key: cord-1015432-ixdzr7h0
authors: Laitman, Andrew M.; Lieberman, Joshua A.; Hoffman, Noah G.; Roychoudhury, Pavitra; Mathias, Patrick C.; Greninger, Alexander L.
title: The SARS-CoV-2 Omicron Variant Does Not Have Higher Nasal Viral Loads Compared to the Delta Variant in Symptomatic and Asymptomatic Individuals
date: 2022-03-28
journal: J Clin Microbiol
DOI: 10.1128/jcm.00139-22
sha: 735744380f980cf3d7ad99647fbd0e4a8a9ff68a
doc_id: 1015432
cord_uid: ixdzr7h0

nan

U nderstanding the mechanism of the rapid spread of the SARS-CoV-2 B.1. 1.529 (Omicron) variant is of great importance to devising public health interventions. Increased viral load has been reported as one cause of increased infectiousness in prior emergent variants and has been associated with symptomatic versus asymptomatic infections (1) . While initial reports have attributed Omicron's exponential growth and increased contagiousness to evasion of humoral memory due to altered spike protein antigens (2, 3) , it is unclear to what extent viral load has contributed to its dominance (4, 5) . Here, we examine whether symptomatic individuals and asymptomatic carriers infected with Omicron demonstrate differences in viral load by examining the reverse transcriptase PCR (RT-PCR) cycle thresholds (C T ) in sequence-confirmed cases, compared with prior infections with the Alpha and Delta variants of SARS-CoV-2.

Since March 2020, the University of Washington Virology Laboratory has performed approximately one-third of the testing for the state of Washington, with a majority of samples collected at open-access community testing sites throughout the state. Samples were collected using anterior nasal swabs observed by health care professionals and tested on four assays (Roche Cobas 6800, Abbott Alinity m, Panther Hologic Fusion, and a Centers for Disease Control and Prevention (CDC) assay-based lab-developed test [6, 7] ). The lowest C T value output from each platform was chosen as the single representative value. The symptomatic status of the individuals presenting to the testing sites was determined from free-text reasons for seeking testing. Using keywords present in such text responses, we categorized individuals as either symptomatic, exposed, or asymptomatic (see Table S1 in the supplemental material). To control for variations in community-wide viral RNA loads, we restricted our analysis to time periods when the Alpha, Delta, and Omicron variants were increasing in prevalence.

We The Omicron infections did not have higher viral loads than those with Delta when stratified by the major PCR platforms used and by symptomatic versus asymptomatic status (Fig. 1) . Consistent with prior reports (4, 5) , the symptomatic individuals across each variant had higher viral loads than did the asymptomatic carriers. Within each clinical category examined, the individuals with Omicron did not have higher viral loads than did those infected with Delta (Wilcoxon rank sum test: symptomatic, P = 2.7e-6; asymptomatic, P = 2.8e-4; exposure, P = 0.01) (Fig. 1) . The viral loads from symptomatic individuals measured on the Abbott platform were significantly lower for Omicron versus Delta infections (P , 0.0001) but were not significantly different on the Roche platform (P = 0.29). The viral loads from asymptomatic individuals trended lower for Omicron infections compared to Delta but were not statistically significant on either the Roche (P = 0.06) or Abbott platforms (P = 0.14). Our data suggest that the spread of Omicron is unlikely to be attributed to higher nasal viral loads compared to prior variants. Limitations to this analysis include the lack of stratification by the specific day of symptom onset, lack of longitudinal data to measure the peak viral load, use of C T as a surrogate for viral load, and restriction of the analysis to only anterior nasal swab viral loads. While recent data suggest that SARS-CoV-2 may be detectable earlier in saliva (8) , our data capturing almost 5,000 sequence-confirmed nasal collections across multiple clinical categories and stratified by PCR platform demonstrate that Omicron is not associated with a higher nasal viral load compared to previous variants.

Supplemental material is available online only. SUPPLEMENTAL FILE 1, XLSX file, 0.2 MB.

The Delta SARS-CoV-2 variant has a higher viral load than the Beta and the historical variants in nasopharyngeal samples from newly diagnosed COVID-19

Activity of convalescent and vaccine serum against SARS-CoV-2 Omicron

SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses

Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19

Epidemiological correlates of PCR cycle threshold values in the detection of SARS-CoV-2

Comparison of commercially available and laboratory-developed assays for in vitro detection of SARS-CoV-2 in clinical laboratories

Performance characteristics of the Abbott Alinity m SARS-CoV-2 assay

Discordant SARS-CoV-2 PCR and rapid antigen test results when infectious: a December 2021 occupational case series

A.L.G. reports central testing contracts with Abbott and research support from Gilead and Merck outside the submitted work.