The rapid spread of SARS-CoV-2 has put the world on alert. The virus belongs to the group of RNA viruses that possess enormous adaptive capacity towards new hosts and environments due to their RNA polymerases lacking proofreading activity. From a diagnostic perspective, the rapid emergence of new virus variants represents a continuous challenge.
Even though multiple random mutations in the SARS-CoV-2 genome have been observed since its first emergence, recent scientific reports have identified two new SARS-CoV-2 variants which raised special attention because of their concerning epidemiological features: higher transmission and infection rates, rapidly replacing prevalent virus lineages and subsequently, becoming the dominant form of the virus regionally.
The new lineage B.1.1.7 first identified in South England, called VUI-202012/01 by Public Health England, is defined by an unusually large number of 23 mutations. Among them, five mutations in ORF1ab, three in Orf8, and two and ten in the genes coding for the spike and nucleocapsid protein (S and N gene), respectively. A special point of concern are the mutations in the S gene that lead to significant changes in this key antigen.
The potential biological impact has been mapped to three mutations, all allocated in the spike protein: N501Y, P681H, and deletion of two amino acids named as del 69-70. The affected amino acids are located in key regions of the protein: receptor binding domain or the furin cleavage site.
The second reported and alarming lineage was initially identified in South Africa, called 501Y.V2 or South African variant. The respective mutations in this strain are of major concern because they could affect the efficacy of current vaccines. This lineage carries among others, two special mutations in the spike protein: E484K and K417N. The E484K mutation has been shown to reduce antibody recognition and therefore, might help the virus to bypass immune protection provided by prior infection or vaccination.
Rapid emergence of mutations in the SARS-CoV-2 genome is a special challenge that we also face as a diagnostic company. In order to provide a premium, accurate, and reliable solution for SARS-CoV-2 detection on a molecular level, we perform constant monitoring of emerging virus variants and evaluate their potential effect on the functionality of our diagnostic solutions.
The performance of the assay is not affected by any of the discovered mutations in the S-gene, ORF1ab or Orf8 appearing in the two rapidly spreading virus variants.
Regarding the reported B.1.1.7 and 501Y.V2 lineages, in silico analysis and alignment of all available SARS-CoV-2 genome sequences confirmed that none of the identified mutations in the N-gene impairs binding of the primer and probes used in our assay. Based on this result, it can be concluded that performance of PhoenixDx SARS-CoV-2 Multiplex and PhoenixDx Cofluenza Kits are not affected by these virus variants.
In summary, PhoenixDx SARS-CoV-2 Multiplex and PhoenixDx Cofluenza Kits detect both new virus variants discussed with equal sensitivity to the reference, wild type SARS-CoV-2, making it a reliable tool for SARS-CoV-2 diagnosis.
Investigation of novel SARS-CoV-2 variant. Variant of Concern 202012/01. Public Health England
Andrew Rambault et.al., Preliminary genomic characterization of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations, Genomic Epidemiology 2020
Houriiyah Tegally et.al., Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa.
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| PhoenixDx® SARS-CoV-2 Multiplex IVD | PhoenixDx® Cofluenza 4-Plex IVD | PhoenixDx® SARS-CoV-2 Mutant Screen [N501Y] | |
| Targets | SARS CoV-2, human RNA | SARS CoV-2, Influenza A , Influenza B, human RNA | SARS-CoV-2 WT/ N501Y Mutant |
| Contents | 50 µl PhoenixDx® RT Enzyme Mix, 750 µl PhoenixDx® SARS-CoV-2 Multiplex Mix, 200 µl SARS-CoV-2 Multiplex TPC | 50 µl PhoenixDx® RT Enzyme Mix, 750 µl PhoenixDx® Cofluenza 4-Plex Mix, 200 µl SARS-CoV-2 Cofluenza TPC | 100 µl 20X RT Enzyme Mix, 400 µl 5X MTS Buffer, 100 µl WT/N501Y Assay Mix, 100 µl TPC SC-2 WT, 100 µl TPC SC-2 Mutant |
| Number of Reactions / Kit | 50 | 50 | 96 |
| Detection Channels | FAM, HEX/VIC, ROX (optional) | FAM, HEX/VIC, ROX, Cy5 | FAM, HEX/VIC, ROX (optional) |
| Storage Temperature | -20°C | -20°C | -20°C |
| Stability | Store all components at -20°C and avoid repeated freeze and thaw cycles (≤ 3 freeze/thaw cycles; prepare aliquotes if required) | ||
| Certification | CE IVD, FDA EUA | CE-IVD | CE IVD |
| Target Genes | N gene, Orf1, RNAse P for human RNA | N gene, Orf1, Influenza A, Influenza B, RNAse P for human RNA | S gene |
| Reaction Time | Hands on time approx. 5-10 min., PCR runtime 60-80 min | Hands on time approx. 5-10 min., PCR runtime 60-80 min | Hands on time approx. 5-10 min., PCR runtime 60-80 min |
| Sample Type | Respiratory specimens including nasopharyngeal / oropharyngeal aspirates or washes, nasopharyngeal /oropharyngeal swabs, bronchoalveolar lavage, tracheal aspirates and sputum. | purified RNA from samples confirmed positive for SARS-CoV-2 | |
| Compatible Nucleic Acid Extraction System | SphaeraMag® DNA/RNA Isolation Kits (Procomcure), Quick-RNA Viral Kits(Zymo Research), bioMérieux NucliSens® systems, QIAamp® Viral RNA Mini Kit, QIAamp® MinElute Virus Spin Kit or RNeasy® Mini Kit (QIAGEN), EZ1 DSP Virus Kit (QIAGEN), Roche MagNA Pure Compact RNA Isolation Kit, Roche MagNA Pure Compact Nucleic Acid Isolation Kit | n/a | |
| Limit of Detection | 11 copies / 20 µl rxn | 11 copies / 20 µl rxn (SARS-CoV-2), 80 copies / 20 µl rxn (Influenza A H3N2), 2 copies / 20 µl rxn (Influenza B) | 5 copies / 20 µl rxn (WT), 15 copies / 20 µl rxn (N501Y) |
| Short Description | All target genes are detected in one reaction through probe-based multiplexing. Suitable for medium to high throughput. | All target genes are detected in one reaction through probe-based multiplexing. Suitable for medium to high throughput. | The kit is used to distinguish between wildtype SARS-CoV-2 and mutant N501Y-SARS-CoV-2 in samples already confirmed positive for SARS-CoV-2. |
| Minimum Quantity Order | 1 | 1 | 1 |
| Catalogue Number | PCCSKU15262 (RUO, FDA EUA), PCCSKU15263 (CE IVD) | PCCSKU15265 | PCCSKU15266 |
| Order here | PhoenixDx® SARS-CoV-2 Multiplex RUO (FDA EUA) PhoenixDx® SARS-CoV-2 Multiplex IVD (CE IVD) | PhoenixDx® Cofluenza 4-Plex IVD | PhoenixDx® SARS-CoV-2 Mutant Screen [N501Y], 96 reactions |
Procomcure Biotech is an ambitious biotech corporation located in Thalgau, Austria. In the heart of the lakeland of Salzburg,we develop innovative, high-tech PCR reagents and technologies for a broad range of applications. From standard endpoint PCR Kits for basic experiments to highly sensitive quantitative PCR reagents to sophisticated One-Step solutions for gene expression analysis, Procomcure’s portfolio offers a solution for any PCR related application.
Procomcure’s unique feature is the development of customized PCR solutions. We develop unique products for unique applications in close cooperation with our customers. With our team of highly skilled experts and state-of-the-art laboratories, we dare to approach any challenge our customers have in mind.
We are certified certified after the ISO Norms ISO 9001:2015 (for the development, distribution and production of molecular biological, cell biological and PCR products) and ISO 13485:2016 for the design, production and distribution of Medical Devices and associated Technical Services.
