AUTHOR=Kairov Ulykbek , Amanzhanova Amina , Karabayev Daniyar , Rakhimova Saule , Aitkulova Akbota , Samatkyzy Diana , Kalendar Ruslan , Kozhamkulov Ulan , Molkenov Askhat , Gabdulkayum Aidana , Sarbassov Dos , Akilzhanova Ainur 

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

JOURNAL=Frontiers in Genetics

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.906318

DOI=10.3389/fgene.2022.906318

ISSN=1664-8021

ABSTRACT=<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’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 (<italic>n</italic> = 189), BA.1 (<italic>n</italic> = 15), BA.2 (<italic>n</italic> = 3), BA.1.15 (<italic>n</italic> = 1), BA.1.17.2 (<italic>n</italic> = 1) omicron lineages, AY.122 (<italic>n</italic> = 119), B.1.617.2 (<italic>n</italic> = 8), AY.111 (<italic>n</italic> = 2), AY.126 (<italic>n</italic> = 1), AY.4 (<italic>n</italic> = 1) delta lineages, one sample B.1.1.7 (<italic>n</italic> = 1) belongs to alpha lineage, and one sample B.1.637 (<italic>n</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.</p>