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Ereqat, Suheir, Alikhan, Nabil-Fareed, Al-Jawabreh, Amer, Matthews, Michaela, Al-Jawabreh, Ahmed, de Oliveira Martins, Leonardo, Trotter, Alexander J., Al-Kaila, Mai, Page, Andrew J., Pallen, Mark J. 
ORCID: https://orcid.org/0000-0003-1807-3657 and Nasereddin, Abedelmajeed
(2024)
Epidemiological characterization and genetic variation of the SARS-CoV-2 Delta variant in Palestine.
Pathogens, 13 (6).
ISSN 2076-0817
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Abstract
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.
| Item Type: | Article |
|---|---|
| Additional Information: | Data Availability Statement: The data in this study are publicly available in the GISAID database (EPI_ISL_10033368-EPI_ISL_10033935). Funding Information: The Quadram Institute authors gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC); their research was funded by the BBSRC Institute Strategic Program Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10352. The Quadram Institute Bioscience BBSRC also funded the Core Capability Grant (project number BB/CCG1860/1). For the purposes of open access publishing, the author has applied a CC-BY public copyright license to any author-accepted manuscript version arising from this submission. |
| Uncontrolled Keywords: | covid-19,genomic epidemiology,mutation,palestine,sars-cov-2,immunology and allergy,molecular biology,immunology and microbiology(all),microbiology (medical),infectious diseases,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/2700/2723 |
| Faculty \ School: | Faculty of Medicine and Health Sciences > Norwich Medical School |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 23 Oct 2024 11:30 |
| Last Modified: | 21 Nov 2024 03:31 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97145 |
| DOI: | 10.3390/pathogens13060521 |
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