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A high scale SARS-CoV-2 profiling by its whole-genome sequencing using Oxford Nanopore Technology in Kazakhstan

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 outb...

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Published in:Frontiers in genetics 2022-09, Vol.13, p.906318-906318
Main Authors: Kairov, Ulykbek, Amanzhanova, Amina, Karabayev, Daniyar, Rakhimova, Saule, Aitkulova, Akbota, Samatkyzy, Diana, Kalendar, Ruslan, Kozhamkulov, Ulan, Molkenov, Askhat, Gabdulkayum, Aidana, Sarbassov, Dos, Akilzhanova, Ainur
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Language:English
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Summary: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’s 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 “Olymp” 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 ( n = 189), BA.1 ( n = 15), BA.2 ( n = 3), BA.1.15 ( n = 1), BA.1.17.2 ( n = 1) omicron lineages, AY.122 ( n = 119), B.1.617.2 ( n = 8), AY.111 ( n = 2), AY.126 ( n = 1), AY.4 ( n = 1) delta lineages, one sample B.1.1.7 ( n = 1) belongs to alpha lineage, and one sample B.1.637 ( n = 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.
ISSN:1664-8021
1664-8021
DOI:10.3389/fgene.2022.906318