{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T20:08:08Z","timestamp":1791230888675,"version":"4.1.0"},"reference-count":28,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,9,2]],"date-time":"2022-09-02T00:00:00Z","timestamp":1662076800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012632","name":"Nazarbayev University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012632","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"abstract":"<jats:p>Severe acute respiratory syndrome (SARS-CoV-2) is responsible for the worldwide pandemic, COVID-19. The original viral whole-genome was sequenced by a high-throughput sequencing approach from the samples obtained from Wuhan, China. Real-time gene sequencing is the main parameter to manage viral outbreaks because it expands our understanding of virus proliferation, spread, and evolution. Whole-genome sequencing is critical for SARS-CoV-2 variant surveillance, the development of new vaccines and boosters, and the representation of epidemiological situations in the country. A significant increase in the number of COVID-19 cases confirmed in August 2021 in Kazakhstan facilitated a need to establish an effective and proficient system for further study of SARS-CoV-2 genetic variants and the development of future Kazakhstan\u2019s genomic surveillance program. The SARS-CoV-2 whole-genome was sequenced according to SARS-CoV-2 ARTIC protocol (EXP-MRT001) by Oxford Nanopore Technologies at the National Laboratory Astana, Kazakhstan to track viral variants circulating in the country. The 500 samples kindly provided by the Republican Diagnostic Center (UMC-NU) and private laboratory KDL \u201cOlymp\u201d were collected from individuals in Nur-Sultan city diagnosed with COVID-19 from August 2021 to May 2022 using real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR). All samples had a cycle threshold (Ct) value below 20 with an average Ct value of 17.03. The overall average value of sequencing depth coverage for samples is 244X. 341 whole-genome sequences that passed quality control were deposited in the Global initiative on sharing all influenza data (GISAID). The BA.1.1 (<jats:italic>n<\/jats:italic> = 189), BA.1 (<jats:italic>n<\/jats:italic> = 15), BA.2 (<jats:italic>n<\/jats:italic> = 3), BA.1.15 (<jats:italic>n<\/jats:italic> = 1), BA.1.17.2 (<jats:italic>n<\/jats:italic> = 1) omicron lineages, AY.122 (<jats:italic>n<\/jats:italic> = 119), B.1.617.2 (<jats:italic>n<\/jats:italic> = 8), AY.111 (<jats:italic>n<\/jats:italic> = 2), AY.126 (<jats:italic>n<\/jats:italic> = 1), AY.4 (<jats:italic>n<\/jats:italic> = 1) delta lineages, one sample B.1.1.7 (<jats:italic>n<\/jats:italic> = 1) belongs to alpha lineage, and one sample B.1.637 (<jats:italic>n<\/jats:italic> = 1) belongs to small sublineage were detected in this study. This is the first study of SARS-CoV-2 whole-genome sequencing by the ONT approach in Kazakhstan, which can be expanded for the investigation of other emerging viral or bacterial infections on the country level.<\/jats:p>","DOI":"10.3389\/fgene.2022.906318","type":"journal-article","created":{"date-parts":[[2022,9,2]],"date-time":"2022-09-02T09:27:39Z","timestamp":1662110859000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":6,"title":["A high scale SARS-CoV-2 profiling by its whole-genome sequencing using Oxford Nanopore Technology in Kazakhstan"],"prefix":"10.3389","volume":"13","author":[{"given":"Ulykbek","family":"Kairov","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amina","family":"Amanzhanova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniyar","family":"Karabayev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saule","family":"Rakhimova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akbota","family":"Aitkulova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diana","family":"Samatkyzy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruslan","family":"Kalendar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ulan","family":"Kozhamkulov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Askhat","family":"Molkenov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aidana","family":"Gabdulkayum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dos","family":"Sarbassov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ainur","family":"Akilzhanova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2022,9,2]]},"reference":[{"key":"B27","doi-asserted-by":"publisher","first-page":"1777","DOI":"10.1007\/s00044-020-02610-8","article-title":"Genomics insights of SARS-CoV-2 (COVID-19) into target-based drug discovery","volume":"29","author":"Chellapandi","year":"2020","journal-title":"Med. Chem. Res."},{"key":"B1","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1016\/j.cytogfr.2021.06.001","article-title":"SARS-CoV-2 mutations and their viral variants","volume":"63","author":"Cosar","year":"2022","journal-title":"Cytokine Growth Factor Rev."},{"key":"B2","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1038\/nature22040","article-title":"Virus genomes reveal factors that spread and sustained the Ebola epidemic","volume":"544","author":"Dudas","year":"2017","journal-title":"Nature"},{"key":"B3","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","article-title":"The nf-core framework for community-curated bioinformatics pipelines","volume":"38","author":"Ewels","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1007\/978-3-030-63761-3_47","article-title":"Retrieval and investigation of data on SARS-CoV-2 and COVID-19 using bioinformatics approach","volume":"1318","author":"Fahmi","year":"2021","journal-title":"Adv. Exp. Med. Biol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"bpaa014","DOI":"10.1093\/biomethods\/bpaa014","article-title":"Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding","volume":"5","author":"Freed","year":"2020","journal-title":"Biol. Methods Protoc."},{"key":"B6","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1186\/s13059-015-0726-x","article-title":"Real-time digital pathogen surveillance - the time is now","volume":"16","author":"Gardy","year":"2015","journal-title":"Genome Biol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"3225","DOI":"10.1007\/s00253-021-11250-w","article-title":"Sequencing of SARS-CoV-2 genome using different nanopore chemistries","volume":"105","author":"Gonzalez-Recio","year":"2021","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"B8","unstructured":"WHO coronavirus disease (COVID-19) dashboard with vaccination data\n            Kazakhstan\n          2022"},{"key":"B9","doi-asserted-by":"publisher","first-page":"2342","DOI":"10.1038\/s41467-019-10280-3","article-title":"Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors","volume":"10","author":"Kirchdoerfer","year":"2019","journal-title":"Nat. Commun."},{"key":"B10","doi-asserted-by":"publisher","first-page":"17492","DOI":"10.1038\/s41598-020-74656-y","article-title":"Rapid genomic characterization of SARS-CoV-2 viruses from clinical specimens using nanopore sequencing","volume":"10","author":"Li","year":"","journal-title":"Sci. Rep."},{"key":"B11","doi-asserted-by":"publisher","first-page":"1537","DOI":"10.1007\/s00438-020-01719-0","article-title":"GC usage of SARS-CoV-2 genes might adapt to the environment of human lung expressed genes","volume":"295","author":"Li","year":"","journal-title":"Mol. Genet. Genomics"},{"key":"B12","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1016\/S0140-6736(20)30251-8","article-title":"Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding","volume":"395","author":"Lu","year":"2020","journal-title":"Lancet"},{"key":"B13","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1186\/s42269-021-00657-0","article-title":"Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021","volume":"45","author":"Nidom","year":"2021","journal-title":"Bull. Natl. Res. Cent."},{"key":"B14","doi-asserted-by":"publisher","first-page":"1261","DOI":"10.1038\/nprot.2017.066","article-title":"Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples","volume":"12","author":"Quick","year":"2017","journal-title":"Nat. Protoc."},{"key":"B15","doi-asserted-by":"publisher","first-page":"1403","DOI":"10.1038\/s41564-020-0770-5","article-title":"A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology","volume":"5","author":"Rambaut","year":"2020","journal-title":"Nat. Microbiol."},{"key":"B28","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ijbiomac.2021.02.071","article-title":"Potential drug targets of SARS-CoV-2: From genomics to therapeutics","volume":"177","author":"Shamsi","year":"2021","journal-title":"Int. J. Biol. Macromol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"E59","DOI":"10.3390\/v11010059","article-title":"From SARS to MERS, thrusting coronaviruses into the spotlight","volume":"11","author":"Song","year":"2019","journal-title":"Viruses"},{"key":"B17","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1016\/S1473-3099(20)30764-7","article-title":"Genomic evidence for reinfection with SARS-CoV-2: A case study","volume":"21","author":"Tillett","year":"2021","journal-title":"Lancet. Infect. Dis."},{"key":"B18","doi-asserted-by":"publisher","first-page":"e2946","DOI":"10.1093\/cid\/ciaa1275","article-title":"Coronavirus disease 2019 (COVID-19) Re-infection by a phylogenetically distinct severe acute respiratory syndrome coronavirus 2 strain confirmed by whole genome sequencing","volume":"73","author":"To","year":"2021","journal-title":"Clin. Infect. Dis."},{"key":"B19","doi-asserted-by":"publisher","first-page":"e2002169","DOI":"10.1002\/smll.202002169","article-title":"Nanopore targeted sequencing for the accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses","volume":"16","author":"Wang","year":"2020","journal-title":"Small"},{"key":"B20","unstructured":"Coronavirus (COVID-19) dashboard\n            Who\n          2022"},{"key":"B21","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1038\/s41586-020-2008-3","article-title":"A new coronavirus associated with human respiratory disease in China","volume":"579","author":"Wu","year":"2020","journal-title":"Nature"},{"key":"B22","doi-asserted-by":"publisher","first-page":"821","DOI":"10.3390\/cells10040821","article-title":"Role of structural and non-structural proteins and therapeutic targets of SARS-CoV-2 for COVID-19","volume":"10","author":"Yadav","year":"2021","journal-title":"Cells"},{"key":"B23","doi-asserted-by":"publisher","first-page":"100096","DOI":"10.1016\/j.lanepe.2021.100096","article-title":"Epidemiology, clinical characteristics, and virologic features of COVID-19 patients in Kazakhstan: A nation-wide retrospective cohort study","volume":"4","author":"Yegorov","year":"2021","journal-title":"Lancet Reg. Health. Eur."},{"key":"B24","doi-asserted-by":"publisher","first-page":"6","DOI":"10.23950\/1812-2892-jcmk-00763","article-title":"COVID-19 outbreak in Kazakhstan: Current status and challenges","volume":"1","author":"Zhalmagambetov","year":"2020","journal-title":"J. Clin. Med. Kaz."},{"key":"B25","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1038\/s41586-020-2012-7","article-title":"A pneumonia outbreak associated with a new coronavirus of probable bat origin","volume":"579","author":"Zhou","year":"2020","journal-title":"Nature"},{"key":"B26","doi-asserted-by":"publisher","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."}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2022.906318\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,2]],"date-time":"2022-09-02T09:27:44Z","timestamp":1662110864000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2022.906318\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,9,2]]},"references-count":28,"alternative-id":["10.3389\/fgene.2022.906318"],"URL":"https:\/\/doi.org\/10.3389\/fgene.2022.906318","relation":{},"ISSN":["1664-8021"],"issn-type":[{"value":"1664-8021","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,9,2]]},"article-number":"906318"}}