A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control

Thornlow, Bryan; Hinrichs, Angie S.; Jain, Mukesh; Dhillon, Navpreet K.; S, La; Jd, Kapp; Anigbogu, I; Cassatt-Johnstone, Molly; McBroome, Jakob; Haeussler, Maximilian; Turakhia, Yatish; Chang, Tsan‐Kuo; He, Olsen; Sanford, Jeremy R.; Stone, Marcia; Vaske, Olena M.; Bjork, Isabel; Akeson, Mark; Shapiro, Beth; Haussler, David; Am, Kilpatrick; Corbett‐Detig, Russ

doi:10.1101/2021.04.05.438352

Cited by 8 publications

(10 citation statements)

References 25 publications

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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%

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Spread of endemic SARS-CoV-2 lineages in Russia

Klink

Safina

Garushyants

et al. 2021

Preprint

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In 2021, the COVID-19 pandemic is characterized by global spread of several lineages with evidence for increased transmissibility. Russia is among the countries with the highest number of confirmed COVID-19 cases, making it a potential hotspot for emergence of novel variants. Here, we show that among the globally significant variants of concern, B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) or P.1 (501Y.V3), none have been sampled in Russia before January 2021. Instead, since summer 2020, the epidemic in Russia has been characterized by the spread of two lineages that are rare elsewhere: B.1.1.317 and a sublineage of B.1.1 including B.1.1.397 (hereafter, B.1.1.397+). In February-March 2021, these lineages reached frequencies of 26.9% (95% C.I.: 23.1%-31.1%) and 32.8% (95% C.I.28.6%-37.2%) respectively in Russia. Their frequency has increased in different parts of Russia. Together with the fact that these lineages carry several spike mutations of interest, this suggests that B.1.1.317 and B.1.1.397+ may be more transmissible than the previously predominant B.1.1, although there is no direct data on change in transmissibility. Comparison of frequency dynamics of lineages carrying subsets of characteristic mutations of B.1.1.317 and B.1.1.397+ suggests that, if indeed some of these mutations affect transmissibility, the transmission advantage of B.1.1.317 may be conferred by the (S:D138Y+S:S477N+S:A845S) combination; while the advantage of B.1.1.397+ may be conferred by the S:M153T change. On top of these lineages, in January 2021, B.1.1.7 emerged in Russia, reaching the frequency of 17.4% (95% C.I.: 12.0%-24.4%) in March 2021. Additionally, we identify three novel distinct lineages, AT.1, and two lineages prospectively named B.1.1.v1 and B.1.1.v2, that have started to spread, together reaching the frequency of 11.8% (95% C.I.: 7.5%-18.1%) in March 2021. These lineages carry combinations of several notable mutations, including the S:E484K mutation of concern, deletions at a recurrent deletion region of the spike glycoprotein (S:Δ140-142, S:Δ144 or S:Δ136-144), and nsp6:Δ106-108 (also known as ORF1a:Δ3675-3677). Community-based PCR testing indicates that these variants have continued to spread in April 2021, with the frequency of B.1.1.7 reaching 21.7% (95% C.I.: 12.3%-35.6%), and the joint frequency of B.1.1.v1 and B.1.1.v2, 15.2% (95% C.I.: 7.6%-28.2%). The combinations of mutations observed in B.1.1.317, B.1.1.397+, AT.1, B.1.1.v1 and B.1.1.v2 together with frequency increase of these lineages make them candidate variants of interest.

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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%

Spread of endemic SARS-CoV-2 lineages in Russia

Klink

Safina

Garushyants

et al. 2021

Preprint

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“…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%

Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy

Baj

Novazzi²,

Ferrante³

et al. 2021

Emerging Microbes & Infections

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The SARS-CoV-2 variant of concern (VOC) "Delta" is currently defined by PANGOLIN as a cluster of 33 different AY sublineages. Delta (in particular B.1.617.2) is largely and rapidly replacing the Alpha VOC as the dominant clade in most countries. To date, variations in the Spike protein of the Delta VOC have largely been limited. We report here the results of a genomic surveillance program from Northern Italy. We identified several Delta sublineages harboring mutations previously reported in GISAID at extremely low frequencies and in different combinations. Two patients (one of them vaccinated) tested positive for a Delta sublineage harboring S71F, T250I, T572I and K854N. More patients tested positive for G769V plus C1248F, A352S, and R158G and C1248F, respectively. Genomic surveillance of Delta variants should be encouraged to anticipate immune escape and deploy countermeasures.

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“…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%

Global Prevalence of Adaptive and Prolonged Infections’ Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein

Lennerstrand

Palanisamy

2021

Viruses

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Several vaccines with varying efficacies have been developed and are currently administered globally to minimize the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite having an RNA-dependent RNA polymerase with a proofreading activity, new variants of SARS-CoV-2 are on the rise periodically. Some of the mutations in these variants, especially mutations on the spike protein, aid the virus in transmission, infectivity and host immune evasion. Further, these mutations also reduce the effectiveness of some of the current vaccines and monoclonal antibodies (mAbs). In the present study, using the available 984,769 SARS-CoV-2 nucleotide sequences on the NCBI database from the end of 2019 till 28 July 2021, we have estimated the global prevalence of so-called ‘adaptive mutations’ and ‘mutations identified in the prolonged infections’, in the receptor-binding domain (RBD) of the spike (S) protein. Irrespective of the geographical region, in the case of the adaptive mutations, N501Y (48.38%) was found to be the dominant mutation followed by L452R (17.52%), T478K (14.31%), E484K (4.69%), S477N (3.29%), K417T (1.64%), N439K (0.7%) and S494P (0.7%). Other mutations were found to be less prevalent (less than 0.7%). Since the last two months, there has been a massive increase of L452R and T478K mutations (delta variant) in certain areas. In the case of prolonged infections’ mutations (long-term SARS-CoV-2 infections), V483A (0.009%) was found to be dominant followed by Q493R (0.009%), while other mutations were found in less than 0.007% of the studied sequences. The data obtained in this study will aid in the development of better infection control policies, thereby curbing the spread of this virus.

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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

Cited by 8 publications

References 25 publications

Spread of endemic SARS-CoV-2 lineages in Russia

Spread of endemic SARS-CoV-2 lineages in Russia

Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy

Global Prevalence of Adaptive and Prolonged Infections’ Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein

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