Novel NUDCD1 gene variant predisposes to severe COVID-19 disease in Asians through modulation of anti-viral DHX15-and MAVS-mediated signaling

Anusha Amali Aseervatham¹Douglas Jie Wen Tay²Yiqi Seow³Marie Loh⁴Sharada Ravikumar1⁵Jocelyn Jin Yu⁶Shaun Loong⁷Siew-Wai Fong⁸Mick Lee⁷Jonathan Jordon Cailu Lim⁶Louis Hanqiang Gan⁷Winston Lian Chye Koh⁹Ying Ding⁶Qi Hui Sam¹⁰Zhaohong Tan¹Rachel Ying Min Tan⁵Chong Boon Lua¹¹Justin Jang Hann Chu¹²Amit Singhal⁸Shyam Prabhakar³Wee Joo Chng¹³Laurent Rénia⁴David Chien Boon Lye⁶Lisa F P Ng⁸Kai Sen Tan¹⁴Roger Foo⁷Chang Chuan Melvin Lee¹¹Barnaby Young⁶Louis Yi Ann Chai^15*

• ¹Division of Infectious Diseases, Department of Medicine,, National University Health System (Singapore), Singapore, Singapore
• ²Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, National University of Singapore, singapore, Singapore
• ³Genomic Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
• ⁴Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
• ⁵Division of Infectious Diseases, Department of Medicine, National University Health System (Singapore), Singapore, Singapore
• ⁶National Centre for Infectious Diseases (NCID), Singapore, Singapore
• ⁷Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
• ⁸A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
• ⁹Bioinformatic Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
• ¹⁰Division of Infectious Diseases, Department of Medicine,, National University Hospital (Singapore) Pte Ltd, Singapore, Singapore
• ¹¹Department of Anaesthesia, National University Health System (Singapore), Singapore, Singapore
• ¹²Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
• ¹³Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University of Singapore, Singapore, Singapore
• ¹⁴Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine,, National University of Singapore, Singapore, Singapore
• ¹⁵National University Health System (Singapore), Singapore, Singapore

BackgroundGenome-wide associative studies can potentially uncover novel pathways which modulate anti-viral immune responses against SARS-CoV-2 or identify drivers of severe disease. To date, these studies have yielded loci mostly in non-functional domains of unknown biological significance and invariably require large sample sizes, potentially missing lower frequency variants, especially in under-represented or minority populations. MethodsTo identify unique genetic traits predisposing to severe COVID-19 in Asians, we employed an alternative strategy of whole exome sequencing from representative cohort of severe versus mild COVID-19 patients. Candidate gene variants were identified by performing logistic regression against top genetic principal components, prioritised for missense variants with likely causal impact. Then, functional sequelae of variants were replicated in-vitro and re-validated in patients ex vivo to demonstrate causality between genotype and clinical phenotype. ResultsOf 136 COVID-19 patients in Singapore (of whom 25% had severe disease), a single nucleotide polymorphism rs2980619 (L252F substitution) belonging to NudC-Domain-Containing-1 (NUDCD1) was highly-placed. Homozygous bearers of variant 252F had higher (3.97x) odds of severe disease. Age >50 years and male sex were significant covariates which increased the odds of severe disease by 3.38x and 3.16x, respectively. We showed in-vitro that variant 252F reduced NUDCD1 activity, leading to reduced antiviral signalling through RNA helicase DHX15 and antiviral signalling adaptor MAVS, reduced activation of NFκB components RelB and p65, and resultant 1-log higher SARS-CoV-2 viral load compared to wild-type L252 cells. Patients bearing 252F had lower NUDCD1, MAVS, and RelB expressions, affirming the above findings. ConclusionThe novel gene variant of NUDCD1 influences COVID-19 severity in Asians through interacting with DHX15 and MAVS, affecting effective response against SARS-CoV-2.