Development of Primer Panels for Whole-Genome Amplification and Sequencing of Human Seasonal Coronaviruses: hCoV-OC43, hCoV-HKU1, hCoV-229E, and hCoV-NL63
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....
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2024-12-01
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| author | Tamila Musaeva Artem Fadeev Maria Pisareva Veronika Eder Andrey Ksenafontov Margarita Korzhanova Valery Tsvetkov Alexander Perederiy Irina Kiseleva Daria Danilenko Dmitry Lioznov Andrey Komissarov |
| author_facet | Tamila Musaeva Artem Fadeev Maria Pisareva Veronika Eder Andrey Ksenafontov Margarita Korzhanova Valery Tsvetkov Alexander Perederiy Irina Kiseleva Daria Danilenko Dmitry Lioznov Andrey Komissarov |
| author_sort | Tamila Musaeva |
| collection | DOAJ |
| description | 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 (900–1100 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 >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. |
| format | Article |
| id | doaj-art-c34055a219d04eac98d91447040bd97e |
| institution | Kabale University |
| issn | 1999-4915 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
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| series | Viruses |
| spelling | doaj-art-c34055a219d04eac98d91447040bd97e2025-01-24T13:52:15ZengMDPI AGViruses1999-49152024-12-011711310.3390/v17010013Development of Primer Panels for Whole-Genome Amplification and Sequencing of Human Seasonal Coronaviruses: hCoV-OC43, hCoV-HKU1, hCoV-229E, and hCoV-NL63Tamila Musaeva0Artem Fadeev1Maria Pisareva2Veronika Eder3Andrey Ksenafontov4Margarita Korzhanova5Valery Tsvetkov6Alexander Perederiy7Irina Kiseleva8Daria Danilenko9Dmitry Lioznov10Andrey Komissarov11Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint Petersburg, RussiaInstitute of Experimental Medicine, 197022 Saint Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint Petersburg, RussiaSmorodintsev Research Institute of Influenza, 197376 Saint Petersburg, RussiaHuman 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 (900–1100 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 >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.https://www.mdpi.com/1999-4915/17/1/13viruseshuman seasonal coronavirusesacute respiratory infectionshCoV-NL63hCoV-229EhCoV-HKU1 |
| spellingShingle | Tamila Musaeva Artem Fadeev Maria Pisareva Veronika Eder Andrey Ksenafontov Margarita Korzhanova Valery Tsvetkov Alexander Perederiy Irina Kiseleva Daria Danilenko Dmitry Lioznov Andrey Komissarov Development of Primer Panels for Whole-Genome Amplification and Sequencing of Human Seasonal Coronaviruses: hCoV-OC43, hCoV-HKU1, hCoV-229E, and hCoV-NL63 Viruses viruses human seasonal coronaviruses acute respiratory infections hCoV-NL63 hCoV-229E hCoV-HKU1 |
| title | Development of Primer Panels for Whole-Genome Amplification and Sequencing of Human Seasonal Coronaviruses: hCoV-OC43, hCoV-HKU1, hCoV-229E, and hCoV-NL63 |
| title_full | Development of Primer Panels for Whole-Genome Amplification and Sequencing of Human Seasonal Coronaviruses: hCoV-OC43, hCoV-HKU1, hCoV-229E, and hCoV-NL63 |
| title_fullStr | Development of Primer Panels for Whole-Genome Amplification and Sequencing of Human Seasonal Coronaviruses: hCoV-OC43, hCoV-HKU1, hCoV-229E, and hCoV-NL63 |
| title_full_unstemmed | Development of Primer Panels for Whole-Genome Amplification and Sequencing of Human Seasonal Coronaviruses: hCoV-OC43, hCoV-HKU1, hCoV-229E, and hCoV-NL63 |
| title_short | Development of Primer Panels for Whole-Genome Amplification and Sequencing of Human Seasonal Coronaviruses: hCoV-OC43, hCoV-HKU1, hCoV-229E, and hCoV-NL63 |
| title_sort | development of primer panels for whole genome amplification and sequencing of human seasonal coronaviruses hcov oc43 hcov hku1 hcov 229e and hcov nl63 |
| topic | viruses human seasonal coronaviruses acute respiratory infections hCoV-NL63 hCoV-229E hCoV-HKU1 |
| url | https://www.mdpi.com/1999-4915/17/1/13 |
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