Tracking the Initial Diffusion of SARS-CoV-2 Omicron Variant in Italy by RT-PCR and Comparison with Alpha and Delta Variants Spreading

Abstract

The emergence of the Omicron SARS-CoV-2 variant caused public health concerns worldwide, raising the need for the improvement of rapid monitoring strategies. The present manuscript aimed at providing evidence of the utility of a diagnostic kit for the routine testing of SARS-CoV-2 infection as a cost-effective method for tracking the Omicron variant in Italy. The study was conducted on patients’ naso-oropharyngeal-swab-derived RNA samples. These samples were subjected to RT-PCR using the TaqPath COVID-19 RT PCR CE IVD kit. Nonparametric testing and polynomial models fitting were used to compare the spreading of Alpha, Delta and Omicron variants. The samples of interest were correctly amplified and displayed the presence of S gene-target failure, suggesting that these patients carry the Omicron variant. The trend of diffusion was found to be significantly different and more rapid compared with that of the Alpha and Delta variants in our cohorts. Overall, these results highlight that the S gene target failure was a very useful tool for the immediate and inexpensive tracking of Omicron variant in the three weeks from the first detection. Thus, our approach could be used as a first-line screening to reduce the time and costs of monitoring strategies, facilitating the management of preventive and counteracting measures against COVID-19.

Identification of SARS CoV‐2 Omicron BA.1 and a novel Delta lineage by rapid methods and partial spike protein sequences in Sulaymaniyah Province, Iraq

“…20 In Italy, the failure of diagnostic kits to target the SARS CoV-2 spike gene was used for rapid and economic screening of the virus's variants including Delta and Omicron. 23 In China, a study showed that the mutations that occurred in VOCs (Beta, Gamma, and Delta) have a negative impact on the sensitivity of commercial diagnostic kits due to mismatches located in the primer/probe nucleotide sequences, however, both Alpha and Omicron have no substantial effects. 25 The efficacies of the previous rapid methods were reduced or failed to identify the K417N, N440K, G446S, and N501Y mutations in the Omicron variant due to intra-primer or -probe mutations such as Q493R, G496S, Q498R, or Y505H; this makes the diagnostic assays be regularly updated.…”

“…13 In Denmark, L452 and 452R markers were putatively used to differentiate between Omicron and Delta variants, respectively. 13 Identifications of both Delta and Omicron variants, by using either rapid molecular methods or sequencing, have been investigated in many countries including the United States, [16][17][18][19] United Kingdom, 3,20 Germany, 21,22 Denmark, 13 Italy, 11,23 Ecuador, 24 China, 25 Taiwan, 6 Belgium, 1 Malaysia, 26 Iran, 27 and Japan. 28 Such rapid molecular methods are uncommon in Iraq and Kurdistan region.…”

Development of a simple genotyping method based on indel mutations to rapidly screen SARS-CoV-2 circulating variants: Delta, Omicron BA.1 and BA.2

“…Interestingly, the previously undetected samples (n=7) were then identified as BA.2, with the first case dating back to late January 2022. Pending the availability of specific Omicron screening assays, Caputo et al showed that the S-gene target failure (SGTF) based method was a very useful tool for tracking the Omicron VOC in Italy within three weeks of the first detection ( Caputo et al, 2022 ). Although the SGTF is widely used to flag potential cases of Omicron BA.1, it is currently not recommended, as the circulating Omicron BA.2 sublineage lacks the Δ69-70 mutation.…”

Validation of reduced S-gene target performance and failure for rapid surveillance of SARS-CoV-2 variants

“…Similarly, other groups targeted PCR results with cycle threshold values � 30 for the N and ORF1ab-genes to reduce the incidence of identifying a sample as exhibiting SGTF in cases where viral load was low, and amplification was near the limit of the detection of the assay. These publications typically focused on smaller sample sizes but did confirm SGTF as a proxy for identification of the Alpha and B.1.1.529/BA.1/BA.1.1 variants through subsequent genome sequencing [8,[12][13][14][15][16]. Similar to our results, the vast majority of samples with SGTF, which were expected to have been caused by commonly circulating variants at the time of the study, were confirmed as Alpha or Omicron B.1.1.529/BA.1/ BA.1.1 via sequencing.…”