2021
DOI: 10.1101/2021.04.05.438352
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A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control

Abstract: We report a SARS-CoV-2 lineage that shares N501Y, P681H, and other mutations with known variants of concern, such as B.1.1.7. This lineage, which we refer to as B.1.x (COG-UK sometimes references similar samples as B.1.324.1), is present in at least 20 states across the USA and in at least six countries. However, a large deletion causes the sequence to be automatically rejected from repositories, suggesting that the frequency of this new lineage is underestimated using public data. Recent dynamics based on 339… Show more

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Cited by 8 publications
(10 citation statements)
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“…It is among the lineage-defining mutations of the B.1.160 (20A.EU2) lineage as well as the B.1.526 lineage that increases in frequency in the USA at rates comparable to those of B.1.1.7 21 . It is also one of the changes defining a newly detected lineage (preliminarily identified as B.1.x) which also contains S:N501Y and S:P681H and seems to spread rapidly in the USA 30 . Independent emergence of N:M234I in several variants of interest may reflect its impact on at least one of multiple functions of the N protein 31 .…”
Section: Resultsmentioning
confidence: 99%
See 1 more Smart Citation
“…It is among the lineage-defining mutations of the B.1.160 (20A.EU2) lineage as well as the B.1.526 lineage that increases in frequency in the USA at rates comparable to those of B.1.1.7 21 . It is also one of the changes defining a newly detected lineage (preliminarily identified as B.1.x) which also contains S:N501Y and S:P681H and seems to spread rapidly in the USA 30 . Independent emergence of N:M234I in several variants of interest may reflect its impact on at least one of multiple functions of the N protein 31 .…”
Section: Resultsmentioning
confidence: 99%
“…21 . It is also one of the changes defining a newly detected lineage (preliminarily identified as B.1.x) which also contains S:N501Y and S:P681H and seems to spread rapidly in the USA 30 . Independent emergence of N:M234I in several variants of interest may reflect its impact on at least one of multiple functions of the N protein 31 .…”
Section: B11317mentioning
confidence: 99%
“…The patient recovered and a follow-up NPS on July 1 was negative. Both the trader and the nurse harboured identical B.1.617.2 sequences, additionally harbouring S71F, T250I, T572I, and K854N [ 4 ].…”
Section: Resultsmentioning
confidence: 99%
“…This mutation was found to be highly prevalent in sequences isolated from Peru (26/127 sequences) followed by sequences isolated from the West Bank (6/62 sequences). The S494P mutation was earlier identified in sequences isolated from Santa Cruz County, USA [68]. This mutation has been predicted to have enhanced binding with the ACE2 receptor [69] and was highly prevalent in sequences isolated from Russia (31/304 sequences), followed by sequences isolated from the USA (5167/300280 sequences).…”
Section: Prevalence Of Adaptive Mutations Until 29 May 2021mentioning
confidence: 97%