A High Scale SARS-CoV-2 Profiling by Its Whole-genome Sequencing Using Oxford Nanopore Technology in Kazakhstan

Overview

Journal Front Genet

Date 2022 Sep 19

PMID 36118859

Authors

Ulykbek Kairov

Amina Amanzhanova

Daniyar Karabayev

Saule Rakhimova

Akbota Aitkulova

Diana Samatkyzy

Ruslan Kalendar

Ulan Kozhamkulov

Askhat Molkenov

Aidana Gabdulkayum

Dos Sarbassov

Ainur Akilzhanova

Affiliations

Soon will be listed here.

Abstract

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

Citing Articles

Universal whole-genome Oxford nanopore sequencing of SARS-CoV-2 using tiled amplicons.

Kalendar R, Kairov U, Karabayev D, Aitkulova A, Tynyshtykbayeva N, Daniyarov A Sci Rep. 2023; 13(1):10334.

PMID: 37365249 PMC: 10293217. DOI: 10.1038/s41598-023-37588-x.

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