Researchers determined the viral loads of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta, Gamma, Alpha, and 20G variants from the saliva samples of coronavirus disease 2019 (COVID-19)-positive individuals in the United States (US). 

The results of this study have been posted to the medRxiv* preprint server.

Background

To date, SARS-CoV-2 has caused over 414 million infections around the world, with over 77 million cases in the US alone. The high viral loads in COVID-19 cases observed during August 2021 in the US might be associated with the rapidly spreading SARS-CoV-2 variants of concern (VOCs), such as Delta and Alpha. The SARS-CoV-2 Alpha and Delta variants demonstrated mutations that enhance their host cell binding affinity. Further, the Delta variant has several additional mutations compared to Alpha, which improves its viral replication within the host, resulting in the quick global spread of this variant.

Thus, the timely detection and isolation of SARS-CoV-2 cases with high viral loads, including presymptomatic or asymptomatic cases, is critical for reducing community outbreaks of COVID-19.

About the study

In this retrospective study, the scientists evaluated the cycle threshold (Ct) values from 1,297 COVID-19-positive saliva samples obtained at the Clemson University testing lab in Upstate South Carolina. 

COVID-19-positive samples were identified using the reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and the SARS-CoV-2 clade data was derived through whole-genome sequencing (WGS) at nearby labs. During COVID-testing, the team collected patient-reported information on exposures and symptoms. 

The data were de-identified before any analyses. The study population included members from the surrounding communities of Clemson University, and students and employees from the University. A mandatory weekly or twice-a-week SARS-CoV-2 test was placed for the employees and students from Clemson University irrespective of their vaccination status. Further, the samples were labeled as symptomatic, exposed, and surveillance, based on the information procured from the participants.

Findings

The results indicate that Delta-infected people had the lowest Ct values, followed by the Alpha, Gamma, and the historic 20G clades. Statistically significant variation in Ct value was observed between the Delta variant and other clades evaluated, which were 20G, Gamma, and Alpha. Similarly, a notable difference in Ct values was seen between the Alpha and 20G variants.

Presymptomatic and asymptomatic SARS-CoV-2-infected individuals demonstrated similar statistical differences in Ct values between the Delta variant and other clades tested, whereas, symptomatic COVID-19 patients did not show statistically valid differences among the SARS-CoV-2 clades evaluated. This finding indicates that the differences in viral load did not exist as the disease progressed to later stages.

Symptomatic patients were more likely to test positive relative to those without symptoms. The average SARS-CoV-2 positivity rate was 12.71% and 0.98% for the symptomatic and surveillance samples, respectively, between January and November 2021. 

Samples from individuals who reported exposure at the community site were more probable to be SARS-CoV-2-positive relative to the non-exposed during the surge of the SARS-CoV-2 Alpha variant in March 2021. Nonetheless, following the emergence of the Delta variant, both the symptomatic and surveillance groups demonstrated a SARS-CoV-2-positivity rate of 10%, possibly because of the extremely high presence of Delta within the community and its high viral load resulting in the exposure of every individual.  

The results of the Kruskal-Wallis test and Welch’s analysis of variance (ANOVA) were similar. Further, Welch’s ANOVA indicated an eight times difference between the viral loads of the SARS-CoV-2 Delta variant and 20G.

Conclusions

The study findings show that the SARS-CoV-2 Delta and Alpha variants demonstrated significantly high viral loads in saliva relative to the more historic SARS-CoV-2 clades, such as 20G. This tendency was particularly noticeable in young and healthy SARS-CoV-2 presymptomatic or asymptomatic participants, indicating that the emerging variants are highly transmissible and spread quickly among younger individuals. Moreover, these individuals are less likely to test for COVID-19, hence were not accurately presented in the previous investigations; however, they play a significant role in the spread of the disease.

Since the SARS-CoV-2 testing in the current study was based on saliva, more participants were inclined to test frequently. Further, the weekly testing approach adopted in the study confirmed that SARS-CoV-2 cases are identified earlier in the infection cycle, usually before the symptom onset, thus lowering the sample size of symptomatic COVID-19 patients. 

The present findings have implications in public health since knowledge about the viral loads of different SARS-CoV-2 variants is significant in COVID-19-related clinical decision-making and informing public policy.

Collectively, the study indicates the higher viral loads of the SARS-CoV-2 Delta variant and provides proof for its rapid spread across the globe. Further, it highlights the significance of accurate surveillance, especially in the light of emerging highly mutated SARS-CoV-2 variants, like Omicron, with high viral loads similar to or greater than the Delta variant.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Written by

Shanet Susan Alex

Shanet Susan Alex, a medical writer, based in Kerala, India, is a Doctor of Pharmacy graduate from Kerala University of Health Sciences. Her academic background is in clinical pharmacy and research, and she is passionate about medical writing. Shanet has published papers in the International Journal of Medical Science and Current Research (IJMSCR), the International Journal of Pharmacy (IJP), and the International Journal of Medical Science and Applied Research (IJMSAR). Apart from work, she enjoys listening to music and watching movies.