Expansion of a SARS-CoV-2 Delta variant with an 872 nt deletion encompassing ORF7a, ORF7b and ORF8, Poland, July to August 2021

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 i...

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Published in:Euro surveillance : bulletin européen sur les maladies transmissibles 2021-09, Vol.26 (39), p.1
Main Authors: Mazur-Panasiuk, Natalia, Rabalski, Lukasz, Gromowski, Tomasz, Nowicki, Grzegorz, Kowalski, Michal, Wydmanski, Witold, Szulc, Piotr, Kosinski, Maciej, Gackowska, Karolina, Drweska-Matelska, Natalia, Grabowski, Jakub, Piotrowska-Mietelska, Anna, Szewczyk, Boguslaw, Bienkowska-Szewczyk, Krystyna, Swadzba, Jakub, Labaj, Pawel, Grzybek, Maciej, Pyrc, Krzysztof
Format: Article
Language:English
Subjects:
COVID-19
Genomics
Genotype & phenotype
Rapid Communication
Severe acute respiratory syndrome coronavirus 2
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Summary: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.
ISSN:1560-7917
1025-496X
1560-7917
DOI:10.2807/1560-7917.ES.2021.26.39.2100902