{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T16:21:20Z","timestamp":1782404480041,"version":"3.54.5"},"reference-count":55,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2024,12,25]],"date-time":"2024-12-25T00:00:00Z","timestamp":1735084800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministry of Health of the Russian Federation","award":["#TVKQ-2024-0003"],"award-info":[{"award-number":["#TVKQ-2024-0003"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Human seasonal coronaviruses (hCoVs) are a group of viruses that affect the upper respiratory tract. While seasonal patterns and the annual variability of predominant hCoV species are well-documented, their genetic and species diversity in St. Petersburg and across Russia remains largely unexplored. In this study, we developed a two-pool, long-amplicon (900\u20131100 bp) PCR primer panel for the whole-genome sequencing of four seasonal hCoV species. The panel was validated using nasopharyngeal swab samples collected within the Global Influenza Hospital Surveillance Network (GIHSN) project. Over a period of six epidemiological seasons from 2017 to 2023, we retrospectively analyzed 14,704 nasopharyngeal swabs collected from patients hospitalized in St. Petersburg clinics. Of these samples, 5010 (34.07%) tested positive for respiratory viruses, with 424 (2.88% of all samples) identified as seasonal human coronaviruses. The assessment of species diversity showed that predominant hCoV species alternate between seasons. Whole-genome sequences for 85 seasonal human coronaviruses (hCoVs) with &gt;70% genome coverage were obtained, including 23 hCoV-OC43, 6 hCoV-HKU1, 39 hCoV-229E, and 17 hCoV-NL63. These represent the first near-complete genomes of seasonal hCoVs from the Russian Federation, addressing a significant gap in the genomic epidemiology of these viruses. A detailed phylogenetic analysis of the sequenced genomes was conducted, highlighting the emergence of hCoV-229E subclades 7b.1 and 7b.2, which carry numerous substitutions in the Spike protein. Additionally, we sequenced a historical hCoV-229E isolate collected in the USSR in 1979, the oldest sequenced 229E virus from Eurasia, and demonstrated that it belongs to Genotype 2. The newly developed PCR-based sequencing protocol for seasonal hCoVs is straightforward and well-suited for genomic surveillance, providing a valuable tool to enhance our understanding of the genetic diversity of human seasonal coronaviruses.<\/jats:p>","DOI":"10.3390\/v17010013","type":"journal-article","created":{"date-parts":[[2024,12,25]],"date-time":"2024-12-25T19:19:32Z","timestamp":1735154372000},"page":"13","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Development of Primer Panels for Whole-Genome Amplification and Sequencing of Human Seasonal Coronaviruses: hCoV-OC43, hCoV-HKU1, hCoV-229E, and hCoV-NL63"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3050-1936","authenticated-orcid":false,"given":"Tamila","family":"Musaeva","sequence":"first","affiliation":[{"name":"Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3558-3261","authenticated-orcid":false,"given":"Artem","family":"Fadeev","sequence":"additional","affiliation":[{"name":"Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1499-9957","authenticated-orcid":false,"given":"Maria","family":"Pisareva","sequence":"additional","affiliation":[{"name":"Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9970-3325","authenticated-orcid":false,"given":"Veronika","family":"Eder","sequence":"additional","affiliation":[{"name":"Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrey","family":"Ksenafontov","sequence":"additional","affiliation":[{"name":"Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2512-2517","authenticated-orcid":false,"given":"Margarita","family":"Korzhanova","sequence":"additional","affiliation":[{"name":"Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5195-9316","authenticated-orcid":false,"given":"Valery","family":"Tsvetkov","sequence":"additional","affiliation":[{"name":"Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5961-1856","authenticated-orcid":false,"given":"Alexander","family":"Perederiy","sequence":"additional","affiliation":[{"name":"Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3892-9873","authenticated-orcid":false,"given":"Irina","family":"Kiseleva","sequence":"additional","affiliation":[{"name":"Institute of Experimental Medicine, 197022 Saint Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6174-0836","authenticated-orcid":false,"given":"Daria","family":"Danilenko","sequence":"additional","affiliation":[{"name":"Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3643-7354","authenticated-orcid":false,"given":"Dmitry","family":"Lioznov","sequence":"additional","affiliation":[{"name":"Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia"},{"name":"Department of Infectious Diseases and Epidemiology, First Pavlov State Medical University, 197022 Saint Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrey","family":"Komissarov","sequence":"additional","affiliation":[{"name":"Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,12,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1467","DOI":"10.1136\/bmj.1.5448.1467","article-title":"Cultivation of a Novel Type of Common-cold Virus in Organ Cultures","volume":"1","author":"Tyrrell","year":"1965","journal-title":"Br. 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