Genomic epidemiology and emergence of SARS-CoV-2 variants of concern in the United Arab Emirates

Alsafar, Habiba; Albreiki, Mohammed; Mousa, Mira; Azman, Syafiq Kamarul; Vurivi, Hema; Waasia, Fathimathuz; Ruta, Dymitr; Al-Hosani, Farida; Almazroui, Shereena; Abuyadek, Rowan; Selvaraj, Francis Amirtharaj; Chaves-Coira, Irene; Zvereff, Val; Abdel-Malek, Mohamed A. Y.; Kaabi, Nawal Al; Uddin, Maimunah; Awadhi, Tayba Al; Marzouqi, Nada Al; Attar, Fatma Al; Shamsi, Safeiya Al; Shehhi, Fatima Al; Alteneiji, Hala; Mohamed, Kalthoom; Muhairi, Noor Al; Alrand, Hussain; Fikri, Asma; Henschel, Andreas

doi:10.1038/s41598-022-16967-w

Cited by 5 publications

(4 citation statements)

References 46 publications

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“…This study was conducted between the periods of May 2020 and June 2020. Different SARS-CoV-2 lineages were circulating in Abu Dhabi during the study period, including B.1 (10%), B.1.1.1 (3%), B.1.1.133 (3%), B.1.36 (12%), B.1.1.74 (9%), B.1.1.263 (5%), B.1.1.315 (4%), and B.1.1.7 (21%) [ 34 ].…”

Section: Discussionmentioning

confidence: 99%

HLA class I associations with the severity of COVID-19 disease in the United Arab Emirates

Tay,

Alnaqbi,

Chehadeh

et al. 2023

PLoS ONE

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SARS-CoV-2 appears to induce diverse innate and adaptive immune responses, resulting in different clinical manifestations of COVID-19. Due to their function in presenting viral peptides and initiating the adaptive immune response, certain Human Leucocyte Antigen (HLA) alleles may influence the susceptibility to severe SARS-CoV-2 infection. In this study, 92 COVID-19 patients from 15 different nationalities, with mild (n = 30), moderate (n = 35), and severe (n = 27) SARS-CoV-2 infection, living in the United Arab Emirates (UAE) were genotyped for the Class I HLA -A, -C, and -B alleles using next-generation sequencing (NGS) between the period of May 2020 to June 2020. Alleles and inferred haplotype frequencies in the hospitalized patient group (those with moderate to severe disease, n = 62) were compared to non-hospitalized patients (mild or asymptomatic, n = 30). An interesting trend was noted between the severity of COVID-19 and the HLA-C*04 (P = 0.0077) as well as HLA-B*35 (P = 0.0051) alleles. The class I haplotype HLA-C*04-B*35 was also significantly associated (P = 0.0049). The involvement of inflammation, HLA-C*04, and HLA-B*35 in COVID-19 severity highlights the potential roles of both the adaptive and innate immune responses against SARS-CoV-2. Both alleles have been linked to several respiratory diseases, including pulmonary arterial hypertension along with infections caused by the coronavirus and influenza. This study, therefore, supports the potential use of HLA testing in prioritizing public healthcare interventions for patients at risk of COVID-19 infection and disease progression, in addition to providing personalized immunotherapeutic targets.

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Section: Discussionmentioning

confidence: 99%

HLA class I associations with the severity of COVID-19 disease in the United Arab Emirates

Tay,

Alnaqbi,

Chehadeh

et al. 2023

PLoS ONE

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“…It was used to identify the first VOCs B.1.1.7 (Alpha), B.1.351 (Beta) and P.1 (Gamma) and those that emerged later on, such as B.1.617.2 (Delta) and Omicron BA.1 and BA.2 lineages associated with enhanced viral transmission and pathogenicity, and immune escape (Akilesh et al, 2021;Alcoba-Florez et al, 2021;Altmann et al, 2021;Hirotsu and Omata, 2021;Nakamichi et al, 2021;Alsafar et al, 2022;Ciuffreda et al, 2022;Harrigan et al, 2022;Lyngse et al, 2022;Wawina-Bokalanga et al, 2022). In fact, the viral WGS is appropriated for the identification of the viral genomic variants that are associated with severe disease patterns (Hoffmann et al, 2021;Hoang et al, 2022;Overton et al, 2022;von Wintersdorff et al, 2022).…”

Section: Virosurveillance: Genomics To Trace Sars-cov-2mentioning

confidence: 99%

Nanomaterials to combat SARS-CoV-2: Strategies to prevent, diagnose and treat COVID-19

Valenzuela-Fernandez

Cabrera-Rodríguez

Ciuffreda

et al. 2022

Front. Bioeng. Biotechnol.

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the associated coronavirus disease 2019 (COVID-19), which severely affect the respiratory system and several organs and tissues, and may lead to death, have shown how science can respond when challenged by a global emergency, offering as a response a myriad of rapid technological developments. Development of vaccines at lightning speed is one of them. SARS-CoV-2 outbreaks have stressed healthcare systems, questioning patients care by using standard non-adapted therapies and diagnostic tools. In this scenario, nanotechnology has offered new tools, techniques and opportunities for prevention, for rapid, accurate and sensitive diagnosis and treatment of COVID-19. In this review, we focus on the nanotechnological applications and nano-based materials (i.e., personal protective equipment) to combat SARS-CoV-2 transmission, infection, organ damage and for the development of new tools for virosurveillance, diagnose and immune protection by mRNA and other nano-based vaccines. All the nano-based developed tools have allowed a historical, unprecedented, real time epidemiological surveillance and diagnosis of SARS-CoV-2 infection, at community and international levels. The nano-based technology has help to predict and detect how this Sarbecovirus is mutating and the severity of the associated COVID-19 disease, thereby assisting the administration and public health services to make decisions and measures for preparedness against the emerging variants of SARS-CoV-2 and severe or lethal COVID-19.

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“…The re-emergence of A-lineage variants correlated with the acquisition of new mutations and lineages. A.27 variants were identified in Germany and France, A.23.1 in Uganda and UAE, and A.2.5 in Panama, Canada and the US [14][15][16][17][18][19]. The A.2.5 variants were also isolated in clinical samples from Johns Hopkins Hospital and Stanford Health Care throughout 2021.…”

Section: Introductionmentioning

confidence: 99%

Convergent Evolution of A-Lineage (Clade 19B) SARS-CoV-2 Spike Sequences with B-Lineage Variants of Concern Affects Virus Replication in a Temperature-Dependent Manner on Human Nasal Epithelial Cell Cultures

Yoon¹,

Anaya²,

Sachithanandham³

et al. 2023

Preprint

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The first three months of the COVID-19 pandemic was dominated by two SARS-CoV-2 lineages: A-lineages (Clade 19B) and B-lineages (Clade 19A). However, with the emergence of the Spike D614G substitution in B.1 lineages (Clade 20A), both early lineages were outcompeted and remained near-extinction from mid-2020 onwards. In early-2021, there was a re-emergence and persistence of novel A-lineage variants with substitutions in the Spike gene resembling those found in Variants of Concern (VOCs). An early A.3 variant (MD-HP00076/2020) and three A.2.5 variants (MD-HP02153/2021, MD-HP05922/2021 and CA-VRLC091/2021) were isolated and characterized for their genomic sequences, antibody neutralization, andin vitroreplication. All A.2.5 isolates had five Spike mutations relative to the A.3 variant sequence: D614G, L452R, Δ141-143, D215A, and ins215AGY. Plaque reduction neutralization assays demonstrated that A.2.5 isolates had a 2.5 to 5-fold reduction in neutralization using contemporaneous COVID-19 convalescent plasma when compared to A.3.In vitroviral characterization in VeroE6 cell lines revealed that the A.3 isolate grew faster and spread more than A.2.5. On VeroE6-TMPRSS2 cells, significant syncytia formation was also observed with the A.2.5 isolates, however Spike cleavage efficiency did not explain these differences. In human nasal epithelial cell (hNEC) cultures, the A.2.5 isolates grew significantly faster and to higher total infectious virus titers than A.3. All A.2.5 lineage isolates grew significantly faster at 37°C than at 33°C irrespective of cell type, and to higher peak titers except compared to A.3. This suggests A.2.5’s adapted to improve replication using similar mutations found in the B-lineage SARS-CoV-2 variants.ImportanceWhile both A- and B-lineage SARS-CoV-2 variants emerged and circulated together during the early months of the pandemic, the B-lineages that acquired Spike D614G eventually outcompeted all other variants. We show that the A-lineage variants eventually evolved mutations including Spike D614G and Spike L452R that improved their in vitro replication in human nasal epithelial cells in a temperature dependent manner, suggesting there are some highly selectable mutation landscapes that SARS-CoV-2 can acquire to adapt to replication and transmission in humans.

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Genomic epidemiology and emergence of SARS-CoV-2 variants of concern in the United Arab Emirates

Cited by 5 publications

References 46 publications

HLA class I associations with the severity of COVID-19 disease in the United Arab Emirates

HLA class I associations with the severity of COVID-19 disease in the United Arab Emirates

Nanomaterials to combat SARS-CoV-2: Strategies to prevent, diagnose and treat COVID-19

Convergent Evolution of A-Lineage (Clade 19B) SARS-CoV-2 Spike Sequences with B-Lineage Variants of Concern Affects Virus Replication in a Temperature-Dependent Manner on Human Nasal Epithelial Cell Cultures

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