{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T05:25:28Z","timestamp":1787030728808,"version":"build-2736575974"},"reference-count":47,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2026,8,15]],"date-time":"2026-08-15T00:00:00Z","timestamp":1786752000000},"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>Lower respiratory tract infections caused by the respiratory syncytial virus (RSV) pose a major global public health challenge. The use of next-generation sequencing technologies enables detailed monitoring of viral genetic variability, which is crucial for evaluating the efficacy of immunoprophylactic measures. In this study, whole-genome sequencing of RSV was performed on 106 samples collected in the Russian Federation between September 2021 and April 2025. Three NGS platforms were employed: Illumina MiSeq, Oxford Nanopore Technologies MinION, and Qitan Tech QNome-3841. Using discrete phylogeographic methods, we estimated a minimum of 45 introduction events into Russia for RSV-A and 39 for RSV-B among the genomes included in the analysis. Most events were represented by a single Russian genome. These results indicate recurrent introductions of RSV into Russia from abroad. Given the limited genomic sampling available, most of these introductions were not associated with detectable transmission within the country.<\/jats:p>","DOI":"10.3390\/v18080901","type":"journal-article","created":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T13:42:17Z","timestamp":1786974137000},"page":"901","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Whole-Genome Sequencing of RSV and Phylogeographic Assessment of Viral Importations into Russia"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2353-5222","authenticated-orcid":false,"given":"German V.","family":"Roev","sequence":"first","affiliation":[{"name":"Central Research Institute of Epidemiology, 111123 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ekaterina V.","family":"Pimkina","sequence":"additional","affiliation":[{"name":"Central Research Institute of Epidemiology, 111123 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-6864-2807","authenticated-orcid":false,"given":"Dmitry V.","family":"Svetlichnyy","sequence":"additional","affiliation":[{"name":"Central Research Institute of Epidemiology, 111123 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-4981-6716","authenticated-orcid":false,"given":"Arina V.","family":"Peresadina","sequence":"additional","affiliation":[{"name":"Central Research Institute of Epidemiology, 111123 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-3217-0963","authenticated-orcid":false,"given":"Maksim I.","family":"Nadtoka","sequence":"additional","affiliation":[{"name":"Central Research Institute of Epidemiology, 111123 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5524-0296","authenticated-orcid":false,"given":"Kamil F.","family":"Khafizov","sequence":"additional","affiliation":[{"name":"Central Research Institute of Epidemiology, 111123 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4228-9044","authenticated-orcid":false,"given":"Vasiliy G.","family":"Akimkin","sequence":"additional","affiliation":[{"name":"Central Research Institute of Epidemiology, 111123 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"103352","DOI":"10.1016\/j.eclinm.2025.103352","article-title":"Global Outbreaks of Respiratory Syncytial Virus Infections from 1960 to 2025: A Systematic Review and Meta-Analysis","volume":"86","author":"Duan","year":"2025","journal-title":"eClinicalMedicine"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2047","DOI":"10.1016\/S0140-6736(22)00478-0","article-title":"Global, Regional, and National Disease Burden Estimates of Acute Lower Respiratory Infections Due to Respiratory Syncytial Virus in Children Younger than 5 Years in 2019: A Systematic Analysis","volume":"399","author":"Li","year":"2022","journal-title":"Lancet"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2138","DOI":"10.1080\/21645515.2017.1337614","article-title":"Product Review on the Monoclonal Antibody Palivizumab for Prevention of Respiratory Syncytial Virus Infection","volume":"13","author":"Resch","year":"2017","journal-title":"Human. Vaccines Immunother."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e70106","DOI":"10.1111\/irv.70106","article-title":"An Improved Rapid and Sensitive Long Amplicon Method for Nanopore-Based RSV Whole-Genome Sequencing","volume":"19","author":"Dong","year":"2025","journal-title":"Influenza Resp. Viruses"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1343","DOI":"10.1056\/NEJMc2506107","article-title":"Clesrovimab in Infants and Children at Increased Risk for Severe RSV Disease","volume":"393","author":"Zar","year":"2025","journal-title":"N. Engl. J. Med."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"evaf093","DOI":"10.1093\/gbe\/evaf093","article-title":"Genome-Wide Analyses of Human Respiratory Syncytial Viruses Provide Insights into Evolutionary Dynamics","volume":"17","author":"Chen","year":"2025","journal-title":"Genome Biol. Evol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2111","DOI":"10.1099\/0022-1317-66-10-2111","article-title":"Two Distinct Subtypes of Human Respiratory Syncytial Virus","volume":"66","author":"Mufson","year":"1985","journal-title":"J. General. Virol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.virusres.2011.09.020","article-title":"Progress in Understanding and Controlling Respiratory Syncytial Virus: Still Crazy after All These Years","volume":"162","author":"Collins","year":"2011","journal-title":"Virus Res."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Pandya, M., Callahan, S., Savchenko, K., and Stobart, C. (2019). A Contemporary View of Respiratory Syncytial Virus (RSV) Biology and Strain-Specific Differences. Pathogens, 8.","DOI":"10.3390\/pathogens8020067"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"e204608","DOI":"10.3201\/eid2706.204608","article-title":"Proposal for Human Respiratory Syncytial Virus Nomenclature below the Species Level","volume":"27","author":"Salimi","year":"2021","journal-title":"Emerg. Infect. Dis."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"105423","DOI":"10.1016\/j.jcv.2023.105423","article-title":"A Simplified, Amplicon-Based Method for Whole Genome Sequencing of Human Respiratory Syncytial Viruses","volume":"161","author":"Dong","year":"2023","journal-title":"J. Clin. Virol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"13531","DOI":"10.1038\/s41598-023-40760-y","article-title":"Genome-Wide Study of Globally Distributed Respiratory Syncytial Virus (RSV) Strains Implicates Diversification Utilizing Phylodynamics and Mutational Analysis","volume":"13","author":"Shishir","year":"2023","journal-title":"Sci. Rep."},{"key":"ref_13","first-page":"90","article-title":"Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being, Moscow, Russia Analysis of the Prevalence and Genetic Diversity of Human Respiratory Syncytial Virus in the Period from 2021 to 2024","volume":"1_2025","author":"Yatsyshina","year":"2025","journal-title":"\u00c8pidemiologi\u00e2 I Infekc. Bolezn. Aktual. Vopr."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Maslov, D.E., Osipov, I.D., Zabelina, D.S., Pak, A.A., and Netesov, S.V. (2026). Respiratory Syncytial Virus Prevalence and Genotypic Distribution in the Countries of the Former Soviet Union: A Systematic Review and Meta-Analysis. Viruses, 18.","DOI":"10.3390\/v18010126"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"btad311","DOI":"10.1093\/bioinformatics\/btad311","article-title":"NanoPack2: Population-Scale Evaluation of Long-Read Sequencing Data","volume":"39","author":"Rademakers","year":"2023","journal-title":"Bioinformatics"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A Flexible Trimmer for Illumina Sequence Data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt Removes Adapter Sequences from High-Throughput Sequencing Reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet j."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: Pairwise Alignment for Nucleotide Sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: A Flexible Suite of Utilities for Comparing Genomic Features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve Years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast Gapped-Read Alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative Genomics Viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"ref_23","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_24","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":"JOSS"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"435","DOI":"10.36233\/0372-9311-554","article-title":"Genomic Surveillance of SARS-CoV-2 in Russia: Insights from the VGARus Platform","volume":"101","author":"Kotov","year":"2024","journal-title":"J. Microbiol. Epidemiol. Immunobiol."},{"key":"ref_26","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."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"D67","DOI":"10.1093\/nar\/gkv1276","article-title":"GenBank","volume":"44","author":"Clark","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1093\/molbev\/msp077","article-title":"FastTree: Computing Large Minimum Evolution Trees with Profiles Instead of a Distance Matrix","volume":"26","author":"Price","year":"2009","journal-title":"Mol. Biol. Evol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"vew007","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the Temporal Structure of Heterochronous Sequences Using TempEst (Formerly Path-O-Gen)","volume":"2","author":"Rambaut","year":"2016","journal-title":"Virus Evol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"veaa087","DOI":"10.1093\/ve\/veaa087","article-title":"RDP5: A Computer Program for Analyzing Recombination in, and Removing Signals of Recombination from, Nucleotide Sequence Datasets","volume":"7","author":"Martin","year":"2021","journal-title":"Virus Evol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2906","DOI":"10.21105\/joss.02906","article-title":"Augur: A Bioinformatics Toolkit for Phylogenetic Analyses of Human Pathogens","volume":"6","author":"Huddleston","year":"2021","journal-title":"J. Open Source Softw."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"vex042","DOI":"10.1093\/ve\/vex042","article-title":"TreeTime: Maximum-Likelihood Phylodynamic Analysis","volume":"4","author":"Sagulenko","year":"2018","journal-title":"Virus Evol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"msag117","DOI":"10.1093\/molbev\/msag117","article-title":"IQ-TREE 3: Phylogenomic Inference Software Using Complex Evolutionary Models","volume":"43","author":"Wong","year":"2025","journal-title":"Mol. Biol. Evol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"4347","DOI":"10.1038\/s41467-023-40057-8","article-title":"Molecular and Phenotypic Characteristics of RSV Infections in Infants during Two Nirsevimab Randomized Clinical Trials","volume":"14","author":"Ahani","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1016\/S1473-3099(24)00570-X","article-title":"Genotypic and Phenotypic Characterisation of Respiratory Syncytial Virus after Nirsevimab Breakthrough Infections: A Large, Multicentre, Observational, Real-World Study","volume":"25","author":"Fourati","year":"2025","journal-title":"Lancet Infect. Dis."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"eaaj1928","DOI":"10.1126\/scitranslmed.aaj1928","article-title":"A Highly Potent Extended Half-Life Antibody as a Potential RSV Vaccine Surrogate for All Infants","volume":"9","author":"Zhu","year":"2017","journal-title":"Sci. Transl. Med."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1093\/infdis\/jiy189","article-title":"Prevalence and Significance of Substitutions in the Fusion Protein of Respiratory Syncytial Virus Resulting in Neutralization Escape From Antibody MEDI8897","volume":"218","author":"Zhu","year":"2018","journal-title":"J. Infect. Dis."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"856","DOI":"10.1016\/S1473-3099(23)00062-2","article-title":"Nirsevimab Binding-Site Conservation in Respiratory Syncytial Virus Fusion Glycoprotein Worldwide between 1956 and 2021: An Analysis of Observational Study Sequencing Data","volume":"23","author":"Wilkins","year":"2023","journal-title":"Lancet Infect. Dis."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"veag002","DOI":"10.1093\/ve\/veag002","article-title":"The S190R Mutation in RSV-A F Protein Impairs Nirsevimab Binding and Neutralization Capacity","volume":"12","author":"Cordela","year":"2026","journal-title":"Virus Evol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"ofac492.019","DOI":"10.1093\/ofid\/ofac492.019","article-title":"94. Pooled Analysis of Nirsevimab Resistance through 150 Days Post Dose in Preterm and Term Infants","volume":"9","author":"Abram","year":"2022","journal-title":"Open Forum Infect. Dis."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/j.virol.2014.02.010","article-title":"Escape from Neutralization by the Respiratory Syncytial Virus-Specific Neutralizing Monoclonal Antibody Palivizumab Is Driven by Changes in on-Rate of Binding to the Fusion Protein","volume":"454\u2013455","author":"Bates","year":"2014","journal-title":"Virology"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"106153","DOI":"10.1016\/j.jinf.2024.106153","article-title":"Genomic Evolution of Human Respiratory Syncytial Virus during a Decade (2013\u20132023): Bridging the Path to Monoclonal Antibody Surveillance","volume":"88","author":"Vila","year":"2024","journal-title":"J. Infect."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1007\/s44197-021-00009-1","article-title":"Age-Specific Etiology of Severe Acute Respiratory Infections and Influenza Vaccine Effectivity in Prevention of Hospitalization in Russia, 2018\u20132019 Season","volume":"11","author":"Sominina","year":"2021","journal-title":"J. Epidemiol. Glob. Health"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"39","DOI":"10.22625\/2072-6732-2022-14-2-39-46","article-title":"Impact of the COVID-19 Pandemic on the Seasonality of Respiratory Syncytial Viral Infection","volume":"14","author":"Babachenko","year":"2022","journal-title":"J. Infectol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"eabe3261","DOI":"10.1126\/science.abe3261","article-title":"Phylogenetic Analysis of SARS-CoV-2 in Boston Highlights the Impact of Superspreading Events","volume":"371","author":"Lemieux","year":"2021","journal-title":"Science"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"11630","DOI":"10.1128\/JVI.01972-15","article-title":"Successive Respiratory Syncytial Virus Epidemics in Local Populations Arise from Multiple Variant Introductions, Providing Insights into Virus Persistence","volume":"89","author":"Agoti","year":"2015","journal-title":"J. Virol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e2501435122","DOI":"10.1073\/pnas.2501435122","article-title":"Tracing SARS-CoV-2 Clusters across Local Scales Using Genomic Data","volume":"122","author":"Lyu","year":"2025","journal-title":"Proc. Natl. Acad. Sci. USA"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/8\/901\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T04:28:09Z","timestamp":1787027289000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/8\/901"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,15]]},"references-count":47,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["v18080901"],"URL":"https:\/\/doi.org\/10.3390\/v18080901","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,15]]}}}