Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine
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Le résumé fourni par la source
The emergence of new SARS-CoV-2 variants in Palestine highlights the need for continuous genetic surveillance and accurate screening strategies. This case series study aimed to investigate the geographic distribution and genetic variation of the SARS-CoV-2 Delta Variant in Palestine in August 2021. Samples were collected at random in August 2021 (n = 571) from eight districts in the West Bank, Palestine. All samples were confirmed as positive for COVID-19 by RT-PCR. The samples passed the quality control test and were successfully sequenced using the ARTIC protocol. The Delta Variant was revealed to have four dominant lineages: B.1.617 (19%), AY.122 (18%), AY.106 (17%), and AY.121 (13%). The study revealed eight significant purely spatial clusters (p < 0.005) distributed in the northern and southern parts of Palestine. Phylogenetic analysis of SARS-CoV-2 genomes (n = 552) showed no geographically specific clades. The haplotype network revealed three haplogroups without any geographic distribution. Chronologically, the Delta Variant peak in Palestine was shortly preceded by the one in the neighboring Israeli community and shortly followed by the peak in Jordan. In addition, the study revealed an extremely intense transmission network of the Delta Variant circulating between the Palestinian districts as hubs (SHR ≈ 0.5), with Al-Khalil, the district with the highest prevalence of COVID-19, witnessing the highest frequency of transitions. Genetic diversity analysis indicated closely related haplogroups, as haplotype diversity (Hd) is high but has low nucleotide diversity (π). However, nucleotide diversity (π) in Palestine is still higher than the global figures. Neutrality tests were significantly (p < 0.05) low, including Tajima’s D, Fu-Li’s F, and Fu-Li’s D, suggesting one or more of the following: population expansion, selective sweep, and natural negative selection. Wright’s F-statistic (Fst) showed genetic differentiation (Fst > 0.25) with low to medium gene flow (Nm). Recombination events were minimal between clusters (Rm) and between adjacent sites (Rs). The study confirms the utility of the whole genome sequence as a surveillance system to track the emergence of new SARS-CoV-2 variants for any possible geographical association and the use of genetic variation analysis and haplotype networking to delineate any minimal change or slight deviation in the viral genome from a reference strain.
Ce résumé expose les affirmations des auteurs. BNTIC ne l’interprète pas comme une validation indépendante des résultats.
Le contrôle bibliographique ouvert
DOI retrouvé dans Crossref DOI retrouvé ; titre concordant.
- Titre Crossref
- Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine
- Date Crossref
- 20/06/2024
- Éditeur
- MDPI AG
- Type
- journal-article
Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude, et il ne compte pas comme une seconde source scientifique indépendante.
Où se fait cette recherche
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Al-Quds University pays non établi dans la noticeUniversité ou école supérieure
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Norwich Research Park pays non établi dans la noticeInstitution
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Quadram Institute pays non établi dans la noticeStructure de recherche
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Arab American University pays non établi dans la noticeUniversité ou école supérieure
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University of East Anglia pays non établi dans la noticeUniversité ou école supérieure
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University of Surrey pays non établi dans la noticeUniversité ou école supérieure
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Bard College pays non établi dans la noticeUniversité ou école supérieure
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Faculty of Medicine Biochemistry and Molecular Biology Department pays non établi dans la noticeUniversité ou école supérieure
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Faculty of Allied Health Sciences Department of Medical Laboratory Sciences pays non établi dans la noticeUniversité ou école supérieure
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Leishmaniases Research Unit pays non établi dans la noticeStructure de recherche
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Ministry of Health of the State of Palestine pays non établi dans la noticeOrganisme public
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School of Veterinary Medicine pays non établi dans la noticeUniversité ou école supérieure
Al-Quds University, Norwich Research Park et Quadram Institute, avec 9 autres affiliations.
Une affiliation ne permet pas de déduire la nationalité d’un auteur.