Investigating the biological and technical origins of unknown bases in the S region of the SARS-CoV-2 Delta variant genome sequences

Borcard, Loïc; Gempeler, Sonja; Terrazos Miani, Miguel A.; Baumann, Christian; Grädel, Carole; Dijkman, Ronald; Suter-Riniker, Franziska; Leib, Stephen L; Bittel, Pascal; Neuenschwander, Stefan; Ramette, Alban (2021). Investigating the biological and technical origins of unknown bases in the S region of the SARS-CoV-2 Delta variant genome sequences (medRxiv). Cold Spring Harbor Laboratory 10.1101/2021.09.09.21262951

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We are reporting on the observation of a large, under-sequenced region of the S gene of the SARS-CoV2 Delta variant genomes, identified in sequences originating from various sequencing centres worldwide (e.g. USA, India, England, Switzerland, France, Germany). This poorly sequenced region was identified from the early phases of the Delta variant spread and the phenomenon is still ongoing. As many commonly-used protocols rely on amplicon-based sequencing procedures, we investigated the likely origin of the issue. We established its biological origin as resulting from mutations in the viral genomes at primer binding sites. We designed and evaluated new PCR primers to circumvent this issue in order to complement the ARTIC v3 set, and validated their performance for the sequencing of circulating Delta variants.

Item Type:

Working Paper

Division/Institute:

04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases

UniBE Contributor:

Borcard, Loïc Vivien; Gempeler, Sonja; Terrazos Miani, Miguel Angel; Baumann, Christian; Grädel, Carole Salome; Dijkman, Ronald; Suter, Franziska Marta; Leib, Stephen; Bittel, Pascal; Neuenschwander, Stefan and Ramette, Alban Nicolas

Subjects:

500 Science > 570 Life sciences; biology
600 Technology > 610 Medicine & health

Series:

medRxiv

Publisher:

Cold Spring Harbor Laboratory

Language:

English

Submitter:

Alban Nicolas Ramette

Date Deposited:

05 Jan 2022 15:34

Last Modified:

05 Jan 2022 15:43

Publisher DOI:

10.1101/2021.09.09.21262951

BORIS DOI:

10.48350/162136

URI:

https://boris.unibe.ch/id/eprint/162136

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