Effective Approaches to Study the Genetic Variability of SARS-CoV-2

Kotov, Ivan A.; Kaptelova, V.V.; Borisova, N. I.; Kolesnikov, A A; Kondrasheva, L. Yu.; Тиванова, Е. В.; Khafizov, K.; Акимкин, В. Г.

doi:10.3390/v14091855

Cited by 4 publications

(4 citation statements)

References 42 publications

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“…Based on the ARTIC protocol, 14 pairs of primer were used for amplifying the spike gene of SARS-CoV-2 to generate amplicons (approximately 400 bp), followed by the short-read Illumina sequencing platform. 33,34 Nonetheless, the second-generation sequencing is limited in terms of incorrect assembly in co-infected samples. In contrast, third-generation single-molecule sequencing based on ONT provides multiple long-read nucleotide sequences with simple library preparation, rapid sequencing and real-time analysis.…”

Section: Discussionmentioning

confidence: 99%

“Nano COVID-19”: Nanopore sequencing of spike gene to identify SARS-CoV-2 variants of concern

Nimsamer,

Sawaswong,

Klomkliew

et al. 2023

Exp Biol Med (Maywood)

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Coronavirus disease 2019 (COVID-19) is a worldwide pandemic infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). World Health Organization (WHO) has defined the viral variants of concern (VOC) which cause more severe disease, higher transmissibility, and reduced vaccine efficacy. In this study, the “Nano COVID-19” workflow based on Oxford nanopore sequencing of the full-length spike gene combined with flexible data analysis options was developed to identify SARS-CoV-2 VOCs. The primers were designed to cover the full-length spike gene and can amplify all VOC strains. The results of VOC identification based on phylogenetic analysis of the full-length spike gene were comparable to the whole genome sequencing (WGS). Compared to the standard VOC identification pipeline, the fast analysis based on Read Assignment, Mapping, and Phylogenetic Analysis in Real Time (RAMPART) and the user-friendly method based on EPI2ME yielded 89.3% and 97.3% accuracy, respectively. The EPI2ME pipeline is recommended for researchers without bioinformatic skills, whereas RAMPART is more suitable for bioinformaticians. This workflow provides a cost-effective, simplified pipeline with a rapid turnaround time. Furthermore, it is portable to point-of-care SARS-CoV-2 VOC identification and compatible with large-scale analysis. Therefore, “Nano COVID-19” is an alternative viral epidemic screening and transmission tracking workflow.

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Section: Discussionmentioning

confidence: 99%

“Nano COVID-19”: Nanopore sequencing of spike gene to identify SARS-CoV-2 variants of concern

Nimsamer,

Sawaswong,

Klomkliew

et al. 2023

Exp Biol Med (Maywood)

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“…Undoubtedly, whole-genome sequencing is by far the most informative and preferred method for pathogen surveillance [ 14 ] with subsequent storage of the results in the VGARus database and deposition in the GISAID. However, the use of less complex (e.g., Sanger sequencing) and cheaper methods (RT-PCR) in the surveillance of SARS-CoV-2 variants has not lost its relevance in some cases.…”

Section: Discussionmentioning

confidence: 99%

“…We used a modified ARTIC v.3.0 panel for whole-genome sequencing, which was modified to account for new genomic changes, as well as a panel of primers for sequencing the S protein gene only, which was described earlier [ 14 ]. Commercial solutions, such as the ATOPlex RNA Library Prep Set from MGI and Midnight kit from ONT (Oxford Nanopore Technologies, Oxford, UK), were used.…”

Section: Methodsmentioning

confidence: 99%

“…In the course of this work, we used protocols for sequencing complete genomes or the S-protein gene, which are described in our previous publications [ 14 , 16 ]. In general, all protocols involve the PCR amplification of parts of the virus genomes followed by sequencing on platforms from Illumina, Thermo Fisher Scientific, Oxford Nanopore Technologies, and MGI.…”

Section: Methodsmentioning

confidence: 99%

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Development and Application of Real-Time PCR-Based Screening for Identification of Omicron SARS-CoV-2 Variant Sublineages

Esman,

Dubodelov,

Khafizov

et al. 2023

Genes

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The Omicron strain is currently the main dominant variant of SARS-CoV-2, with a large number of sublineages. In this article, we present our experience in tracing it in Russia using molecular diagnostic methods. For this purpose, different approaches were used; for example, we developed multiprimer panels for RT-PCR and Sanger and NGS sequencing methods. For the centralized collection and analysis of samples, the VGARus database was developed, which currently includes more than 300,000 viral sequences.

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Genomic surveillance of SARS-CoV-2 in Russia: insights from the VGARus platform

Kotov,

Agletdinov,

Roev

et al. 2024

Journal of microbiology, epidemiology and immunobiology

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Introduction. In response to the COVID-19 pandemic in the Russian Federation, comprehensive response measures were taken. One of these measures was the development of a viral genome aggregation platform (VGARus) to monitor virus variability. The aim of this paper is to describe the role of the VGARus platform in tracking genetic variation in SARS-CoV-2. Materials and methods. VGARus utilizes sequencing data and bioinformatics tools to monitor genetic variations in SARS-CoV-2. The viral genomes were aligned using NextClade, which also translated them into amino acids and identified mutations. The viral variability over time was analyzed by counting the number of amino acid changes compared to the reference sequence. Results. The analysis of data within VGARus enabled the identification of new virus variants, contributing to improved diagnostic tests and vaccine development. The platform allowed for the prediction of epidemiologic trends, facilitating a rapid response to changes in the epidemiologic situation. For example, using VGARus, an increase in COVID-19 incidence was accurately predicted in the summer of 2022 and early 2023, which were associated with the emergence of Omicron subvariants BA.5 and XBB. Data from the platform helps validate the effectiveness of primers and DNA probes to ensure high diagnostic accuracy and reduce the risk of false negatives. Conclusion. VGARus demonstrates the growing role of genomic surveillance in combating COVID-19 and improving preparedness for future infectious disease outbreaks. The platform is a powerful tool for generating evidence-based solutions to combat a pandemic and mitigate its health, economic and societal impacts. It provides the ability to promptly obtain information on the epidemiologic situation in a particular region of the Russian Federation, use genomic data for phylogenetic analysis, compare the mutational spectrum of SARS-CoV-2 sequences with foreign samples. VGARus data allow for both retrospective analysis and predictive hypotheses. For example, we can clearly see the dynamics of the change of different virus variants: sequences belonging to the Alpha, Beta, Delta, Omicron lineages and many less common ones, clearly form the upsurges of morbidity, the interaction of which is reflected in the epidemiological picture. It is also currently being expanded to monitor other pathogens, increasing its public health relevance.

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Effective Approaches to Study the Genetic Variability of SARS-CoV-2

Cited by 4 publications

References 42 publications

“Nano COVID-19”: Nanopore sequencing of spike gene to identify SARS-CoV-2 variants of concern

“Nano COVID-19”: Nanopore sequencing of spike gene to identify SARS-CoV-2 variants of concern

Development and Application of Real-Time PCR-Based Screening for Identification of Omicron SARS-CoV-2 Variant Sublineages

Genomic surveillance of SARS-CoV-2 in Russia: insights from the VGARus platform

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