Infection with the SARS-CoV-2 Delta Variant is Associated with Higher Recovery of Infectious Virus Compared to the Alpha Variant in both Unvaccinated and Vaccinated Individuals

Abstract

Abstract Background The SARS-CoV-2 variant of concern (VOC) B.1.617.2 (Delta) displaced B.1.1.7 (Alpha) and is associated with increases in COVID-19 cases, greater transmissibility, and higher viral RNA loads but data is lacking regarding the infectious virus load and antiviral antibody levels in the nasal tract. Methods Whole genome sequencing, cycle threshold (Ct) values, infectious virus, anti-SARS-CoV-2 IgG levels, and clinical chart reviews were combined to characterize SARS-CoV-2 lineages circulating in the National Capital Region between January and September 2021 and differentiate infections in vaccinated and unvaccinated individuals by the Delta, Alpha, and B.1.2 variants. Results The Delta variant displaced the Alpha variant to constitute 99% of the circulating lineages in the National Capital Region by August, 2021. In Delta infections, 28.5% were breakthrough cases in fully vaccinated individuals compared to 4% in the Alpha infected cohort. Breakthrough infections in both cohorts were associated with comorbidities, but only Delta infections were associated with a significant increase in the median days after vaccination . More than 74% of Delta samples had infectious virus compared to less than 30% from the Alpha cohort. The recovery of infectious virus with both variants was associated with low levels of local SARS-CoV-2 IgG. Conclusions Infection with the Delta variant was associated with more frequent recovery of infectious virus in vaccinated and unvaccinated individuals compared to the Alpha variant but was not associated with an increase in disease severity in fully vaccinated individuals. Infectious virus was correlated with the presence of low amounts of antiviral IgG in the nasal specimens.