Journal
MICROORGANISMS
Volume 10, Issue 2, Pages -Publisher
MDPI
DOI: 10.3390/microorganisms10020268
Keywords
SARS-CoV-2; delta variant; omicron variant; N gene target failure; diagnostic assay; sequence; NGS; nucleocapsid deletion
Categories
Funding
- Italian Ministry of Research [FISR2020IP_04758]
- EuCARE project European cohorts of patients and schools to advance response to epidemics - EC under HORIZON-HLTH-2021-CORONA-01 [101046016]
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This study reports a case of an Italian male infected with Delta sublineage AY.4 carrying an atypical deletion that causes N gene target failure. The importance of performing SARS-CoV-2 sequencing and characterizing new mutations/deletions that could affect the interpretation of molecular diagnostic tests is underscored.
Herein, we report a case of an Italian male infected by Delta sublineage AY.4 harboring an atypical deletion, leading to a N gene target failure (NGTF) by a commercial molecular assay for SARS-CoV-2 diagnosis (Allplex(TM) SARS-CoV-2 Assay, Seegene). A 59-year-old unvaccinated patient was hospitalized for pulmonary embolism, with first negative results obtained by both molecular and antigen tests. After several days of viral negativity, he presented positive results for E and RdRP/S genes, but negative in N gene. Negativity in N gene was repeatedly confirmed in the following days. Suspecting an infection by the Omicron variant, SARS-CoV-2 genome sequencing was rapidly performed from nasopharyngeal swab by MiSeq and revealed the presence of the Delta sublineage AY.4 variant with an atypical deletion of six nucleotides, leading to G214-G215 deletion in the Nucleocapsid, thus responsible for NGTF. The analysis of GISAID sequences (N = 2,618,373 12 January 2022) showed that G214-G215 deletion is rarely occurring in most circulating Delta lineages and sublineages in the globe and Europe, with an overall prevalence never exceeding 0.2%. Hence, this study highlights the importance to perform SARS-CoV-2 sequencing and to characterize novel mutations/deletions that could jeopardize the proper interpretation of molecular diagnostic tests. Based on these assumptions, the role of deletions in the recently identified Omicron variant deserves further investigation.
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