{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T01:04:09Z","timestamp":1760231049794,"version":"build-2065373602"},"reference-count":41,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2022,8,24]],"date-time":"2022-08-24T00:00:00Z","timestamp":1661299200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Significant efforts are being made in many countries around the world to respond to the COVID-19 pandemic by developing diagnostic reagent kits, identifying infected people, determining treatment methods, and finally producing effective vaccines. However, novel coronavirus variants may potentially reduce the effectiveness of all these efforts, demonstrating increased transmissibility and abated response to therapy or vaccines, as well as the possibility of false negative results in diagnostic procedures based on nucleic acid amplification methods. Since the end of 2020, several variants of concern have been discovered around the world. When information about a new, potentially more dangerous strain of pathogen appears, it is crucial to determine the moment of its emergence in a region. Eventually, that permits taking timely measures and minimizing new risks associated with the spreading of the virus. Therefore, numerous nations have made tremendous efforts to identify and trace these virus variants, which necessitates serious technological processes to sequence a large number of viral genomes. Here, we report on our experience as one of the primary laboratories involved in monitoring SARS-CoV-2 variants in Russia. We discuss the various approaches used, describe effective protocols, and outline a potential technique combining several methods to increase the ability to trace genetic variants while minimizing financial and labor costs.<\/jats:p>","DOI":"10.3390\/v14091855","type":"journal-article","created":{"date-parts":[[2022,8,24]],"date-time":"2022-08-24T02:55:34Z","timestamp":1661309734000},"page":"1855","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Effective Approaches to Study the Genetic Variability of SARS-CoV-2"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2416-5689","authenticated-orcid":false,"given":"Ivan","family":"Kotov","sequence":"first","affiliation":[{"name":"FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia"},{"name":"Moscow Institute of Physics and Technology, National Research University, 115184 Dolgoprudny, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0952-0830","authenticated-orcid":false,"given":"Valeriia","family":"Saenko","sequence":"additional","affiliation":[{"name":"FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9672-0648","authenticated-orcid":false,"given":"Nadezhda","family":"Borisova","sequence":"additional","affiliation":[{"name":"FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3480-953X","authenticated-orcid":false,"given":"Anton","family":"Kolesnikov","sequence":"additional","affiliation":[{"name":"FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0147-4262","authenticated-orcid":false,"given":"Larisa","family":"Kondrasheva","sequence":"additional","affiliation":[{"name":"FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1286-2612","authenticated-orcid":false,"given":"Elena","family":"Tivanova","sequence":"additional","affiliation":[{"name":"FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5524-0296","authenticated-orcid":false,"given":"Kamil","family":"Khafizov","sequence":"additional","affiliation":[{"name":"FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4228-9044","authenticated-orcid":false,"given":"Vasily","family":"Akimkin","sequence":"additional","affiliation":[{"name":"FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,8,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1001\/jama.2020.2648","article-title":"Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72 314 Cases From the Chinese Center for Disease Control and Prevention","volume":"323","author":"Wu","year":"2020","journal-title":"JAMA"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1437","DOI":"10.1001\/jama.2020.3864","article-title":"Diagnostic Testing for the Novel Coronavirus","volume":"323","author":"Sharfstein","year":"2020","journal-title":"JAMA"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"e52","DOI":"10.7861\/clinmed.2020-0912","article-title":"A case of COVID-19 reinfection in the UK","volume":"21","author":"West","year":"2021","journal-title":"Clin. Med."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1390","DOI":"10.1017\/ice.2021.224","article-title":"Severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection in asymptomatic vaccinated healthcare workers","volume":"42","author":"Damiani","year":"2021","journal-title":"Infect Control. Hosp. Epidemiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"eabn4947","DOI":"10.1126\/science.abn4947","article-title":"Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa","volume":"376","author":"Pulliam","year":"2022","journal-title":"Science"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"103130","DOI":"10.1016\/j.amsu.2021.103130","article-title":"The mystery of COVID-19 reinfections: A global systematic review and meta-analysis","volume":"72","author":"Dhillon","year":"2021","journal-title":"Ann. Med. Surg."},{"key":"ref_7","first-page":"e19102","article-title":"Equivalency of Protection From Natural Immunity in COVID-19 Recovered Versus Fully Vaccinated Persons: A Systematic Review and Pooled Analysis","volume":"13","author":"Shenai","year":"2021","journal-title":"Cureus"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Flacco, M.E., Martellucci, C.A., Baccolini, V., De Vito, C., Renzi, E., Villari, P., and Manzoli, L. (2022). Risk of reinfection and disease after SARS-CoV-2 primary infection: Meta-analysis. Eur. J. Clin. Invest., e13845.","DOI":"10.1111\/eci.13845"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2115","DOI":"10.1001\/jama.2021.5607","article-title":"S-Gene Target Failure as a Marker of Variant B.1.1.7 Among SARS-CoV-2 Isolates in the Greater Toronto Area, December 2020 to March 2021","volume":"325","author":"Flacco","year":"2021","journal-title":"JAMA"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"104969","DOI":"10.1016\/j.jcv.2021.104969","article-title":"Evaluation of two RT-PCR screening assays for identifying SARS-CoV-2 variants","volume":"143","author":"Migueres","year":"2021","journal-title":"J. Clin. Virol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.ijmmb.2021.01.003","article-title":"TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2","volume":"39","author":"Borkakoty","year":"2021","journal-title":"Indian J. Med. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1496","DOI":"10.3201\/eid2705.210397","article-title":"Detecting Rapid Spread of SARS-CoV-2 Variants, France, January 26\u2013February 16, 2021","volume":"27","author":"Roquebert","year":"2021","journal-title":"Emerg. Infect Dis."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e0031521","DOI":"10.1128\/Spectrum.00315-21","article-title":"Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance","volume":"9","author":"Zelyas","year":"2021","journal-title":"Microbiol. Spectr."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e0092621","DOI":"10.1128\/JCM.00926-21","article-title":"Mutation-Specific SARS-CoV-2 PCR Screen: Rapid and Accurate Detection of Variants of Concern and the Identification of a Newly Emerging Variant with Spike L452R Mutation","volume":"59","author":"Wang","year":"2021","journal-title":"J. Clin. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"e0084521","DOI":"10.1128\/JCM.00845-21","article-title":"A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants","volume":"59","author":"Banada","year":"2021","journal-title":"J. Clin. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.ijid.2022.07.042","article-title":"An isothermal lab-on-phone test for easy molecular diagnostic of SARS-CoV-2 near patient and in less than 1 hour","volume":"123","author":"Doria","year":"2022","journal-title":"Int. J. Infect. Dis."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"5907","DOI":"10.1007\/s00216-022-04156-7","article-title":"Point-of-care COVID-19 testing: Colorimetric diagnosis using rapid and ultra-sensitive ramified rolling circle amplification","volume":"414","author":"Choi","year":"2022","journal-title":"Anal. Bioanal. Chem."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2302","DOI":"10.1056\/NEJMoa2006100","article-title":"Spread of SARS-CoV-2 in the Icelandic Population","volume":"382","author":"Gudbjartsson","year":"2020","journal-title":"N. Engl. J. Med."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1405","DOI":"10.1038\/s41591-020-0997-y","article-title":"Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands","volume":"26","author":"Nieuwenhuijse","year":"2020","journal-title":"Nat. Med."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1263","DOI":"10.1016\/S1473-3099(20)30562-4","article-title":"Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: A prospective genomic surveillance study","volume":"20","author":"Meredith","year":"2020","journal-title":"Lancet Infect. Dis."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"e00807-19","DOI":"10.1128\/mSphere.00807-19","article-title":"Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing","volume":"5","author":"Li","year":"2020","journal-title":"mSphere"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1038\/nprot.2017.066","article-title":"Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples","volume":"12","author":"Quick","year":"2017","journal-title":"Nat. Protoc."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"910955","DOI":"10.3389\/fmicb.2022.910955","article-title":"A Rapid, Whole Genome Sequencing Assay for Detection and Characterization of Novel Coronavirus (SARS-CoV-2) Clinical Specimens Using Nanopore Sequencing","volume":"13","author":"Li","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Bushnell, B., Rood, J., and Singer, E. (2017). BBMerge\u2014Accurate paired shotgun read merging via overlap. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0185056"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"3773","DOI":"10.21105\/joss.03773","article-title":"Nextclade: Clade assignment, mutation calling and quality control for viral genomes","volume":"6","author":"Aksamentov","year":"2021","journal-title":"J. Open Source Softw."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"269","DOI":"10.36233\/0507-4088-72","article-title":"Monitoring the spread of the SARS-CoV-2 (Coronaviridae: Coronavirinae: Betacoronavirus; Sarbecovirus) variants in the Moscow region using targeted high-throughput sequencing","volume":"66","author":"Borisova","year":"2021","journal-title":"Vopr. Virusol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"veac017","DOI":"10.1093\/ve\/veac017","article-title":"The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia","volume":"8","author":"Klink","year":"2022","journal-title":"Virus Evol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"815389","DOI":"10.3389\/fmed.2022.815389","article-title":"SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines","volume":"9","author":"Thakur","year":"2022","journal-title":"Front. Med."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Gohl, D.M., Garbe, J., Grady, P., Daniel, J., Watson, R.H., Auch, B., Nelson, A., Yohe, S., and Beckman, K.B. (2020). A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2. BMC Genom., 21.","DOI":"10.1186\/s12864-020-07283-6"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1038\/s41598-018-36612-9","article-title":"PrimerROC: Accurate condition-independent dimer prediction using ROC analysis","volume":"9","author":"Johnston","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_34","first-page":"121","article-title":"Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351\/501Y-V2","volume":"6","author":"Hill","year":"2021","journal-title":"Wellcome Open Res."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"100682","DOI":"10.1016\/j.genrep.2020.100682","article-title":"Genomic characterization of a novel SARS-CoV-2","volume":"19","author":"Khailany","year":"2020","journal-title":"Gene Rep."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"593548","DOI":"10.3389\/fmicb.2020.593548","article-title":"Genetic Spectrum and Distinct Evolution Patterns of SARS-CoV-2","volume":"11","author":"Liu","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"612571","DOI":"10.3389\/fgene.2020.612571","article-title":"SARS-CoV-2 Genomes From Oklahoma, United States","volume":"11","author":"Narayanan","year":"2020","journal-title":"Front. Genet."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Shrestha, L.B., Foster, C., Rawlinson, W., Tedla, N., and Bull, R.A. (2022). Evolution of the SARS-CoV-2 omicron variants BA.1 to BA.5: Implications for immune escape and transmission. Rev. Med. Virol., e2381.","DOI":"10.1002\/rmv.2381"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1038\/s41467-020-20880-z","article-title":"Genomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia","volume":"12","author":"Komissarov","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"104910","DOI":"10.1016\/j.meegid.2021.104910","article-title":"A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern","volume":"92","author":"Bezerra","year":"2021","journal-title":"Infect. Genet. Evol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.46234\/ccdcw2021.255","article-title":"GISAID\u2019s Role in Pandemic Response","volume":"3","author":"Khare","year":"2021","journal-title":"China CDC Wkly."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/14\/9\/1855\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T00:14:19Z","timestamp":1760141659000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/14\/9\/1855"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,8,24]]},"references-count":41,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2022,9]]}},"alternative-id":["v14091855"],"URL":"https:\/\/doi.org\/10.3390\/v14091855","relation":{},"ISSN":["1999-4915"],"issn-type":[{"type":"electronic","value":"1999-4915"}],"subject":[],"published":{"date-parts":[[2022,8,24]]}}}