Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France

ABSTRACT

While the SARS-CoV-2 genome has remained relatively stable since its emergence, genomic deletions are a frequently described evolutionary pattern of previous coronaviruses with significant impacts on outbreaks. This was the case in with both the SARS and MERS epidemics and has also recently been described with the massive surveillance of the SARS-CoV-2 genome since its emergence. During routine molecular surveillance of SARS-CoV-2 performed at the National Reference Center of Respiratory Viruses (Lyon, France) (n=229 sequences collected Feb-April 2020), two frameshifting deletions were detected in the open reading frame 6, starting at the same position (27267). While a 26-nucleotide deletion variant (D26) was only found in one nasopharyngeal sample in March 2020, the 34-nucleotide deletion variant D34) was found within a single geriatric hospital unit in 5/9 patients and one health care worker in April 2020. Phylogeny analysis strongly suggested a nosocomial transmission between patients for D34, with potential fecal transmission, as D34 was also identified in a stool sample. No difference in disease severity was observed within the patients hospitalized in the geriatric unit and infected with WT (n=4) or D34 (n=5). In vitro characterization of D26 and D34 revealed comparable replication kinetics with the wild-type (WT), but differential host immune responses. While interferon-stimulated genes were similarly upregulated after infection withWTand ORF6 deletion variants, the latter specifically induced overexpression of 9 genes coding for inflammatory cytokines in the NF-kB pathway, including CCL2/MCP1, PTX3, and TNF, for which high plasma levels of these cytokines have been associated with severe Covid-19. Given the heterogeneous clinical manifestations of Covid-19 and the growing global prevelance of certain SARS-CoV-2 variants, our findings emphasize the need to monitor the occurrence of ORF6 deletions and assess their impact on the host immune response.