TY - JOUR
T1 - Genotype-phenotype correlation identified a novel SARS-CoV-2 variant possibly linked to severe disease
AU - Loney, Tom
AU - Khansaheb, Hamda
AU - Ramaswamy, Sathishkumar
AU - Harilal, Divinlal
AU - Deesi, Zulfa Omar
AU - Varghese, Rupa Murthy
AU - Belal Al Ali, Aydah
AU - Khadeeja, Anees
AU - Al Suwaidi, Hanan
AU - Alkhajeh, Abdulmajeed
AU - Mohamed AlDabal, Laila
AU - Uddin, Mohammed
AU - Al Faresi, Mubarak
AU - Joshi, Madhvi
AU - Senok, Abiola
AU - Nowotny, Norbert
AU - Alsheikh-Ali, Alawi
AU - Abou Tayoun, Ahmad
N1 - Funding Information:
This work was supported by internal funds from the College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences (to AAT, grant no. MBRU‐CM‐RG2020‐04).
Publisher Copyright:
© 2021 Wiley-VCH GmbH.
PY - 2022/3
Y1 - 2022/3
N2 - The geographic location and heterogeneous multi-ethnic population of Dubai (United Arab Emirates; UAE) provide a unique setting to explore the global molecular epidemiology of SARS-CoV-2 and relationship between different viral strains and disease severity. We systematically selected (i.e. every 100th individual in the central Dubai COVID-19 database) 256 patients by age, sex, disease severity and month to provide a representative sample of laboratory-confirmed COVID-19 patients (nasopharyngeal swab PCR positive) during the first wave of the UAE outbreak (January to June 2020). Sociodemographic and clinical data were extracted from medical records and full SARS-CoV-2 genome sequences extracted from nasopharyngeal swabs were analysed. Older age was significantly associated with COVID-19-associated hospital admission and mortality. Overweight/obese or diabetic patients were 3–4 times more likely to be admitted to hospital and intensive care unit (ICU). Sequencing data showed multiple independent viral introductions into the UAE from Europe, Iran and Asia (29 January–18 March), and these early strains seeded significant clustering consistent with almost exclusive community-based transmission between April and June 2020. Majority of sequenced strains (N = 60, 52%) were from the European cluster consistent with the higher infectivity rates associated with the D614G mutation carried by most strains in this cluster. A total of 986 mutations were identified in 115 genomes, 272 were unique (majority were missense, n = 134) and 20/272 mutations were novel. A missense (Q271R) and synonymous (R41R) mutation in the S and N proteins, respectively, were identified in 2/27 patients with severe COVID-19 but not in patients with mild or moderate disease (0/86; p =.05, Fisher's Exact Test). Both patients were women (51–64 years) with no significant underlying health conditions. The same two mutations were identified in a healthy 37-year-old Indian man who was hospitalized in India due to COVID-19. Our findings provide evidence for continued community-based transmission of the European strains in the Dubai population and highlight new mutations that might be associated with severe disease in otherwise healthy adults.
AB - The geographic location and heterogeneous multi-ethnic population of Dubai (United Arab Emirates; UAE) provide a unique setting to explore the global molecular epidemiology of SARS-CoV-2 and relationship between different viral strains and disease severity. We systematically selected (i.e. every 100th individual in the central Dubai COVID-19 database) 256 patients by age, sex, disease severity and month to provide a representative sample of laboratory-confirmed COVID-19 patients (nasopharyngeal swab PCR positive) during the first wave of the UAE outbreak (January to June 2020). Sociodemographic and clinical data were extracted from medical records and full SARS-CoV-2 genome sequences extracted from nasopharyngeal swabs were analysed. Older age was significantly associated with COVID-19-associated hospital admission and mortality. Overweight/obese or diabetic patients were 3–4 times more likely to be admitted to hospital and intensive care unit (ICU). Sequencing data showed multiple independent viral introductions into the UAE from Europe, Iran and Asia (29 January–18 March), and these early strains seeded significant clustering consistent with almost exclusive community-based transmission between April and June 2020. Majority of sequenced strains (N = 60, 52%) were from the European cluster consistent with the higher infectivity rates associated with the D614G mutation carried by most strains in this cluster. A total of 986 mutations were identified in 115 genomes, 272 were unique (majority were missense, n = 134) and 20/272 mutations were novel. A missense (Q271R) and synonymous (R41R) mutation in the S and N proteins, respectively, were identified in 2/27 patients with severe COVID-19 but not in patients with mild or moderate disease (0/86; p =.05, Fisher's Exact Test). Both patients were women (51–64 years) with no significant underlying health conditions. The same two mutations were identified in a healthy 37-year-old Indian man who was hospitalized in India due to COVID-19. Our findings provide evidence for continued community-based transmission of the European strains in the Dubai population and highlight new mutations that might be associated with severe disease in otherwise healthy adults.
KW - COVID-19
KW - Q271R
KW - SARS-CoV-2
KW - molecular phylogeny
KW - mutation
KW - whole genome sequencing
UR - http://www.scopus.com/inward/record.url?scp=85101089266&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85101089266&partnerID=8YFLogxK
U2 - 10.1111/tbed.14004
DO - 10.1111/tbed.14004
M3 - Article
C2 - 33506644
AN - SCOPUS:85101089266
SN - 1865-1674
VL - 69
SP - 465
EP - 476
JO - Transboundary and Emerging Diseases
JF - Transboundary and Emerging Diseases
IS - 2
ER -