Emergence of New SARS-CoV2 Omicron Variants after the Change of Surveillance and Control Strategy
In January 2022, there was a global and rapid surge of the Omicron variant of SARS-CoV-2 related to more transmission. This coincided with an increase in the incidence in Asturias, a region where rapid diagnosis and containment measures had limited the circulation of variants. Methods: From January...
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| Format: | Article |
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MDPI AG
2022-09-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/10/10/1954 |
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| author | José María González Alba Zulema Pérez-Martínez José A. Boga Susana Rojo-Alba Juan Gómez de Oña Marta E. Alvarez-Argüelles Garbriel Martín Rodríguez Isabel Costales Gonzalez Ismael Huerta González Eliecer Coto Santiago Melón García |
| author_facet | José María González Alba Zulema Pérez-Martínez José A. Boga Susana Rojo-Alba Juan Gómez de Oña Marta E. Alvarez-Argüelles Garbriel Martín Rodríguez Isabel Costales Gonzalez Ismael Huerta González Eliecer Coto Santiago Melón García |
| author_sort | José María González Alba |
| collection | DOAJ |
| description | In January 2022, there was a global and rapid surge of the Omicron variant of SARS-CoV-2 related to more transmission. This coincided with an increase in the incidence in Asturias, a region where rapid diagnosis and containment measures had limited the circulation of variants. Methods: From January to June 2022, 34,591 variants were determined by the SNP method. From them, 445 were characterized by the WGS method and classified following pangolin program and phylogenic analysis. Results: The Omicron variant went from being detected in 2438 (78%) samples in the first week of January 2021 to 4074 (98%) in the third week, according to the SNP method. Using the WGS method, 159 BA.1 (35.7%), 256 BA.2 (57.6%), 1 BA.4 (0.2%) and 10 BA.5 (2.2%) Omicron variants were found. Phylogenetic analysis detected that three new sub-clades, BA.2,3.5, BA.2.56 and BF1, were circulating. Conclusions: The increase in the incidence of SARS-CoV2 caused the circulation of new emerging variants. Viral evolution calls for continuous genomic surveillance. |
| first_indexed | 2024-03-09T19:45:53Z |
| format | Article |
| id | doaj.art-f887c75f56de45659af518fba58be987 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T19:45:53Z |
| publishDate | 2022-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-f887c75f56de45659af518fba58be9872023-11-24T01:26:01ZengMDPI AGMicroorganisms2076-26072022-09-011010195410.3390/microorganisms10101954Emergence of New SARS-CoV2 Omicron Variants after the Change of Surveillance and Control StrategyJosé María González Alba0Zulema Pérez-Martínez1José A. Boga2Susana Rojo-Alba3Juan Gómez de Oña4Marta E. Alvarez-Argüelles5Garbriel Martín Rodríguez6Isabel Costales Gonzalez7Ismael Huerta González8Eliecer Coto9Santiago Melón García10Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, SpainUnit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, SpainUnit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, SpainUnit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, SpainInstituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, SpainUnit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, SpainUnit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, SpainUnit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, SpainEpidemiological Surveillance Department, 33011 Oviedo, SpainInstituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, SpainUnit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, SpainIn January 2022, there was a global and rapid surge of the Omicron variant of SARS-CoV-2 related to more transmission. This coincided with an increase in the incidence in Asturias, a region where rapid diagnosis and containment measures had limited the circulation of variants. Methods: From January to June 2022, 34,591 variants were determined by the SNP method. From them, 445 were characterized by the WGS method and classified following pangolin program and phylogenic analysis. Results: The Omicron variant went from being detected in 2438 (78%) samples in the first week of January 2021 to 4074 (98%) in the third week, according to the SNP method. Using the WGS method, 159 BA.1 (35.7%), 256 BA.2 (57.6%), 1 BA.4 (0.2%) and 10 BA.5 (2.2%) Omicron variants were found. Phylogenetic analysis detected that three new sub-clades, BA.2,3.5, BA.2.56 and BF1, were circulating. Conclusions: The increase in the incidence of SARS-CoV2 caused the circulation of new emerging variants. Viral evolution calls for continuous genomic surveillance.https://www.mdpi.com/2076-2607/10/10/1954Omicronnew variantssurveillancephylogenetic analysis |
| spellingShingle | José María González Alba Zulema Pérez-Martínez José A. Boga Susana Rojo-Alba Juan Gómez de Oña Marta E. Alvarez-Argüelles Garbriel Martín Rodríguez Isabel Costales Gonzalez Ismael Huerta González Eliecer Coto Santiago Melón García Emergence of New SARS-CoV2 Omicron Variants after the Change of Surveillance and Control Strategy Microorganisms Omicron new variants surveillance phylogenetic analysis |
| title | Emergence of New SARS-CoV2 Omicron Variants after the Change of Surveillance and Control Strategy |
| title_full | Emergence of New SARS-CoV2 Omicron Variants after the Change of Surveillance and Control Strategy |
| title_fullStr | Emergence of New SARS-CoV2 Omicron Variants after the Change of Surveillance and Control Strategy |
| title_full_unstemmed | Emergence of New SARS-CoV2 Omicron Variants after the Change of Surveillance and Control Strategy |
| title_short | Emergence of New SARS-CoV2 Omicron Variants after the Change of Surveillance and Control Strategy |
| title_sort | emergence of new sars cov2 omicron variants after the change of surveillance and control strategy |
| topic | Omicron new variants surveillance phylogenetic analysis |
| url | https://www.mdpi.com/2076-2607/10/10/1954 |
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