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Detection of non-B.1.1.7 Spike ∆69/70 sequences (B.1.375) in the United States

Multiple SARS-CoV-2 variants are circulating globally, however, phenotypic differences, if any, have yet to be described for the majority of these variants. Routine surveillance sequencing of SARS-CoV-2 is critical for identifying and tracking new mutations. Most notably, two recently emerged lineages, termed B.1.1.7 (also known as 20B/501Y.V1, and Variant of Concern (VOC) 202012/01), and B.1.351 (20C/501Y.V2), have become “variants of concern.”

B.1.1.7 lineage (20B/501Y.V1) has 17 amino acid substitutions relative to the initial SARS-CoV-2 genome sequence. In particular, investigations have focused on mutations in the Spike attachment protein, including deletions of amino acids 69 and 70 (S ∆69/70), N501Y, and P681H, as well as ORF8 Q27stop. The B.1.1.7 lineage is thought to have increased transmissibility based on recent epidemiological and phylogenetic data1.

The Spike ∆69/70 deletion prevents the oligonucleotide probe used in the commercial Applied Biosystems TaqPath COVID-19 assay (ThermoFisher) from binding its target sequence, leading to what has been termed “S gene dropout” or “S gene target failure,” that is, a lack of signal from the S gene amplicon, together with successful amplification of other two SARS-CoV-2 gene targets2. It was quickly recognized that this S gene target failure could be used as a proxy for B.1.1.7 lineage viruses, at least when B.1.1.7 had already reached some prevalence in the community3. Because the S ∆69/70 deletion occurs in other genetic backgrounds in addition to B.1.1.7, sequencing is necessary to confirm the genetic lineage of a virus with S gene target failure, particularly in regions where B.1.1.7 is not already known to circulate. However, viruses displaying S gene target failure in the U.S. should be prioritized for follow-up sequencing as the proportion of these failures attributable to B.1.1.7 viruses appears to vary geographically4.


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