Comparative phylodynamics reveals the evolutionary history of SARS-CoV-2 emerging variants in the Arabian Peninsula

Author:

Alkhamis Moh A1ORCID,Fountain-Jones Nicholas M2ORCID,Khajah Mohammad M3,Alghounaim Mohammad45,Al-Sabah Salman K56ORCID

Affiliation:

1. Department of Epidemiology and Biostatistics, Faculty of Public Health, Health Sciences Centre, Kuwait University , Street 109, Jabriya Campus, Safat, Kuwait City 13110, Kuwait

2. School of Natural Sciences, University of Tasmania , Hobart, Dynnyrne, TAS 7000, Australia

3. Systems and Software Development Department, Kuwait Institute for Scientific Research , Al-Jaheth Street, Shuwaikh, Safat, Kuwait City 13109, Kuwait

4. Departement of Pediatrics, Amiri Hospital, Ministry of Health , Main street, Kuwait City 13041, Kuwait

5. Jaber Al-Ahmad Al-Sabah Hospital, Ministry of Health , South Surra street, Kuwait City 13094, Kuwait

6. Department of Surgery, Faculty of Medicine, Health Sciences Center, Kuwait University , Street 109, Jabriya Campus, Safat, Kuwait City 13110, Kuwait

Abstract

Abstract Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to be responsible for an unprecedented worldwide public health and economic catastrophe. Accurate understanding and comparison of global and regional evolutionary epidemiology of novel SARS-CoV-2 variants are critical to guide current and future interventions. Here, we utilized a Bayesian phylodynamic pipeline to trace and compare the evolutionary dynamics, spatiotemporal origins, and spread of five variants (Alpha, Beta, Delta, Kappa, and Eta) across the Arabian Peninsula. We found variant-specific signatures of evolution and spread that are likely linked to air travel and disease control interventions in the region. Alpha, Beta, and Delta variants went through sequential periods of growth and decline, whereas we inferred inconclusive population growth patterns for the Kappa and Eta variants due to their sporadic introductions in the region. Non-pharmaceutical interventions imposed between mid-2020 and early 2021 likely played a role in reducing the epidemic progression of the Beta and the Alpha variants. In comparison, the combination of the non-pharmaceutical interventions and the rapid rollout of vaccination might have shaped Delta variant dynamics. We found that the Alpha and Beta variants were frequently introduced into the Arab peninsula between mid-2020 and early 2021 from Europe and Africa, respectively, whereas the Delta variant was frequently introduced between early 2021 and mid-2021 from East Asia. For these three variants, we also revealed significant and intense dispersal routes between the Arab region and Africa, Europe, Asia, and Oceania. In contrast, the restricted spread and stable effective population size of the Kappa and the Eta variants suggest that they no longer need to be targeted in genomic surveillance activities in the region. In contrast, the evolutionary characteristics of the Alpha, Beta, and Delta variants confirm the dominance of these variants in the recent outbreaks. Our study highlights the urgent need to establish regional molecular surveillance programs to ensure effective decision making related to the allocation of intervention activities targeted toward the most relevant variants.

Funder

Kuwait Foundation for the Advancement of Science

Publisher

Oxford University Press (OUP)

Subject

Virology,Microbiology

Reference70 articles.

1. COVID-19 in the Gulf Cooperation Council Member States: An Evidence of Effective Response;Al Awaidy;Oman Medical Journal,2021

2. Molecular Epidemiology of COVID-19 in Oman: A Molecular and Surveillance Study for the Early Transmission of COVID-19 in the Country;Al-Mahruqi;International Journal of Infectious Diseases,2021

3. The Proximal Origin of SARS-CoV-2;Andersen;Nature Medicine,2020

4. Classification of Sandstorms in Saudi Arabia;Arishi;Atmospheric and Climate Sciences,2021

5. Epidemiological, Demographic, and Clinical Characteristics of 47 Cases of Middle East Respiratory Syndrome Coronavirus Disease from Saudi Arabia: A Descriptive Study;Assiri;The LancetInfectious Diseases,2013

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