Natalia Mazur-Panasiuk1,* , Lukasz Rabalski2,* , Tomasz Gromowski1,3 , Grzegorz Nowicki4 , Michal Kowalski5 , Witold Wydmanski5 , Piotr Szulc5 , Maciej Kosinski2 , Karolina Gackowska2 , Natalia Drweska-Matelska4 , Jakub Grabowski4 , Anna Piotrowska-Mietelska6 , Boguslaw Szewczyk2 , Krystyna Bienkowska-Szewczyk7 , Jakub Swadzba6 , Pawel Labaj5 , Maciej Grzybek8 , Krzysztof Pyrc1
Routine genomic surveillance on samples from COVID-19 patients collected in Poland during summer 2021 revealed the emergence of a SARS-CoV-2 Delta variant with a large 872 nt deletion. This change, confirmed by Sanger and deep sequencing, causes complete loss of ORF7a, ORF7b, and ORF8 genes. The index case carrying the deletion is unknown. The standard pipeline for sequencing may mask this deletion with a long stretch of N’s. Effects of this deletion on phenotype or immune evasion needs further study.
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Routine genomic surveillance on samples from COVID-19 patients collected in Poland during summer 2021 revealed the emergence of a SARS-CoV-2 Delta variant with a large 872 nt deletion. This change, confirmed by Sanger and deep sequencing, causes complete loss of ORF7a, ORF7b, and ORF8 genes. The index case carrying the deletion is unknown. The standard pipeline for sequencing may mask this deletion with a long stretch of N’s. Effects of this deletion on phenotype or immune evasion needs further study.
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