SARS-CoV-2 variants of concern Alpha and Delta show increased viral load in saliva

Abstract

Background Higher viral loads in SARS-CoV-2 infections may be linked to more rapid spread of emerging variants of concern (VOC). Rapid detection and isolation of cases with highest viral loads, even in pre- or asymptomatic individuals, is essential for the mitigation of community outbreaks. Methods and findings In this study, we analyze Ct values from 1297 SARS-CoV-2 positive patient saliva samples collected at the Clemson University testing lab in upstate South Carolina. Samples were identified as positive using RT-qPCR, and clade information was determined via whole genome sequencing at nearby commercial labs. We also obtained patient-reported information on symptoms and exposures at the time of testing. The lowest Ct values were observed among those infected with Delta (median: 22.61, IQR: 16.72–28.51), followed by Alpha (23.93, 18.36–28.49), Gamma (24.74, 18.84–30.64), and the more historic clade 20G (25.21, 20.50–29.916). There was a statistically significant difference in Ct value between Delta and all other clades (all p.adj<0.01), as well as between Alpha and 20G (p.adj<0.05). Additionally, pre- or asymptomatic patients (n = 1093) showed the same statistical differences between Delta and all other clades (all p.adj<0.01); however, symptomatic patients (n = 167) did not show any significant differences between clades. Our weekly testing strategy ensures that cases are caught earlier in the infection cycle, often before symptoms are present, reducing this sample size in our population. Conclusions COVID-19 variants Alpha and Delta have substantially higher viral loads in saliva compared to more historic clades. This trend is especially observed in individuals who are pre- or asymptomatic, which provides evidence supporting higher transmissibility and more rapid spread of emerging variants. Understanding the viral load of variants spreading within a community can inform public policy and clinical decision making.

Infections with the SARS-CoV-2 Delta variant exhibit fourfold increased viral loads in the upper airways compared to Alpha or non-variants of concern

“…Nevertheless, it has to be noted that the former study 5 comprised a much smaller dataset (62 samples harboring Delta variant vs 63 samples harboring clade 19A/19B isolates) which was part of an outbreak and compared the Delta variant to a mixture of samples harboring nextstrain clade 19A/19B variants, which did not harbor the D614G mutation that enhances infectivity [13][14][15] and were much closer related to the original Wuhan strain than the non-VOC isolates in our study. In agreement with our study, King et al 16 also reported a more subtle increase in viral load for saliva samples harboring the Delta variant since the median CT value was about 1.3 values lower compared to Alpha and about three CT values lower compared to non-VOC samples. This study also observed a significant increase in viral load when comparing Alpha to non-VOC, which was only observed in the WGS dataset in our study.…”

“…In agreement with our study, King et al . 16 also reported a more subtle increase in viral load for saliva samples harboring the Delta variant since the median CT value was about 1.3 values lower compared to Alpha and about three CT values lower compared to non-VOC samples. This study also observed a significant increase in viral load when comparing Alpha to non-VOC, which was only observed in the WGS dataset in our study.…”

“…This study also observed a significant increase in viral load when comparing Alpha to non-VOC, which was only observed in the WGS dataset in our study. Several studies have suggested that the increase in viral load for the Delta variant compared to previous variants could reflect an enhanced replication rate for this variant in the airways of infected individuals 16 , 17 . Indeed, in vitro infection experiments in both cell culture and organoid models have shown that the Delta variant has a significantly higher replication rate compared to the Alpha and the wild-type variant harboring the D614G mutation 18 , 19 .…”

Predicting COVID-19 Infected Individuals in a Defined Population from Wastewater RNA Data

“…In the diagnostic lab, the first Alpha cases were detected on February 22 and March 1, 2021. 31 Over the next 3 weeks, the number of Alpha cases increased rapidly. On the date the Alpha variant was detected in the wastewater, Alpha cases made up 45% of the diagnosed cases in the lab.…”

“…Starting in January, samples from the Clemson diagnostic lab were sequenced to measure the prevalence of different variants in the clinical tests. 31 Beginning with the March 2, 2021 samples, SiREM estimated the relative quantity of VOCs using RT-qPCR targeting specific S gene mutation sites. The assay targeted the N501Y and A580D mutation sites.…”