Researchers have found that a deletion in the SARS-CoV-2 genome, which has been detected in Singapore and other countries, is associated with a milder infection.
A 382-nucleotide deletion
Since the outbreak of the SARS-CoV-2, researchers have made efforts to map the diversity of the virus and to determine variants with a selective advantage. A cluster of cases were detected in Singapore early this year with a 382-nucleotide deletion (Δ382) in the SARS-CoV-2 genome. The deletion results in a truncated open reading frame (ORF) 7b. This removes the ORF8 transcription-regulatory sequence and therefore eliminates ORF8 transcription. The variant successfully transmitted during the early stages of the pandemic but was not detected after March 2020. Other deletions in ORF8 have been reported across Bangladesh, Australia and Spain.
The biological function of the ORF8 protein in SARS-CoV-2 is unclear. However, recent research has indicated that ORF8 mediates immune evasion by downregulating MHC-I molecules. In a study, published in The Lancet, researchers compared clinical outcomes and immune responses from patients infected with wild-type and Δ382 SARS-CoV-2.
Wild–type vs Deletion
The team retrospectively identified individuals who had been screened for the Δ382 variant and recruited to the PROTECT study. PROTECT is a prospective observational cohort study conducted at seven public hospitals in Singapore. The study aimed to recruit all individuals hospitalised with confirmed SARS-CoV-2 from the seven hospitals to clinically characterise COVID-19. They collected clinical, laboratory and radiological data from each patient’s electronic medical record. They also obtained serial blood and respiratory samples that were taken during hospitalisation and after discharge. Individuals infected with the Δ382 variant were compared with those infected with wild-type SARS-CoV-2.
Out of 251 samples where SARS-CoV-2 was detected, 131 (52%) had been enrolled in the PROTECT study and had clinical data available for further analysis. Among them, 92 (70%) were infected with wild-type virus only, 10 (8%) had a mixture of both and 29 (22%) had only the Δ382 variant.
A multivariable logistic regression model revealed that the Δ382 variant was associated with less severe infection in terms of hypoxia requiring supplemental oxygen. Specifically, in the Δ382 variant group, 0% of patients required supplemental oxygen, whereas 28% of the wild-type only group did. The team also observed that patients infected with the Δ382 variant had lower concentration of proinflammatory cytokines, chemokines and growth factors. These factors are strongly associated with severe COVID-19.
ORF8 hotspot for mutations
The repeated emergence of SARS-CoV-2 deletions in ORF8 implies that this region is important for viral adaptation to humans. Previous studies have reported that ORF8 is strongly immunogenic and that antibodies are produced against ORF8 during early infection. The analysis from this study suggests that the Δ382 variant out-competed the wild-type virus.
This study indicates that ORF8 deletions appear to result in milder COVID-19 infection with less systemic release of proinflammatory cytokines. Further understanding of these variants and their effects on SARS-CoV-2 pathogenesis could have implications for drug and vaccine development.
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