Detection of a characteristic melting profile of a SARS-CoV-2 Kappa variant in Italy using the SARS-CoV-2 Variants ELITe MGB® Kit

Background: Although more than a year has passed since the start of the pandemic, SARS-CoV-2 infection still represents a major challenge for public health all over the world due to viral genome capability of gaining rapid mutations. Whole-genome sequencing (WGS) is the gold standard for variant identification, but it is time consuming and relatively expensive. For this reason, assays targeting multiple regions of the SARS-CoV-2 genome may be useful for a rapid traceability of either known or new variants, anyway, not all the manufacturers are able to sustain the rapid development of variants. Objective: We tested forty nasopharyngeal swabs, resulted positive for the presence of SARS-CoV-2 RNA at low cycle threshold (CT < 25), with SARS-CoV-2 Variants ELITe MGB (R) Kit, which was designed to identify Nigerian variant, possible UK variant and South African or Brazilian variant. Results: During the analysis, we noted an atypical melting curve, different from the other variants recognizable by the kit. The subsequent WGS reported this variant as Kappa, so we assess the possibility of suspecting the presence of a Kappa variant using SARS-CoV-2 Variants ELITe MGB (R) Kit. Conclusions: Rapid variant screening followed by WGS offers the opportunity to study mutation dynamics and quickly identify possible variants of interest (VOI) and/or variants of concern (VOC), which is crucial in virus spreading control. Furthermore, an accurate analysis of the melting peak could be useful to suspect the presence of new variants.

Automated summary

Whole-genome sequencing is the gold standard for identifying SARS-CoV-2 variants, but it is time consuming and expensive. Therefore, assays targeting multiple regions of the SARS-CoV-2 genome may be useful for rapid tracing of known or new variants. In this study, a variant detection kit was used to test forty nasopharyngeal swabs, resulting in the identification of an unprecedented variant, which was confirmed as Kappa variant through subsequent whole-genome sequencing.