1. Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study
- Author
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Laurent Rénia, Siti Naqiah Amrun, Danielle E. Anderson, Timothy Barkham, Tze Minn Mak, Yun Shan Goh, Lisa F. P. Ng, Yi-Hao Chan, Yee Sin Leo, Wycliffe E. Wei, Seow Yen Tan, Cheryl Yi-Pin Lee, Vernon J. Lee, Raymond T. P. Lin, Barnaby Edward Young, Louisa Sun, Siew-Wai Fong, Purnima Parthasarathy, Lin-Fa Wang, Louis Yi Ann Chai, Shirin Kalimuddin, Yuan Yi Constance Chen, Bernett Lee, Surinder Pada, Gavin J. D. Smith, David C. Lye, Sebastian Maurer-Stroh, Li Wei Ang, and Yvonne C. F. Su
- Subjects
Adult ,Respiratory Therapy ,medicine.medical_specialty ,Pneumonia, Viral ,Genome, Viral ,030204 cardiovascular system & hematology ,Virus Replication ,Logistic regression ,Severity of Illness Index ,Article ,Betacoronavirus ,Open Reading Frames ,03 medical and health sciences ,0302 clinical medicine ,Internal medicine ,Severity of illness ,Clinical endpoint ,Humans ,Medicine ,Prospective Studies ,030212 general & internal medicine ,Hypoxia ,Prospective cohort study ,Pandemics ,Aged ,Singapore ,SARS-CoV-2 ,business.industry ,Medical record ,COVID-19 ,Odds ratio ,General Medicine ,Middle Aged ,medicine.disease ,Pneumonia ,Coronavirus Infections ,business ,Gene Deletion ,Cohort study - Abstract
Summary 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.
- Published
- 2020
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