Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study

Abstract

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with a 382-nucleotide deletion (∆382) in the open reading frame 8 (ORF8) region of the genome have been detected in Singapore and other countries. We investigated the effect of this deletion on the clinical features of infection.

Methods: We retrospectively identified patients who had been screened for the ∆382 variant and recruited to the PROTECT study-a prospective observational cohort study conducted at seven public hospitals in Singapore. We collected clinical, laboratory, and radiological data from patients' electronic medical records and serial blood and respiratory samples taken during hospitalisation and after discharge. Individuals infected with the ∆382 variant were compared with those infected with wild-type SARS-CoV-2. Exact logistic regression was used to examine the association between the infection groups and the development of hypoxia requiring supplemental oxygen (an indicator of severe COVID-19, the primary endpoint). Follow-up for the study's primary endpoint is completed.

Findings: Between Jan 22 and March 21, 2020, 278 patients with PCR-confirmed SARS-CoV-2 infection were screened for the ∆382 deletion and 131 were enrolled onto the study, of whom 92 (70%) were infected with the wild-type virus, ten (8%) had a mix of wild-type and ∆382-variant viruses, and 29 (22%) had only the ∆382 variant. Development of hypoxia requiring supplemental oxygen was less frequent in the ∆382 variant group (0 [0%] of 29 patients) than in the wild-type only group (26 [28%] of 92; absolute difference 28% [95% CI 14-28]). After adjusting for age and presence of comorbidities, infection with the ∆382 variant only was associated with lower odds of developing hypoxia requiring supplemental oxygen (adjusted odds ratio 0·07 [95% CI 0·00-0·48]) compared with infection with wild-type virus only.

Interpretation: The ∆382 variant of SARS-CoV-2 seems to be associated with a milder infection. The observed clinical effects of deletions in ORF8 could have implications for the development of treatments and vaccines.

Funding: National Medical Research Council Singapore.

Figure 1

Capillary electrophoresis of the ORF8 gene showing differences across the duration of disease in four patients co-infected with wild-type and the Δ382 variant of severe acute respiratory syndrome coronavirus 2 Approximate band sizes were 880 bp for the wild-type virus and 500 bp for the Δ382 variant. Nuclease-free water was used as a non-template negative control for PCR1. This resultant reaction was used as the negative control for the nested reaction. Δ382=382-nucleotide deletion. M=100-bp marker.

Figure 2

Concentrations of 45 immune mediators quantified using a 45-plex microbead-based immunoassay Heatmap of immune mediator levels in plasma samples of patients infected with either wild-type (n=64), Δ382 variant (n=25), or mixed wild-type and Δ382 variant severe acute respiratory syndrome coronavirus 2 (n=8; indicated by asterisks in figure) during the first collection timepoint upon hospital admission (median 8 days from symptom onset). Each colour represents the relative concentration of a particular analyte (blue=low concentration; red=high concentration). Δ382=382-nucleotide deletion.

Figure 3

Chain of transmission between cases as established by epidemiological investigations Δ382=382-nucleotide deletion. *Possible epidemiological links were identified when individuals with COVID-19 had a common physical location or timing but direct interaction could not be clearly established; possible epidemiological links would also reflect transmissions that have arisen from close contact between a case and a few possible sources in the same cluster.