Results: Higher baseline plasma viral loads were associated with poorer clinical outcomes, and decreases in viral RNA and antigen in blood but not the upper respiratory tract correlated with enhanced benefit from remdesivir. The treatment effect of remdesivir was most pronounced in patients with elevated baseline nucleocapsid antigen levels: the recovery rate ratio was 1.95 (95% CI, 1.40-2.71) for levels >245 pg/mL vs 1.04 (95% CI, .76-1.42) for levels <245 pg/mL. Remdesivir also accelerated the rate of viral RNA and antigen clearance in blood, and patients whose blood levels decreased were more likely to recover and survive.

Conclusions: Reductions in SARS-CoV-2 RNA and antigen levels in blood correlated with clinical benefit from antiviral therapy.

Clinical trial registration: NCT04280705 (ClinicalTrials.gov).

Keywords: COVID-19; SARS-CoV-2; antiviral efficacy; clinical trial; remdesivir.

Figure 1.

Distribution of baseline viral loads by disease severity and correlation with other biomarkers. A, Distribution of baseline viral loads by assay categorized by disease severity. Box plots indicate the median (line) and IQR (box). Wilcoxon P values assess differences in medians between disease severity groups, and proportions of samples are shown below each assay's limit of quantification (LOQ; illustrated by size of bottom circle). RNA values below the assay LOQ of 1.79 log₁₀ copies/mL were set as half the LOQ (1.49 log₁₀ copies/mL) when measurements were above the lower limit of detection and one-quarter the LOQ (1.19 log₁₀ copies/mL) when RNA was not detected; nucleocapsid antigen values below the assay LOQ of 3 pg/mL were set as half the LOQ (1.5 pg/mL). B, Matrix heat map of Pearson correlations between baseline biomarker levels among all patients in the primary cohort. *P < .05. **P < .01. ***P < .001. Coefficient estimates are provided in Supplementary Table 4. CRP, C-reactive protein; IL-6, interleukin 6.

Figure 2.

Distribution of baseline viral loads by assay according to the clinical outcome: A, recovery; B, mortality. Box plots indicate the median (line) and IQR (box). Wilcoxon P values assess differences in medians between disease severity groups, and proportions of samples are shown below each assay's limit of quantification (LOQ; illustrated by size of bottom circle). RNA values below the assay LOQ of 1.79 log₁₀ copies/mL were set as half the LOQ (1.49 log₁₀ copies/mL) when measurements were above the lower limit of detection and one-quarter the LOQ (1.19 log₁₀ copies/mL) when RNA was not detected; nucleocapsid antigen values below the assay LOQ of 3 pg/mL were set as half the LOQ (1.5 pg/mL).

Figure 3.

Impact of remdesivir on clinical outcomes according to viral load subgroups. Forest plots illustrate subgroup analyses of Cox models to evaluate for a differential effect of remdesivir on (A) recovery and (B) mortality based on baseline viral load or presence of antispike antibodies. Viral load measurements were dichotomized at median values per assay: 2.39 log₁₀ pg/mL (245 pg/mL) for serum nucleocapsid, 2.09 log₁₀ copies/mL (123 copies/mL) for plasma RNA, and 3.41 log₁₀ copies/mL (2570 copies/mL) for upper respiratory RNA. P values for treatment interaction are shown. HR, hazard ratio; PLC, placebo; RDV, remdesivir; RRR, recovery rate ratio.

Figure 4.

Virologic efficacy of remdesivir vs placebo. A, Differences in mean daily rate of change of viral load among patients with moderate/severe disease by treatment arm. P values are shown for differences in adjusted daily rate of change when normalized to baseline level. For calculations, RNA values below the assay limit of quantification (LOQ) of 1.79 log₁₀ copies/mL were set as half the LOQ (1.49 log₁₀ copies/mL) when measurements were above the lower limit of detection (LLOD) and one-quarter the LOQ (1.19 log₁₀ copies/mL) when RNA was not detected. B, Bar plot of patients with increasing or persistently elevated viral loads measured through 5 days of treatment. Relative risk (RR) of an increasing viral load comparing remdesivir and placebo recipients are shown with corresponding P values.

Figure 5.

Time to recovery comparing patients with increasing vs decreasing viral loads. Kaplan-Meier curve analyses compare patients with decreasing viral loads (blue) and those with increasing or persistently elevated viral loads (red) through the first 5 days of treatment. P values represent test of the log-rank statistic.