Ct values of different SARS CoV2 variants: a single center observational study from Innsbruck, Austria

To the Editor,

The PCR method from nasopharyngeal swab medium is considered as gold standard of diagnostic methods for SARS-CoV2 virus detection due to its highest sensitivity and specificity [1]. The Ct value generated by real-time-PCR is in principle reflecting the quantity of viral RNA load but not directly equivalent as it is a non-standardized measured variable and subjected to several factors [2]. Although caution should be used in interpreting viral load and Ct values especially across different PCR test systems, reporting of Ct values may have important clinical implications and benefit [3, 4].

Initial reports suggested that the new Omicron variant was associated with higher viral copy numbers in addition to increased infectivity [5], [6], [7], [8]. Whether the Omicron variant, in contrast to other preceding Variants of Concern (VOC), has higher virus concentrations in the oropharynx compared to the nasopharynx, as initially suspected, is currently still controversial [9, 10].

In the period from March 2020 to April 2022, a number of 217,882 samples from outpatients and inpatients were examined by qPCR at the university hospital Innsbruck, Austria, of which 16,873 samples tested positive for SARS CoV2. On average, 2.2 samples were taken per positively tested patient during the course of the study (Figure 1). Beginning from January 2021 all patients were additionally subjected to PCR-based screening for SARS CoV2 VOC (Alpha, Alpha + E484K mutation, Beta, Gamma, Delta, Omicron BA.1 and BA.2). Patients in whom no variant could be determined (e.g. due to low virus loads) were excluded from the evaluation. Throughout the course of the pandemic the SARS-CoV2 PCR was determined using the same Roche Cobas SARS-CoV-2 assay (94.7% of the examinations, targets ORF1a/b and E-gene), Roche Liat SARS-CoV-2 assay (5.3%, ORF1a/b and N-gene) or Altona SARS-CoV2 Realstar assay (0.1%, E- and S-gene). SARS-CoV2 variant determination was performed using Roche cobas^® SARS-CoV-2 Variant Set 1 and TIB MBIOL melting curve PCR for the main characteristic mutations (e.g. N501Y, E484K, del69/70, L452R, L371S/L373P, P681H and others). The accuracy of variant typing was confirmed by next-generation sequencing and participation in national external quality assurance programs.

Figure 1:

Median Ct value of different SARS CoV2 VOC compared with wild-type.

Numbers of patients tested per subgroup see Supplementary Table 1. Horizontal black lines indicate median with IQR. As global test, comparing all subgroups for Ct values a Kruskal–Wallis test was used as ANOVA on ranks and Dunn’s test for the post hoc comparisons. All VOC revealed a significant difference (p<0.05) compared to SARS CoV2 wild-type, except Beta and Gamma variant.

The statistical evaluation includes the determination of medians and confidence intervals of the Ct value results for assessment. The Kruskal–Wallis test was used to assess the statistical difference of the Ct values of the individual virus variants and smear localizations. A p-value <0.05 was considered statistically significant. All statistical analyses were performed using MedCalc 19.6.1 statistical software.

In the population studied, 36.3% of patients had the wild-type variant, 6.0% the Alpha, 0.4% the Alpha + E484K, 0.5% Beta, 0.2% the Gamma, 12.2% the Delta, 21.8% the Omicron BA.1 and 21.2% the Omicron BA.2 variant. The distribution of male to female patients was 49.0–51.0%.

Ct values of different SARS-CoV2 variants: The Ct values of the different SARS-CoV2 variants only differ partially. The median Ct values of the wild-type variant are significantly higher than Alpha, Alpha + E484K, Delta, Omicron BA.1 and Omicron BA.2. The subgroups of Beta and Gamma also show lower median Ct values compared with wild-type, but are not statistically significant due to the insufficient number of cases (see Supplementary Table 1). While the median Ct values of the Alpha variant are significantly higher than Delta and Omicron BA.2, there is no significant difference between the first Omicron BA.1 and the previously predominant Delta variant.

Ct values of different smear collection techniques: With regard to the smear collection, it is evident that generally lower Ct values are detectable with the nasopharyngeal smear collection. This observation was also confirmed in a separate evaluation of the wild-type, Alpha, Delta, Omicron BA.1 and BA.2 variants except for the groups AlphaE484K, Beta and Gamma variants (too low sample numbers). In our study, we observed 39 patients undergoing a SARS-CoV2 reinfection with another variant. The largest proportion of reinfections occurred from wild-type to Omicron BA.1 and BA.2 (71% in total). On average, the second infection occurred 388 days after the initial infection. The median Ct values of the second infection (25.0) were generally higher compared to the first infection (23.0) but not statistically significantly different due to the insufficient number of cases.

Our study shows that, contrary to initial assumptions, there is no significant difference in Ct values between the first Omicron BA.1 variant and the previously dominant Delta variant in our collective in contrast to the second Omicron BA.2 variant, which reveals significantly lower Ct values than any other preceding variant. Assuming that the Ct Value within a constant method approximately reflects the viral load, our data suggest that the higher prevalence of Omicron BA.1 in contrast to the previously dominating Delta variant was primarily due to an increased infectivity whereas the BA.2 variant might also have the advantage of a higher viral load. Nevertheless, it should be borne in mind the Ct value alone cannot be considered as a reliable surrogate marker of infectivity as it is still unclear whether it correlates with the number of infectious virus particles. Moreover, infectivity is also influenced by other factors such as host immunity.

In addition, we cannot confirm that the oropharyngeal swab reveals lower Ct values than the nasopharyngeal swab for PCR detection with Omicron. Thus, in our study the oropharyngeal swab had no advantage in sensitivity compared to the nasopharyngeal swab. From this point of view the nasopharyngeal swab should be retained as the gold standard or a combination of pooled nasal and throat swabs.

In all cases of patients with reinfection by a second variant, we could detect a tendency toward higher Ct values at diagnosis of the second infection although the second infection were produced by variants with usually higher viral loads. Whether a possible immunity due to the initial infection is causal for the higher Ct value in the second infection cannot be verified from our data due to the small number of cases and other influencing factors and therefore remains questionable.

The limitations of the present study lie in the consideration of only one center. The results should therefore be confirmed in further longitudinal studies. The variability of the Ct values due to differences in smear collection or stage of disease cannot be ruled out. The strength of the present study lies in the large number of cases over a broad time span and the simultaneous systematic determination of the SARS-CoV2 variant.

The SARS-CoV2 pandemic has shown that the respective SARS-CoV2 variant has clear influences on virulence and viral load in affected patients. Knowledge of the variant-specific properties are therefore of immanent importance and must continue to be continuously monitored.