Dynamics of viral shedding during ancestral or Omicron BA.1 SARS-CoV-2 infection and enhancement of pre-existing immunity during breakthrough infections

Abstract

Omicron variant is circulating in the presence of a globally acquired immunity unlike the ancestral SARS-CoV-2 isolate. Herein, we investigated the normalized viral load dynamics and viral culture status in 44 fully vaccinated healthcare workers (HCWs) infected with the Omicron BA.1 variant. Viral load dynamics of 38 unvaccinated HCWs infected with the 20A variant during the first pandemic wave was also studied. We then explored the impact of Omicron infection on pre-existing immunity assessing anti-RBD IgG levels, neutralizing antibody titres against 19A, Delta and Omicron isolates, as well as IFN-γ release following cell stimulation with SARS-CoV-2 peptides. We reported that two weeks after diagnosis a greater proportion of HCWs infected with 20A (78.9%, 15/19) than with Omicron BA.1 (44.7%, 17/38; p = 0.02) were still positive by RT-qPCR. We found that Omicron breakthrough infections led to an overall enhancement of vaccine-induced humoral and cellular immunity as soon as a median [interquartile range] of 8 [7-9] days post symptom onset. Among samples with similar high viral loads, non-culturable samples exhibited higher neutralizing antibody titres and anti-RBD IgG levels than culturable samples. Additionally, Omicron infection led to an enhancement of antibodies neutralization capacity against other SARS-CoV-2 isolates. Taken together, the results suggest that Omicron BA.1 vaccine breakthrough infection is associated with a faster viral clearance than that of the ancestral SARS-CoV-2, in addition this new variant leads to a rapid enhancement of the humoral response against multiple SARS-CoV-2 variants, and of the cellular response.

Keywords: Omicron; SARS-CoV-2; infectiousness; vaccine-immunity; viral culture; viral shedding.

Figure 1.

Study design for Omicron-infected healthcare workers (HCWs). A total of 44 HCWs were included. Blood samples were collected for 32 HCWs who completed all 3 visits; 12 HCWs missed at least one of the follow-up visits, nasopharyngeal swabs only were collected.

Figure 2.

Viral kinetics and viral load according to viral culture status for 20A- and Omicron- infected healthcare workers. Kinetics of viral infection caused by the SARS-CoV-2 20A variant or the Omicron variant (A). The mean number of HCWs sampled per day was three for 20A-infected HCWs and six for Omicron-infected HCWs. Curves representing the kinetic of the viral infection by the first wave variant 20A (in orange), or by the Omicron variant (in blue); within the first 20 days following symptom onset. The light-coloured area around the curves represents the confidence interval of each curve. Box plots represent the median [interquartile range, IQR] of the normalized SARS-CoV-2 viral loads (log₁₀ cp/10⁶ cells) stratified according to viral culture status for the Omicron variant (B) and the 20A variant (C) among SARS-CoV-2 positive samples. The median [IQR] of the normalized viral load was compared between culturable and non-culturable samples for Omicron-infected HCWs (7.4 [6.6–8.2] log₁₀ cp/10⁶ cells vs. 4.7 [3.3–5.4] log₁₀ cp/10⁶ cells, p < 0.0001; B) as well as for 20A-infected HCWs (6.6 [5.4–7.4] log₁₀ cp/10⁶ cells vs. 3.5 [2.9–4.6] log₁₀ cp/10⁶ cells, p < 0.0001; C). Comparisons were made using the Mann–Whitney U-test. ****p < 0.0001.

Figure 3.

Immunological parameters assessed up to 2 weeks post Omicron infection. A chemiluminescence immunoassay (CLIA) was performed in order to determine anti-RBD IgG levels (A), expressed in binding antibody units/mL (n = 96). The dotted line represents the threshold of positivity (≥21.8 BAU/mL). Neutralizing antibody titres (PRNT₅₀) against the Omicron (B), 19A (C) and Delta (D) isolates (n = 96). The dotted line represents the threshold of positivity (a titre ≥ 20). Fold reduction were calculated for Omicron in comparison to 19A and Delta. Bar plot represents the mean fold change with standard deviation at diagnosis (n = 21), 1 week after (n = 32) and 2 weeks after (n = 32) (E). An Interferon Gamma Release Assay was performed to assess T cell function following stimulation with a restricted pool of peptides (RPP) derived from SARS-CoV-2 structural proteins (n = 72) (F). The dotted line represents the threshold of positivity (≥0.08 IU/mL). For all three experiments (A–D, F), box plots represent the median [IQR] for each parameter and before-and-after scatter plots represent the evolution of the parameter for each patient individually. Samples were obtained at diagnosis, 1 week after diagnosis, and 2 weeks after diagnosis. Comparisons were made using the Friedman test followed by Dunn’s multiple comparison test. *p = 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001; ^#p < 0.1.

Figure 4.

Anti-RBD IgG levels and neutralizing antibody titres stratified according to isolation status among HCWs infected with Omicron. Samples having a similar high viral load (≥6 log₁₀ cp/10⁶ cells) were selected. A chemiluminescence immunoassay (CLIA) was performed in order to determine anti-RBD IgG levels, expressed here in binding antibody unit/mL (BAU/mL) and stratified according to culture status (A). The dotted line represents the threshold of positivity (≥21.8 BAU/mL). A 50% plaque reduction neutralization test (PRNT₅₀) was conducted to determine the neutralizing antibody titre of each sample against the live Omicron variant and stratified according to culture status (B). The dotted line represents the threshold of positivity (a titre ≥ 20). For both experiments, box plots represent the median [IQR] for each parameter and before-and-after scatter plots represent the evolution of the parameter for each patient individually. Comparisons were made using the Mann–Whitney U-test. **p < 0.01.