Infection With the Severe Acute Respiratory Syndrome Coronavirus 2 (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

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.

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

“…Recovery of infectious virus on cell culture was less frequent in the Omicron group with no significant impact of vaccination with the exception of the Delta individuals who received a booster dose, this group showed a significantly reduced recovery of infectious virus when compared to the Delta fully vaccinated and unvaccinated groups. Consistent with our previously reported observations (11), samples with successful recovery of infectious virus on cell culture correlated with less IgG levels in the respiratory samples. In this study, we also report a significant increase of IgG in samples collected from patients who received a booster dose.…”

“…A significant increase in the recovery of infectious virus from specimens of patients infected with the Delta variant as compared to the Omicron was noted for both fully vaccinated (87% vs 69%, p < 0.04) and unvaccinated (82% vs 60%, p = 0.008) groups (Figure 3A). Consistent with our previously published reports (Figure 3C and (11,14)), and since lower Ct values have been associated with positive CPE, we compared samples with Ct values less than 20 for both Delta and Omicron groups (N; Table 1). Our analysis showed that the Delta infection was associated a significant increase in samples with positive CPE compared to Omicron (87% vs 70%, p = 0.001) however, no significant differences were seen between boosted, fully vaccinated, or unvaccinated groups (Figure 3B).…”

“…Clinical and vaccination data for patients whose samples were characterized by whole genome sequencing was bulk extracted as previously detailed in (11). Repeat tests from the same patient were excluded as were results with uncharacterized genomes due to insufficient quality (n=347).…”

“…Respiratory samples were tested, undiluted, with the EUROIMMUN Anti-SARS-CoV-2 ELISA (IgG) following the package insert (https://www.fda.gov/media/137609/download) as we described previously (11). The assay detects antibodies to the SARS-CoV-2 S1 domain of the spike protein.…”

“…We previously showed that SARS-CoV-2 IgG levels in the upper respiratory tract are higher in samples from vaccinated individuals and correlate with less recovery of infectious virus on cell culture (11). To compare the anti-SARS-CoV-2 IgG levels between patients who received a booster and fully vaccinated patients, ELISA was performed on upper respiratory samples from the Omicron and Delta infected groups.…”