In the past two months, three distinct SARS-CoV-2 variants of concern have been detected and are now the subject of intense study: B.1.1.7, B.1.351, and P.1. B.1.1.7 is thought to have emerged in the UK in November 2020 and is likely significantly more transmissible than preexisting variants of SARS-CoV-2. B.1.351 was first detected in South Africa in October 2020 and seems to have an ability to escape the neutralizing antibody response elicited by previous infection and reduce the efficacy of vaccines in development. P.1 was first detected in Brazil in January 2020 and, like B.1.351, seems like it is able to escape the neutralizing antibody response elicited by previous infection. All three of these variants have a S:N501 mutation that differentiates them from other variants.
According to data from the recently launched CoVariants.org, the three variants in question — B.1.1.7, B.1.351, P.1 — are steadily increasing as a proportion of overall sequenced SARS-CoV-2 cases in the US.
The proportion of S:N501 among all sequenced SARS-CoV-2 samples submitted to the GISAID database in the US for the week of 2021-01-11 (2021-01-11 to 2021-01-17, inclusive) was 0.05, or 5%. Note that data for previous weeks are backfilled with sequences uploaded at later dates, so these percentages might change slightly over time — in other words, there is a lag between sequence collection and sequence upload.
In response to an increased incidence of S:N501 variants, public health officials may promote mitigation measures, further focus on contact tracing, and increase the rate of genomic sequencing.
Data sources and more information:
- Distribution of S:N501 per country
- US COVID-19 Cases Caused by Variants
- Emergence of SARS-CoV-2 B.1.1.7 Lineage — United States, December 29, 2020–January 12, 2021
- The Global Initiative on Sharing Avian Influenza Data (GISAID) website - https://www.gisaid.org/
- Next Strain - https://nextstrain.org/
- S gene dropout patterns in SARS-CoV-2 tests suggest spread of the H69del/V70del mutation in the US
- Helix SARS-CoV-2 Viral Sequencing Trends
What will be the percent of S:N501 sequences in the U.S. among all positive SARS-CoV-2 samples submitted to the GISAID database of genetic sequences between 2021-03-29 and 2021-04-04 (inclusive)?
This question will resolve as the percentage of US S:N501 sequences among all positive SARS-CoV-2 samples submitted for genomic sequencing to the GISAID database between 2021-03-29 and 2021-04-04 (inclusive), as displayed on the "Distribution of S:N501 per country" plot on following website: https://covariants.org/variants/S.N501. This website pulls data from GISAID and makes it publicly accessible. This percentage will be accessed no sooner than 2021-04-12.