SARS-CoV-2 RNAaemia predicts clinical deterioration and extrapulmonary complications from COVID-19

Abstract

Background: The determinants of COVID-19 disease severity and extrapulmonary complications (EPCs) are poorly understood. We characterise the relationships between SARS-CoV-2 RNAaemia and disease severity, clinical deterioration, and specific EPCs.

Methods: We used quantitative (qPCR) and digital (dPCR) PCR to quantify SARS-CoV-2 RNA from nasopharyngeal swabs and plasma in 191 patients presenting to the Emergency Department (ED) with COVID-19. We recorded patient symptoms, laboratory markers, and clinical outcomes, with a focus on oxygen requirements over time. We collected longitudinal plasma samples from a subset of patients. We characterised the role of RNAaemia in predicting clinical severity and EPCs using elastic net regression.

Findings: 23·0% (44/191) of SARS-CoV-2 positive patients had viral RNA detected in plasma by dPCR, compared to 1·4% (2/147) by qPCR. Most patients with serial measurements had undetectable RNAaemia 10 days after onset of symptoms, but took 16 days to reach maximum severity, and 33 days for symptoms to resolve. Initially RNAaemic patients were more likely to manifest severe disease (OR 6·72 [95% CI, 2·45 - 19·79]), worsening of disease severity (OR 2·43 [95% CI, 1·07 - 5·38]), and EPCs (OR 2·81 [95% CI, 1·26 - 6·36]). RNA load correlated with maximum severity (r = 0·47 [95% CI, 0·20 - 0·67]).

Interpretation: dPCR is more sensitive than qPCR for the detection of SARS-CoV-2 RNAaemia, which is a robust predictor of eventual COVID-19 severity and oxygen requirements, as well as EPCs. Since many COVID-19 therapies are initiated on the basis of oxygen requirements, RNAaemia on presentation might serve to direct early initiation of appropriate therapies for the patients most likely to deteriorate.

Figure 1.. Pairwise Pearson’s correlations between measures of nasopharyngeal (NP) and plasma SARS-CoV-2 RNA load.

Colors reflect absolute pairwise correlation, as qPCR cycle thresholds are expected to be inversely proportional to SARS-CoV-2 RNA concentrations as measured by dPCR. Plasma RNA concentration by dPCR at enrollment (“Plasma dPCR day 0”) is modestly negatively correlated (r = −0·30) with qPCR Ct on the same specimen, moderately correlated with plasma dPCR on day 3/7 (r = 0·42), and poorly correlated with RNA concentration in the nasopharynx (r = 0·16), suggesting that RNAaemia is weakly related to nasopharyngeal viral load. NP = nasopharyngeal swab. qPCR = quantitative PCR. dPCR = digital PCR.

Figure 2.. Distribution of discrete and binned WHO severity scores.

We classified the maximum severity of 147 SARS-CoV-2 presentations using a modified WHO score, as follows: 1 = asymptomatic infection, 2 = symptomatic infection not requiring admission, 3 = admitted without supplemental oxygen, 4 = admitted, requiring oxygen by nasal cannula, 5 = admitted, requiring oxygen by high-flow nasal cannula, 6 = admitted, requiring mechanical ventilation, 7 = admitted, requiring mechanical ventilation and vasopressors or renal replacement therapy, 8 = death from COVID-related cause. A. Distribution of WHO scores. B. Distribution of binned (mild, moderate, severe) scores.

Figure 3.. SARS-CoV-2 RNAaemia and clinical severity.

A. RNAaemic patients had higher mean maximum WHO scores (4·80) than non-RNAaemic patients (3·24, difference = 1·56 [95% CI of difference, 1·00 – 2·11]). 40·9% of RNAaemic patients developed severe disease, compared to 10·2% of non-RNAaemic patients (difference = 30·7% [95% CI of difference, 13·9% - 47·5%]). 4·5% of initially RNAaemic patients had mild disease, compared to 35·4% of non-RNAaemic patients (difference = 30·8% [95% CI of difference, 19·5% - 42·2%]). The same proportion (54·5%) of both RNAaemic and non-RNAaemic patients had disease of moderate severity. B. Among patients with detectable RNAaemia at time of enrollment (n=44), patients with higher plasma RNA concentrations manifested more severe disease (r = 0·47 [95% CI, 0·20 – 0·67]). RNA concentrations in RNAaemic patients were distributed approximately log-normally, so were log-scaled for depiction and calculation of correlation. Dashed blue line shows linear correlation between log-scaled plasma RNA concentration and maximum clinical severity.

Figure 4.. Dynamics of SARS-CoV-2 RNAaemia and clinical severity, by modified WHO score.

A. Serial plasma SARS-CoV-2 RNA concentrations and WHO scores for each of the 27 patients with longitudinal samples. Plasma RNA concentration (red gradient) and WHO scores (blue gradient) are shown with respect to the number of days since the reported onset of symptoms (not date of study enrollment) for each patient. Patients who died in the hospital are highlighted in bold and italics. Specimens with undetectable RNAaemia are represented as. Most (14/27) patients had undetectable RNAaemia by day 10, while the same proportion took 16 days to reach maximum severity, and 33 days for resolution of symptoms. B. Aggregate RNA and clinical dynamics in the 30 days following onset of symptoms. Loess regression curves represent trends in RNA and clinical dynamics. RNAaemia peaked 3 days after symptom onset, while clinical severity peaked at 14 days.

Figure 5.. Trajectories of patient severity, by RNAaemia on initial presentation.

36·4% (16/44) of initially RNAaemic patients, and 19·0% (28/147) of non-RNAaemic patients worsened in severity after initial presentation (difference = 17·4% [95% CI of difference, 0·3% - 34·4%]). RNAaemic patients worsened by a median of three points on the modified WHO scale, compared to one point for non-RNAaemic patients (p = 0·02, Wilcoxon rank-sum test with continuity correction). Day zero represents day of patient enrollment. Values prior to day zero are based on patient’s first reported day of symptoms. Values after day zero are based on the date of each patient’s maximum WHO score. Red trajectories are those that increase in severity after presentation, by modified WHO score.

Figure 6.. Presence of extrapulmonary complications, by RNAaemia.

56·8% (25/44) of patients RNAaemic on enrollment patients developed one or more extrapulmonary complications by hospital discharge, compared to 30·6% (45/147) of non-RNAaemic patients (difference in proportions = 26·2% [95% CI, 8·3% - 44·1%]). RNAaemic patients tended toward higher rates of extrapulmonary complications across systems, though only differences in rates of hepatobiliary (HB), haematologic, and immunologic complications were individually statistically significant at p < 0·05 (chi-squared tests for equality of proportions with continuity correction). CV = cardiovascular, HB = hepatobiliary.