Assay quickly identifies the E484K, N501Y mutations and K417 wildtype found in U.K., South Africa, and Brazil lineages of SARS-CoV-2
Transplantation was severely affected by the COVID pandemic in the first part of 2020. Several molecular diagnostic labs, including HLA labs, have started testing the novel coronavirus. While there were over hundred different SARS-CoV-2 detection kits available, there was a demand for faster testing with less consumables and without RNA-extraction. RNA extraction kits were on short supply and RNA-extraction extended the turn-around time and reduced lab throughput. Omixon was among the first in Europe to bring to market a CE-marked direct detection kit for SARS-CoV-2, developed in collaboration with SeqOnce Biosciences. This product allowed some of the largest labs in Central Europe to double testing throughput during the second wave of the pandemic.
A third wave of coronavirus cases in London, UK, Northern Ireland, Denmark, Portugal, Brazil and South Africa were linked to more infectious new variants of SARS-CoV-2. The common feature of these variants is the N501Y mutation in the spike protein. Studies from Imperial College estimate that the new variant in the UK infects 50% more people or increases the reproduction rate by 50%. Laboratories reported higher copy numbers in samples taken from people infected with the new variant. There is an observation of higher mortality rate, but it is unknown whether it is specifically linked to the new variant. The variants originated in South Africa and Brazil had additional new mutations in the 484 and 417 positions. These mutations were shown to appear independently in several lineages of the virus. They are particularly concerning since they not only impact the effectiveness of therapeutic antibodies but also that of vaccines. Vaccines made by Novavax, Johnson&Johnson and AstraZeneca all showed severely reduced efficacy against the infection by the new variant of SARS-CoV-2 in South Africa.
Since the mutations in the 501, 484 and 417 positions are the result of convergent evolution, they may appear independently anywhere in the world. For this reason, testing the presence of these mutations in infected individuals provides local public health authorities crucial information for decision making about local non-pharmaceutical interventions.
The extension to the AzureSeq-200 CE One-step RT-qPCR Assay to Detect SARS-CoV-2 E484K N501Y mutations and K417 wildtype enables molecular testing laboratories to identify the most common combinations of the three crucial mutation positions. The assay can be used as a reflexive testing for samples identified as positive with AzureSeq-200 CE One-step RT-qPCR Assay or other SARS-CoV-2 detection kit. The new kit extension enables the monitoring of the progression of the variants in and reports it as a first line estimation to the authorities to make appropriate decisions.
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