Then novel virus was renamed SARS-CoV-2 by the International Committee on Taxonomy of Viruses (ICTV) due to its genetic relevance to earlier verified coronaviruses ( Lu et al., 2020). Nevertheless, genomic examination of samples obtained from the infected patients confirmed the novel disease as coronavirus (2019-nCoV) pneumonia ( Zhou et al., 2020). Primarily, initial clinical symptoms, such as sore throat, fever, weakness, and respiratory distress resembled viral pneumonia. Originated in Wuhan, the capital of Hubei province in late December 2019, SARS-CoV-2 immediately propagated across the world causing infectious pneumonia. The global coronavirus disease 2019 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which is responsible for the severe acute respiratory syndrome ( Wu et al., 2020 Zhu et al., 2020) that led to the death of 6.3 million people by July 2022 ( WHO 2022). 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. 341 whole-genome sequences that passed quality control were deposited in the Global initiative on sharing all influenza data (GISAID). The overall average value of sequencing depth coverage for samples is 244X. All samples had a cycle threshold (Ct) value below 20 with an average Ct value of 17.03. 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). 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. 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. 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. Real-time gene sequencing is the main parameter to manage viral outbreaks because it expands our understanding of virus proliferation, spread, and evolution.
The original viral whole-genome was sequenced by a high-throughput sequencing approach from the samples obtained from Wuhan, China. Severe acute respiratory syndrome (SARS-CoV-2) is responsible for the worldwide pandemic, COVID-19.
1Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.Ulykbek Kairov 1* † ‡, Amina Amanzhanova 1 † ‡, Daniyar Karabayev 1 † ‡, Saule Rakhimova 1 ‡, Akbota Aitkulova 2 ‡, Diana Samatkyzy 1 ‡, Ruslan Kalendar 1 ‡, Ulan Kozhamkulov 1 ‡, Askhat Molkenov 1 ‡, Aidana Gabdulkayum 1 ‡, Dos Sarbassov 1,2 ‡ and Ainur Akilzhanova 1* ‡
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