{"id":16141,"date":"2022-01-14T12:52:37","date_gmt":"2022-01-14T20:52:37","guid":{"rendered":"https:\/\/admin.acceleratingscience.com\/clinical-conversations\/?p=16141"},"modified":"2022-02-14T20:08:55","modified_gmt":"2022-02-15T04:08:55","slug":"taqpath-covid-19-diagnostic-tests-detect-the-omicron-variant-and-all-its-lineages","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/clinical-conversations\/taqpath-covid-19-diagnostic-tests-detect-the-omicron-variant-and-all-its-lineages\/","title":{"rendered":"TaqPath COVID-19 Diagnostic Tests Detect the Omicron Variant and All its Lineages"},"content":{"rendered":"

Based on a multi-target design<\/a> that compensates for emerging SARS-CoV-2 variants and mutations, the Applied Biosystems TaqPathTM<\/sup> COVID-19 diagnostic tests can detect<\/strong> the Omicron Variant of Concern (VOC) and all its currently known lineages. In fact, the TaqPath COVID-19 diagnostic tests can detect all currently known SARS-CoV-2 among patients\u2019 samples.<\/p>\n

Independent of the currently known variants, the tests can determine whether a patient\u2019s sample is positive or negative for the virus. The TaqPathTM<\/sup> COVID-19 diagnostic tests listed in Table 1 will show a specific detection pattern for the majority of Omicron variant isolates. \u00a0Using this detection pattern as a proxy can help identify<\/strong> the Omicron variant.<\/p>\n

Table 1: <\/strong>TaqPath COVID-19 Diagnostic Tests <\/strong><\/p>\n\n\n\n\n\n\n\n\n\n\n\n
TaqPath COVID-19 Assay<\/strong><\/td>\nCat #<\/strong><\/td>\nDetects SARS-CoV-2 (Including Omicron B.1.1.529, BA. 1, BA.2 and BA. 3) <\/strong><\/td>\nDetects S Gene Target Failure (SGTF)<\/strong><\/p>\n

(Detection Pattern Suggestive of Omicron BA. 1 and BA. 3)<\/strong><\/td>\n<\/tr>\n

Products with US FDA\u2019s Emergency Use Authorization (EUA)*<\/strong><\/td>\n<\/tr>\n
TaqPath COVID-19 Combo Kit*<\/td>\nEUA<\/td>\nA47814<\/td>\nYES <\/strong><\/td>\nYES<\/strong><\/td>\n<\/tr>\n
TaqPath COVID-19 Combo Kit Advanced*<\/td>\nEUA<\/td>\nA47813<\/td>\n<\/tr>\n
TaqPath COVID\u201119 High\u2011Throughput Combo Kit for use with Amplitude Solution*<\/td>\nEUA<\/td>\nA49869<\/td>\n<\/tr>\n
TaqPath COVID-19 Pooling Kit*<\/td>\nEUA<\/td>\nA49918<\/td>\n<\/tr>\n
Products Complied with EU\u2019s CE-IVD Requirements**<\/strong><\/td>\n<\/tr>\n
TaqPath COVID-19 CE-IVD RT-PCR Kit**<\/td>\nCE-IVD<\/td>\nA48067<\/td>\nYES <\/strong><\/td>\nYES<\/strong><\/td>\n<\/tr>\n
TaqPath COVID-19 HT Kit for use with Amplitude Platform**<\/td>\nCE-IVD<\/td>\nA50883<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

* For In Vitro Diagnostic Use. For Emergency Use Authorization Only.<\/p>\n

**CE-IVD. For In Vitro Diagnostic Use.<\/p>\n

The first case of Omicron and its subsequent lineages <\/em><\/strong><\/p>\n

The first case of the Omicron VOC was reported in November of 2021 and designated as B.1.1.529 (pangolin lineage, also known as 21M). This new variant has more than 30 mutations in the spike protein alone.\u00a0Since its first discovery, multiple variations of the Omicron virus have been identified that share the majority of mutations but also harbor their own unique sequence changes. The three sub-lineages identified so far include BA.1 (also known as 21K), BA.2 (also known as 21L), and BA.3 (Table 2).[1]<\/a> \u00a0\u00a0\u00a0<\/strong><\/p>\n

Table 2: Sub-Lineages of Omicron B.1.1.529 (Pangolin Lineage, Also Known as 21M) and Their Detection Pattern<\/strong><\/p>\n\n\n\n\n\n\n
Name of Omicron Sub-Lineages\u00a0<\/strong><\/td>\nAlso Known As\u00a0<\/strong><\/td>\nShows SGTF Detection Pattern by <\/strong><\/p>\n

TaqPath COVID-19 Assay<\/strong><\/td>\n<\/tr>\n

BA.1<\/td>\n21K<\/td>\nYES<\/strong><\/td>\n<\/tr>\n
BA.2<\/td>\n21L<\/td>\nNO\u00a0<\/strong><\/td>\n<\/tr>\n
BA.3<\/td>\n\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 –<\/td>\nYES<\/strong><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n

The 69-70 deletion in the spike protein, a mutation that presents in the majority of the currently circulating Omicron cases worldwide, helps identify the potential presence of the VOC when using any of the TaqPath COVID-19 diagnostic tests listed in Table 1 on patients\u2019 samples. This mutation is present in BA.1 (21K) and BA.3, but not in BA.2 (21L) lineage.1<\/sup><\/p>\n

The worldwide and country-specific prevalence of the Omicron variant and its lineages can be tracked using World Health Organization (WHO)\u2019s Tracking SARS-CoV-2 Variants<\/a>, WHO\u2019s Technical Brief and Priority Actions for Member States<\/a>, Outbreak.info<\/a> hosted by Scripps Research, or the ROSALIND tracker<\/a> hosted by ROSALIND, Inc. The BA.1 (21K) lineage of Omicron, which has the 69-70 deletion in the spike protein and presents the S Gene Target Failure (SGTF) detection pattern by TaqPath COVID-19 Assay, is currently the most prevalent worldwide. It accounts for >98% of sequences submitted to Global Initiative on Sharing Avian Influenza Data (GISAID) as of 7 January 2022. BA.2 and BA.3 only account for a minority of the submitted sequences worldwide.1 <\/sup><\/p>\n

The WHO, the US Food and Drug Administration (FDA), the US Centers for Disease Control and Prevention (CDC), and the European Centre for Disease Prevention and Control (ECDC) have all reported that using SGTF of PCR assays as a proxy for the variant helps in identifying Omicron. 1[2]<\/a>[3]<\/a>[4]<\/a><\/sup><\/p>\n

TaqPath detects all currently known SARS-CoV-2, including different lineages of the Omicron variant<\/em><\/strong><\/p>\n

The Applied Biosystems TaqPath COVID-19 diagnostic tests are capable of detecting samples infected with different Omicron variants. The tests detect SARS-CoV-2 infections by identifying the presence of three gene targets from the orf1a\/b, S, and N regions of the virus. The COVID-19 Interpretive Software algorithms utilize the results from all three targets to generate a final call, and a positive result is called if at least two of the three SARS-CoV-2 targets are detected.<\/p>\n

Figure 1: Multi-Target Design of the TaqPath COVID-19 Diagnostic Tests Listed in Table 1<\/strong><\/p>\n

\"\"<\/p>\n

For the BA.1 and BA.3 lineages of the Omicron variant B.1.1.529, the TaqPath COVID-19 diagnostic tests detect both the orf1ab and N genes while showing a negative signal for the S gene target. This S Gene Target Failure (SGTF)<\/strong> is also known as S Gene Advantage<\/strong> as it can be used as a marker suggestive of the Omicron variants<\/a>. The Delta variant, currently the predominant variant worldwide, does not have the S gene 69-70del mutation in the majority of the cases and the S gene is detected by the TaqPath COVID-19 Kits. It is important to note that the 69-70del mutation may also exist in other mutants, and a dropout of the S gene signal could also be caused by other reasons.<\/p>\n

For the Omicron variant BA.2 and other SARS-CoV-2 variants without the spike protein mutations, the TaqPath COVID-19 diagnostic tests detect all three gene targets from the orf1a\/b, S, and N regions of the virus.<\/p>\n

In summary, the TaqPath COVID-19 diagnostic tests can detect all currently known SARS-CoV-2 variants. The S Gene Advantage has already helped detect the Alpha variant<\/a>, and the WHO, US CDC, European CDC, and African CDC have all reported that using S Gene Target Failure (SGTF) of PCR assays as a proxy for the variant helps in identifying Omicron, and the CDCs have specifically recognized the TaqPath assay for these findings. Both the ECDC and US FDA recommend further characterizing specimens which show S-gene dropout using sequencing.<\/p>\n

What to do if SGTF is observed?<\/em><\/strong><\/p>\n

Samples that are associated with the S gene dropout reflect either a resurgence of the Alpha variant, a new or emerging mutant that interferes with the S gene detection, or the presence of the new Omicron variant (B.1.1.529, BA.1 and BA. 3). Given that the majority of currently circulating SARS-CoV-2 are the Delta variant which does not produce the SGTF profile, any sample with S gene dropout should be seen as signal to characterize the sample for the presence of Omicron. Due to the novelty and potential risks associated with the new Omicron variant, the WHO, CDC, and ECDC recommend further characterizing specimens with S gene dropout using sequencing.<\/p>\n

<\/div>\n

 <\/p>\n

For surveillance purposes, confirming various variants by genotyping may be performed using the following:<\/em><\/strong><\/p>\n

For Genotyping with existing qPCR equipment:<\/h3>\n