{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T22:42:11Z","timestamp":1783636931221,"version":"3.55.0"},"reference-count":26,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2024,11,29]],"date-time":"2024-11-29T00:00:00Z","timestamp":1732838400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"STDF","award":["46654"],"award-info":[{"award-number":["46654"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>The COVID-19 pandemic caused by the SARS-CoV-2 virus continues to circulate worldwide, causing the deaths of millions of people. The continuous circulation of the virus, its genetic diversity, the emergence of new variants with increased transmissibility, and\/or the capacity of the virus to escape from the immune system constitute a major public health concern. In our study, we aimed to characterize SARS-CoV-2 strains in Iraq from the first introduction until the end of 2023, and to identify their variants, lineages, clades, and mutation patterns. All published Iraqi full genome sequences (2020\u20132023) were obtained from Global Initiative on Sharing All Influenza Data (GISAID) and subjected to molecular characterization along with 19 samples of full genome sequences that were collected during the fifth and sixth waves of the SARS-CoV-2 pandemic in this study. Next-generation sequencing was performed using an Illumina MiSeq system, and phylogenetic analysis was performed for all the Iraqi sequences. Three established global platforms, GISAID, Nextstrain, and PANGO, were used for the classification of isolates into distinct clades, variants, and lineages. Six wave peaks of COVID-19 cases have been identified in Iraq, resulting in approximately 2,400,000 cumulative confirmed cases and more than 25,000 deaths. Our study revealed patterns of circulation and dominance of SARS-CoV-2 clades and their lineages in the pandemic waves in the country.<\/jats:p>","DOI":"10.3390\/pathogens13121051","type":"journal-article","created":{"date-parts":[[2024,12,2]],"date-time":"2024-12-02T03:50:57Z","timestamp":1733111457000},"page":"1051","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Genomic Diversity and Evolution of Identified SARS-CoV-2 Variants in Iraq"],"prefix":"10.3390","volume":"13","author":[{"given":"Ahmed A.","family":"Al-Mankhee","sequence":"first","affiliation":[{"name":"Al Hussein Teaching Hospital, Al Bat\u2019haa 64011, Thi Qar, Iraq"},{"name":"Department of Microbiology, Faculty of Science, Ain Shams University, Cairo 11566, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2159-2511","authenticated-orcid":false,"given":"Yassmin","family":"Moatasim","sequence":"additional","affiliation":[{"name":"Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmed","family":"El Taweel","sequence":"additional","affiliation":[{"name":"Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mokhtar","family":"Gomaa","sequence":"additional","affiliation":[{"name":"Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Omar A.","family":"Rabiee","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Faculty of Science, Ain Shams University, Cairo 11566, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3905-5482","authenticated-orcid":false,"given":"Marwa M.","family":"Gado","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Faculty of Science, Ain Shams University, Cairo 11566, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmed B.","family":"Barakat","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Faculty of Science, Ain Shams University, Cairo 11566, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5615-3212","authenticated-orcid":false,"given":"Mohamed A.","family":"Ali","sequence":"additional","affiliation":[{"name":"Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8798-2240","authenticated-orcid":false,"given":"Rabeh","family":"El-Shesheny","sequence":"additional","affiliation":[{"name":"Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,11,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1056\/NEJMoa2001017","article-title":"A novel coronavirus from patients with pneumonia in China, 2019","volume":"382","author":"Zhu","year":"2020","journal-title":"N. Engl. J. Med."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","article-title":"Nextstrain: Real-time tracking of pathogen evolution","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Aileni, M., Rohela, G.K., Jogam, P., Soujanya, S., and Zhang, B. (2022). Biotechnological perspectives to combat the COVID-19 pandemic: Precise diagnostics and inevitable vaccine paradigms. Cells, 11.","DOI":"10.3390\/cells11071182"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Lin, L., Liu, Y., Tang, X., and He, D. (2021). The disease severity and clinical outcomes of the SARS-CoV-2 variants of concern. Front. Public Health, 9.","DOI":"10.3389\/fpubh.2021.775224"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1038\/s41586-021-03426-1","article-title":"Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7","volume":"593","author":"Davies","year":"2021","journal-title":"Nature"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Noureddine, F.Y., Chakkour, M., El Roz, A., Reda, J., Al Sahily, R., Assi, A., Joma, M., Salami, H., Hashem, S., and Harb, B. (2021). The Emergence of SARS-CoV-2 Variant(s) and Its Impact on the Prevalence of COVID-19 Cases in the Nabatieh Region, Lebanon. Med. Sci., 9.","DOI":"10.1101\/2021.04.08.21255005"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1001\/jama.2020.27124","article-title":"Genetic variants of SARS-CoV-2\u2014What do they mean?","volume":"325","author":"Lauring","year":"2021","journal-title":"JAMA"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1038\/s41591-022-01836-w","article-title":"An early warning system for emerging SARS-CoV-2 variants","volume":"28","author":"Subissi","year":"2022","journal-title":"Nat. Med."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Janik, E., Niemcewicz, M., Podogrocki, M., Majsterek, I., and Bijak, M. (2021). The emerging concern and interest SARS-CoV-2 variants. Pathogens, 10.","DOI":"10.3390\/pathogens10060633"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1038\/s41564-021-00932-w","article-title":"SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse","volume":"6","author":"Konings","year":"2021","journal-title":"Nat. Microbiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/s41588-022-01033-y","article-title":"Global landscape of SARS-CoV-2 genomic surveillance and data sharing","volume":"54","author":"Chen","year":"2022","journal-title":"Nat. Genet."},{"key":"ref_12","unstructured":"Public Health England (2024, January 24). Public Health England. Investigation of Novel SARS-CoV-2 Variant: Variant of Concern 202012\/01. Technical Briefing 3, Available online: https:\/\/assets.publishing.service.gov.uk\/government\/uploads\/system\/uploads\/attachment_data\/file\/959360\/Variant_of_Concern_VOC_202012_01_Technical_Briefing_3.pdf."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1038\/s41576-021-00408-x","article-title":"The biological and clinical significance of emerging SARS-CoV-2 variants","volume":"22","author":"Tao","year":"2021","journal-title":"Nat. Rev. Genet."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e237","DOI":"10.1017\/S0950268821002430","article-title":"SARS-CoV-2 variants and effectiveness of vaccines: A review of current evidence","volume":"149","author":"Tatsi","year":"2021","journal-title":"Epidemiol. Infect."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1016\/j.cmi.2021.10.005","article-title":"Comparing COVID-19 vaccines for their characteristics, efficacy and effectiveness against SARS-CoV-2 and variants of concern: A narrative review","volume":"28","author":"Fiolet","year":"2022","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_16","unstructured":"Rambaut, A., Loman, N., Pybus, O., Barclay, W., Barrett, J., Carabelli, A., Connor, T., Peacock, T., Robertson, D.L., and Volz, E. (2024, January 24). Preliminary Genomic Characterisation of an Emergent SARS-CoV-2 Lineage in the UK Defined by a Novel Set of Spike Mutations. Available online: https:\/\/virological.org\/t\/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations\/563."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"eabg3055","DOI":"10.1126\/science.abg3055","article-title":"Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England","volume":"372","author":"Davies","year":"2021","journal-title":"Science"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"e02979-21","DOI":"10.1128\/mbio.02979-21","article-title":"The impact of evolving SARS-CoV-2 mutations and variants on COVID-19 vaccines","volume":"13","author":"McLean","year":"2022","journal-title":"mBio"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Duong, B.V., Larpruenrudee, P., Fang, T., Hossain, S.I., Saha, S.C., Gu, Y., and Islam, M.S. (2022). Is the SARS CoV-2 omicron variant deadlier and more transmissible than delta variant?. Int. J. Environ. Res. Public Health, 19.","DOI":"10.3390\/ijerph19084586"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1016\/S1473-3099(22)00141-4","article-title":"Severity of omicron variant of concern and effectiveness of vaccine boosters against symptomatic disease in Scotland (EAVE II): A national cohort study with nested test-negative design","volume":"22","author":"Sheikh","year":"2022","journal-title":"Lancet Infect. Dis."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"e2381","DOI":"10.1002\/rmv.2381","article-title":"Evolution of the SARS-CoV-2 omicron variants BA. 1 to BA. 5: Implications for immune escape and transmission","volume":"32","author":"Shrestha","year":"2022","journal-title":"Rev. Med. Virol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"22","DOI":"10.37652\/juaps.2022.172362","article-title":"Challenges facing Iraq to tackle the spread of COVID-19: An overview","volume":"14","author":"Alsayed","year":"2020","journal-title":"J. Univ. Anbar Pure Sci."},{"key":"ref_23","unstructured":"World Health Organization (2022). World Health Organization Coronavirus (COVID-19) Dashboard, World Health Organization. Available online: https:\/\/data.who.int\/dashboards\/covid19\/cases?n=c."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3773","DOI":"10.21105\/joss.03773","article-title":"Nextclade: Clade assignment, mutation calling and quality control for viral genomes","volume":"6","author":"Aksamentov","year":"2021","journal-title":"J. Open Source Softw."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1038\/s41586-022-04462-1","article-title":"Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant","volume":"603","author":"Suzuki","year":"2022","journal-title":"Nature"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1038\/s41422-022-00617-x","article-title":"Peptide-based pan-CoV fusion inhibitors maintain high potency against SARS-CoV-2 Omicron variant","volume":"32","author":"Xia","year":"2022","journal-title":"Cell Res."}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/13\/12\/1051\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T16:42:47Z","timestamp":1760114567000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/13\/12\/1051"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,29]]},"references-count":26,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["pathogens13121051"],"URL":"https:\/\/doi.org\/10.3390\/pathogens13121051","relation":{},"ISSN":["2076-0817"],"issn-type":[{"value":"2076-0817","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,11,29]]}}}