Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Detection of SARS-CoV-2 Δ426 ORF8 Deletion Mutant Cluster in NGS Screening

Riccardo Cecchetto
ORCID logo ,
Emil Tonon
,
Nicoletta Medaina
,
Giona Turri
,
Erica Diani
* ORCID logo ,
Pier Paolo Piccaluga
ORCID logo ,
Angela Salomoni
,
Michela Conti
,
Evelina Tacconelli
,
Anna Lagni
ORCID logo ,
Virginia Lotti
ORCID logo ,
Mosè Favarato
,
Davide Gibellini
Version 1 : Received: 3 August 2023 / Approved: 4 August 2023 / Online: 4 August 2023 (13:34:25 CEST)

A peer-reviewed article of this Preprint also exists.

Cecchetto, R.; Tonon, E.; Medaina, N.; Turri, G.; Diani, E.; Piccaluga, P.P.; Salomoni, A.; Conti, M.; Tacconelli, E.; Lagni, A.; Lotti, V.; Favarato, M.; Gibellini, D. Detection of SARS-CoV-2 Δ426 ORF8 Deletion Mutant Cluster in NGS Screening. Microorganisms 2023, 11, 2378. Cecchetto, R.; Tonon, E.; Medaina, N.; Turri, G.; Diani, E.; Piccaluga, P.P.; Salomoni, A.; Conti, M.; Tacconelli, E.; Lagni, A.; Lotti, V.; Favarato, M.; Gibellini, D. Detection of SARS-CoV-2 Δ426 ORF8 Deletion Mutant Cluster in NGS Screening. Microorganisms 2023, 11, 2378.

Abstract

Next generation sequencing (NGS) from SARS-CoV-2-positive swabs collected during the last months of 2022 revealed a large deletion between ORF7b and ORF8 (426 nt) in six patients infected with the BA.5.1 Omicron variant. This extensive genome loss removed a large part of these two genes, maintaining in frame the first 22 aminoacids of ORF7b and the last 3 aminoacids of ORF8. Interestingly, the deleted region was flanked by 2 small repeats, likely involved in the formation of a hairpin structure. Similar rearrangements, comparable in size and location to the deletion, were also identified in 15 sequences in the NCBI database. In this group, 7 out of 15 cases from the USA and Switzerland presented both the BA.5.1 variant and the same 426 nuclotides deletion. It is noteworthy that 3 out of 6 cases were detected in patients with immunodeficiency and is conceivable that this clinical condition could promote the replication and selection of these mutations.

Keywords

SARS-CoV-2; genomic surveillance; NGS; deletion; variants.; clusters

Subject

Medicine and Pharmacology, Epidemiology and Infectious Diseases

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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