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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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Autores principales: Kairov, Ulykbek, Amanzhanova, Amina, Karabayev, Daniyar, Rakhimova, Saule, Aitkulova, Akbota, Samatkyzy, Diana, Kalendar, Ruslan, Kozhamkulov, Ulan, Molkenov, Askhat, Gabdulkayum, Aidana, Sarbassov, Dos, Akilzhanova, Ainur
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9479076/
https://www.ncbi.nlm.nih.gov/pubmed/36118859
http://dx.doi.org/10.3389/fgene.2022.906318
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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
author_facet Kairov, Ulykbek
Amanzhanova, Amina
Karabayev, Daniyar
Rakhimova, Saule
Aitkulova, Akbota
Samatkyzy, Diana
Kalendar, Ruslan
Kozhamkulov, Ulan
Molkenov, Askhat
Gabdulkayum, Aidana
Sarbassov, Dos
Akilzhanova, Ainur
author_sort Kairov, Ulykbek
collection PubMed
description 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.
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spelling pubmed-94790762022-09-17 A high scale SARS-CoV-2 profiling by its whole-genome sequencing using Oxford Nanopore Technology in Kazakhstan Kairov, Ulykbek Amanzhanova, Amina Karabayev, Daniyar Rakhimova, Saule Aitkulova, Akbota Samatkyzy, Diana Kalendar, Ruslan Kozhamkulov, Ulan Molkenov, Askhat Gabdulkayum, Aidana Sarbassov, Dos Akilzhanova, Ainur Front Genet Genetics 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. Frontiers Media S.A. 2022-09-02 /pmc/articles/PMC9479076/ /pubmed/36118859 http://dx.doi.org/10.3389/fgene.2022.906318 Text en Copyright © 2022 Kairov, Amanzhanova, Karabayev, Rakhimova, Aitkulova, Samatkyzy, Kalendar, Kozhamkulov, Molkenov, Gabdulkayum, Sarbassov and Akilzhanova. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Kairov, Ulykbek
Amanzhanova, Amina
Karabayev, Daniyar
Rakhimova, Saule
Aitkulova, Akbota
Samatkyzy, Diana
Kalendar, Ruslan
Kozhamkulov, Ulan
Molkenov, Askhat
Gabdulkayum, Aidana
Sarbassov, Dos
Akilzhanova, Ainur
A high scale SARS-CoV-2 profiling by its whole-genome sequencing using Oxford Nanopore Technology in Kazakhstan
title A high scale SARS-CoV-2 profiling by its whole-genome sequencing using Oxford Nanopore Technology in Kazakhstan
title_full A high scale SARS-CoV-2 profiling by its whole-genome sequencing using Oxford Nanopore Technology in Kazakhstan
title_fullStr A high scale SARS-CoV-2 profiling by its whole-genome sequencing using Oxford Nanopore Technology in Kazakhstan
title_full_unstemmed A high scale SARS-CoV-2 profiling by its whole-genome sequencing using Oxford Nanopore Technology in Kazakhstan
title_short A high scale SARS-CoV-2 profiling by its whole-genome sequencing using Oxford Nanopore Technology in Kazakhstan
title_sort high scale sars-cov-2 profiling by its whole-genome sequencing using oxford nanopore technology in kazakhstan
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9479076/
https://www.ncbi.nlm.nih.gov/pubmed/36118859
http://dx.doi.org/10.3389/fgene.2022.906318
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