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Ereqat S, Alikhan NF, Al-Jawabreh A, Matthews M, Al-Jawabreh A, de Oliveira Martins L, Trotter AJ, Al-Kaila M, Page AJ, Pallen MJ, Nasereddin A. Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine. Pathogens 2024; 13:521. [PMID: 38921818 PMCID: PMC11206313 DOI: 10.3390/pathogens13060521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/29/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
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.
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Affiliation(s)
- Suheir Ereqat
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al-Quds University, Abu Dis, Jerusalem P.O. Box 51000, Palestine; (S.E.); (A.N.)
| | - Nabil-Fareed Alikhan
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (N.-F.A.); (L.d.O.M.); (A.J.T.); (A.J.P.); (M.J.P.)
| | - Amer Al-Jawabreh
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Arab American University, Jenin P.O. Box 240, Palestine
- Leishmaniases Research Unit, Jericho P5840227, Palestine
| | - Michaela Matthews
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (N.-F.A.); (L.d.O.M.); (A.J.T.); (A.J.P.); (M.J.P.)
| | - Ahmed Al-Jawabreh
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al-Quds University, Abu Dis, Jerusalem P.O. Box 51000, Palestine; (S.E.); (A.N.)
- Ministry of Health of the State of Palestine, Ramallah P6028100, Palestine;
| | - Leonardo de Oliveira Martins
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (N.-F.A.); (L.d.O.M.); (A.J.T.); (A.J.P.); (M.J.P.)
| | - Alexander J. Trotter
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (N.-F.A.); (L.d.O.M.); (A.J.T.); (A.J.P.); (M.J.P.)
| | - Mai Al-Kaila
- Ministry of Health of the State of Palestine, Ramallah P6028100, Palestine;
| | - Andrew J. Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (N.-F.A.); (L.d.O.M.); (A.J.T.); (A.J.P.); (M.J.P.)
| | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (N.-F.A.); (L.d.O.M.); (A.J.T.); (A.J.P.); (M.J.P.)
- University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, UK
| | - Abedelmajeed Nasereddin
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al-Quds University, Abu Dis, Jerusalem P.O. Box 51000, Palestine; (S.E.); (A.N.)
- Al-Quds Bard College, Al-Quds University, East Jerusalem P.O. Box 20002, Palestine
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Nasir A, Aamir UB, Kanji A, Bukhari AR, Ansar Z, Ghanchi NK, Masood KI, Samreen A, Islam N, Ghani S, Syed MA, Wassan M, Mahmood SF, Hasan Z. Tracking SARS-CoV-2 variants through pandemic waves using RT-PCR testing in low-resource settings. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001896. [PMID: 37262051 PMCID: PMC10234525 DOI: 10.1371/journal.pgph.0001896] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/05/2023] [Indexed: 06/03/2023]
Abstract
COVID-19 resulted in extensive morbidity and mortality worldwide. SARS-CoV-2 evolved rapidly, with increasing transmission due to Variants of Concern (VOC). Identifying VOC became important but genome submissions from low-middle income countries (LMIC) remained low leading to gaps in genomic epidemiology. We demonstrate the use of a specific mutation RT-PCR based approach to identify VOC in SARS-CoV-2 positive samples through the pandemic in Pakistan. We selected 2150 SARS-CoV-2 PCR positive respiratory specimens tested between April 2021 and February 2022, at the Aga Khan University Hospital Clinical Laboratories, Karachi, Pakistan. Commercially available RT-PCR assays were used as required for mutations in Spike protein (N501Y, A570D, E484K, K417N, L452R, P681R and deletion69_70) to identify Alpha, Beta, Gamma, Delta, and Omicron variants respectively. Three pandemic waves associated with Alpha, Delta and Omicron occurred during the study period. Of the samples screened, VOC were identified in 81.7% of cases comprising mainly; Delta (37.2%), Alpha (29.8%) and Omicron (17.1%) variants. During 2021, Alpha variants were predominant in April and May; Beta and Gamma variants emerged in May and peaked in June; the Delta variant peaked in July and remained predominant until November. Omicron (BA.1) emerged in December 2021 and remained predominant until February 2022. The CT values of Alpha, Beta, Gamma and Delta were all significantly higher than that of Omicron variants (p<0.0001). We observed VOC through the pandemic waves using spike mutation specific RT-PCR assays. We show the spike mutation specific RT-PCR assay is a rapid, low-cost and adaptable for the identification of VOC as an adjunct approach to NGS to effectively inform the public health response. Further, by associating the VOC with CT values of its diagnostic PCR we gain information regarding the viral load of samples and therefore the level of transmission and disease severity in the population.
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Affiliation(s)
- Asghar Nasir
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | | | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Ali Raza Bukhari
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zeeshan Ansar
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Najia Karim Ghanchi
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Kiran Iqbal Masood
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Azra Samreen
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Nazneen Islam
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Samina Ghani
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - M. Asif Syed
- Department of Health, Government of Sindh, Karachi, Pakistan
| | - Mansoor Wassan
- Department of Health, Government of Sindh, Karachi, Pakistan
| | | | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
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Seadawy MG, Binsuwaidan R, Alotaibi B, El-Masry TA, El-Harty BE, Gad AF, Elkhatib WF, El-Bouseary MM. The Mutational Landscape of SARS-CoV-2 Variants of Concern Recovered From Egyptian Patients in 2021. Front Microbiol 2022; 13:923137. [PMID: 35875574 PMCID: PMC9300961 DOI: 10.3389/fmicb.2022.923137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/16/2022] [Indexed: 11/22/2022] Open
Abstract
In December 2019, a mysterious viral pneumonia first developed in Wuhan, China, resulting in a huge number of fatal cases. This pneumonia, which was named COVID-19, was attributed to a novel coronavirus, SARS-CoV-2. The emerging SARS-CoV-2 mutations pose the greatest risk to human health because they could result in an increase in the COVID-19 severity or the failure of current vaccines. One of these notable mutations is the SARS-CoV-2 Delta variant (B.1.617) that was first detected in India and has rapidly expanded to 115 countries worldwide. Consequently, in this study, we performed next-generation sequencing and phylogenetic analysis of SARS-CoV-2 during the third wave of the pandemic to determine the SARS-CoV-2 variants of concern (VOC) prevalence in Egypt. We observed several mutational patterns, revealing that SARS-CoV-2 evolution has expanded in Egypt with a considerable increase in the number of VOC. Therefore, the Egyptian authorities should take an appropriate approach to investigate the compatibility of already employed vaccines with this VOC and to examine the efficacy of the existing therapeutic regimen against new SARS-CoV-2 variants.
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Affiliation(s)
- Mohamed G. Seadawy
- Biological Prevention Department, Egypt Army, Cairo, Egypt
- Mohamed G. Seadawy, , orcid.org/0000-0001-6102-723X
| | - Reem Binsuwaidan
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Badriyah Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Thanaa A. El-Masry
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | | | - Ahmed F. Gad
- Biological Prevention Department, Egypt Army, Cairo, Egypt
| | - Walid F. Elkhatib
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Galala University, New Galala City, Egypt
| | - Maisra M. El-Bouseary
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
- *Correspondence: Maisra M. El-Bouseary, , orcid.org/0000-0001-6503-0719
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