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% B.1.1.7 among all S gene dropout samples?


SARS-CoV-2 lineage B.1.1.7, otherwise known as Variant of Concern 202012/01 (VOC), is a novel SARS-CoV-2 strain that originated in the United Kingdom in late summer/early fall 2020. A recent pre-print estimates B.1.1.7 to be 56% more transmissible (95% Crl: 50%-74%) compared to preexisting variants. A second pre-print finds that the new variant has “an additive increase in R that ranged between 0.4 and 0.7, and alternatively as a multiplicative increase in R that ranged between 50% and 75%."

The B.1.1.7 strain is characterized by 17 new mutations. One of these mutations, S.H69- (a deletion of H69), can be detected via PCR diagnostic testing. If the PCR test shows an S gene dropout, where the S probe of the RT-PCR test cannot bind to the S gene due to B.1.1.7's H69 deletion, then the sample has the potential to be the B.1.1.7 strain — at that point, further sequencing would be needed to determine if a second mutation is present: the N501Y (S:N501Y) mutation.

In the UK, B.1.1.7 is so widespread that a PCR test that shows S-gene dropout alone is a strong indicator the sample is the B.1.1.7 variant — recent data indicates ~98% of S gene dropout samples in the UK are B.1.1.7. To date, B.1.1.7 is not widespread enough in the United States to consider a sample with a S gene dropout synonymous with the B.1.1.7 variant.

As of 2020-01-04, the genomic repository and analysis platform NextStrain, which uses viral samples submitted to GISAID, reported 381 samples with an S-gene dropout (S.H69-) have been sequenced and uploaded in the United States. Among samples with an S-gene dropout in the U.S., 1.84% (7/381) percent were identified as B.1.1.7 in a NextStrain/GISAID database maintained by the Neher Lab. Please note that there is a lag between sequence collection and sequence upload — so the number of sequences to date will be backfilled once those sequences are uploaded.

Data sources and more information:

What will be the percent of B.1.1.7 among all S gene dropout SARS-CoV-2 samples submitted for genomic sequencing surveillance in the US between 2021-02-01 and 2021-02-15?

This NextStrain page on S:N501Y as a proportion of overall S gene dropout samples in the US will be consulted for resolution. To access this data, scroll to the bottom of the page and download “selected metadata.” In this Excel sheet, please consult the “Pangolin Lineage” column to find B.1.1.7 samples. Samples that have a “collection data” date between 2021-02-01 and 2021-02-15 (inclusive) will be considered. We will compute the proportion by dividing the number of B.1.1.7 samples by the total number of samples (which are all 69del samples) in the spreadsheet. NextStrain will be accessed in the last week of February (the week ending on 2021-02-27) for resolution.

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