A Quick Displacement of the SARS-CoV-2 variant Delta with Omicron: Unprecedented Spike in COVID-19 Cases Associated with Fewer Admissions and Comparable Upper Respiratory Viral Loads

Abstract

Background The increase in SARS-CoV-2 infections in December 2021 in the United States was driven primarily by the Omicron variant which largely displaced the Delta over a three week span. Outcomes from infection with the Omicron remain uncertain. We evaluate whether clinical outcomes and viral loads differ between Delta and Omicron infections during the period when both variants were co-circulating. Methods Remnant clinical specimens from patients that tested positive for SARS-CoV-2 after standard of care testing between the last week of November and the end of December 2021were used for whole viral genome sequencing. Cycle threshold values (Ct) for viral RNA, the presence of infectious virus, and levels of respiratory IgG were measured, and clinical outcomes were obtained. Differences in each measure were compared between variants stratified by vaccination status. Results The Omicron variant displaced the Delta during the study period and constituted 95% of the circulating lineages by the end of December 2021. Patients with Omicron infections (N= 1121) were more likely to be vaccinated compared to patients with Delta (N = 910), but were less likely to be admitted, require ICU level care, or succumb to infection regardless of vaccination status. There was no significant difference in Ct values based on the lineage regardless of the vaccination status. Recovery of infectious virus in cell culture was reduced in boosted patients compared to fully vaccinated without a booster and unvaccinated when infected with the Delta lineage. However, in patients with Omicron infections, recovery of infectious virus was not affected by vaccination. Conclusions Omicron infections of vaccinated individuals are expected, yet admissions are less frequent. Admitted patients might develop severe disease comparable to Delta. Efforts for reducing the Omicron transmission are required as even though the admission risk is lower, the numbers of infections continue to be high.

Evaluation of the role of home rapid antigen testing to determine isolation period after infection with SARS-CoV-2

“…In addition, though RAT performance is in some studies less accurate in detection of the Omicron variant, the Flowflex™ has been shown to detect Omicron with reasonable sensitivity 23 . Similarly, while the decreased ability to culture Omicron has been reported 24 our culture assay system utilizing Caco2 cells overexpressing Ace2 and TMPRSS2 has good sensitivity for culturing SARS-CoV-2 variants including Omicron, 19,21 (JHC, unpublished data). Finally, and perhaps most significantly, both rapid antigen testing and culture are only proxies for transmission and correlates, not determinant, of infectiousness and transmissibility in vivo.…”

Pulmonary lesions following inoculation with the SARS-CoV-2 Omicron BA.1 (B.1.1.529) variant in Syrian golden hamsters

“…This increased shedding in part has been suggested to contribute to in the increased spread of these variants [19]. However, recent analysis of human specimens are indicative for no major differences in shedding between the SARS-CoV-2 variants Delta and Omicron BA.1 [20]. We demonstrated that the kinetics of viral genome shedding were not significantly different between Delta and Omicron BA.…”

“…The copyright holder for this preprint this version posted March 15, 2022. ; https://doi.org/10.1101/2022.03.15.484448 doi: bioRxiv preprint recent analysis of human specimens are indicative for no major differences in shedding between the SARS-CoV-2 variants Delta and Omicron BA.1 [20]. We demonstrated that the kinetics of viral genome shedding were not significantly different between Delta and Omicron BA.1 infected hamsters.…”

Detection of the Omicron variant of SARS-CoV-2 in international travelers returning to Venezuela

“…Differences in viral levels between Omicron and Delta VOCs may also affect the detection of positive samples. RNA levels have been reported to be lower for the Omicron VOC when compared to Delta VOC [ 7 , 8 ], but higher in another more recent study [ 9 ], or similar in another one [ 10 ]. In the present study, the same Ct values were observed for Delta and Omicron VOCs, probably due to the type of sample analyzed (from travelers originally negative, retested 1–3 days later).…”