Impact of time elapsed since full vaccination on SARS-CoV-2 RNA load in Delta-variant breakthrough COVID-19.

To the Editor,

We recently commented on the study by Teyssou and colleagues showing substantial differences across SARS-CoV-2 variants of concern RNA loads in the upper respiratory tract (URT). Regarding the Delta variant, we reported a trend towards higher viral loads in non-vaccinated individuals with COVID-19 compared to those vaccinated with a variety of COVID-19 vaccines. A number of studies concur on that although SARS-CoV-2 RNA loads in the upper respiratory tract of individuals with Delta variant breakthrough infection are comparable to those found in unvaccinated infected individuals, viral RNA clearance seemingly proceeds at a faster rate in the former subjects.3, 4, 5, 6 Nevertheless, analyzes in these studies were not stratified by either time elapsed since full COVID-19 vaccination3, 4, 5 or clinical status (asymptomatic vs. symptomatic) at the time of RT-PCR diagnosis.3, 4, 5, 6 Here, we add nuances to the aforementioned assumption by showing that among patients with breakthrough COVID-19, both the magnitude and dynamics of Delta variant RNA load in URT are markedly affected by time elapsed since full COVID-19 vaccination.

The current observational study included a convenience sample of 107 individuals (57 female; median age, 62 years; range, 50–94) who developed breakthrough COVID-19 at a median of 65 days (range, 17–199) after completion of the vaccination schedule with Comirnaty® (n = 73), Spikevax® (n = 13), Vaxzebria® (n = 12) or Janssen COVID-19 vaccine (n = 9). Diagnosis of SARS-CoV-2 infection was achieved by RT-PCR (TaqPath COVID-19 Combo Kit; Thermo Fisher Scientific, MS, USA)) in nasopharyngeal specimens collected within the first 4 days after symptoms onset. SARS-CoV-2 RNA loads were estimated using the AMPLIRUN® TOTAL SARS-CoV-2 RNA Control (Vircell SA, Granada, Spain), and are reported as copies/ml throughout the study. Delta variant involvement was identified by whole-genome sequencing.

None of the participants in our sample had an immunosuppressive condition or was under immunosuppressive therapy at the time of symptoms onset. Most patients presented with mild disease (n = 105), whereas 16 had to be hospitalized (one in the intensive care unit). We arbitrarily stratified participants according to time elapsed between full vaccination and symptoms onset into three groups, which were balanced regarding participant numbers: Group 1: 15–45 days, Group 2: 46–90 days and Group 3: 91–200 days (Supplementary Table 1). Participants differed significantly across groups in age and hospitalization rate (older age and more hospital admissions in Group 3) and vaccine used, but were comparable regarding time interval between symptoms onset and RT-PCR diagnosis (median, 2 days) and sex. Taking the cohort as a whole, we noticed an increase in initial SARS-CoV-2 RNA loads in NP, positively associated with time since vaccination, irrespective of the vaccine used (Fig. 1 A), although a clear trend towards lower initial SARS-CoV-2 RNA load was observed in participants in Group 1 compared to the other two groups. By analyzing SARS-CoV-2 RNA load trajectory over time since symptom onset (Fig. 1B) we observed a seemingly faster viral RNA load decay in patients in Group 1. To rule out bias related to vaccine used, we next performed a similar analysis restricted to subjects vaccinated with Comirnaty®, the vaccine used in the majority of participants in the current cohort (Supplementary Table 2). As depicted in Figure 2C, initial SARS-CoV-2 RNA loads gradually increased with time elapsed since vaccination, with significant differences in viral loads between participants in Groups 1 and 3 (P = 0.03). Again, viral load decrease appeared faster in patients in Group 1 than in the other two study groups (Fig. 1D).

Fig. 1

SARS-CoV-2 Delta variant RNA load in the upper respiratory tract of individuals with breakthrough COVID-19 according to time elapsed since full vaccination. (A) Box-Whisker plot depicting initial SARS-CoV-2 RNA loads in all participants; (B) Kinetics of SARS-CoV-2 RNA load over the first 4 days after symptoms in all participants; (C) Box-Whisker plot depicting initial SARS-CoV-2 RNA loads in participants vaccinated with the Comirnaty® vaccine; (D) Kinetics of SARS-CoV-2 RNA load over the first 4 days after symptoms in participants vaccinated with the Comirnaty® vaccine. P values are shown for comparisons (Mann-Whitney U test or Kruskal-Wallis test, as appropriate).

Beyond the relatively modest sample size, our study has several further limitations. First, Delta variant peak RNA loads may have been reached before symptoms appeared, and not uniformly across participants in the study groups. Second, patients in Group 3 were much older than those in the remaining groups; it is possible that elderly individuals may exhibit different kinetics of SARS-CoV-2 Delta variant RNA load in URT, post-vaccination waning of immune responses, or both, compared to patients in the remaining study groups. Third, sequential NP specimens from participants were not available for analyzes.

Our data highlight the impact of time elapsed since full vaccination on the magnitude and decay kinetics of SARS-CoV-2 RNA loads in URT in COVID-19 patients during Delta variant breakthrough infections, and are in line with results published in a recent study. How dissimilarities in viral loads translate into differences in infectiousness needs to be assessed. Disappearance of vaccine-elicited immune responses over time likely account for our findings, which should be verified in larger studies due to their potential public health implications.

CRediT authorship contribution statement

Paula de Michelena: Data curation, Formal analysis, Writing – review & editing. Ignacio Torres: . Eliseo Albert: Data curation, Formal analysis, Writing – review & editing. Alma Bracho: Methodology, Writing – review & editing. Fernando González-Candelas: Methodology, Writing – review & editing. David Navarro: Conceptualization, Formal analysis, Writing – original draft, Writing – review & editing.

Declaration of Competing Interest

The authors declare no conflicts of interest.