The Single-Nucleotide Polymorphism (SNP) Validity to Detect Omicron Variants
Introduction. Mutation of SARS-CoV-2 has generated several variants of concern (VOC) which spread promptly worldwide. These emerging variants affected global strategies to overcome COVID-19. Variants of SARS-CoV-2 are determined by the whole genome sequencing (WGS) assay, which is time-consuming, wi...
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| Format: | Article |
| Language: | English |
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Wiley
2023-01-01
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| Series: | Advances in Virology |
| Online Access: | http://dx.doi.org/10.1155/2023/6618710 |
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| author | Lia Gardenia Partakusuma Luhung Budiailmiawan null Budiman Ida Parwati null Aryati Basti Andriyoko Louisa Markus Corine Niswara Cut Nur Cinthia Alamanda |
| author_facet | Lia Gardenia Partakusuma Luhung Budiailmiawan null Budiman Ida Parwati null Aryati Basti Andriyoko Louisa Markus Corine Niswara Cut Nur Cinthia Alamanda |
| author_sort | Lia Gardenia Partakusuma |
| collection | DOAJ |
| description | Introduction. Mutation of SARS-CoV-2 has generated several variants of concern (VOC) which spread promptly worldwide. These emerging variants affected global strategies to overcome COVID-19. Variants of SARS-CoV-2 are determined by the whole genome sequencing (WGS) assay, which is time-consuming, with limited availability (only in several laboratories). Hence, a faster and more accessible examination is needed. The single-nucleotide polymorphism (SNP) method is one of the options for genomic variation surveillance that can help provide an answer to this challenge. This study aims to determine the validity of the SNP method with PCR to detect omicron variants of SARS-CoV-2 compared with the gold standard, WGS. Methods. This is a diagnostic analysis of 140 confirmed COVID-19 nasopharyngeal samples taken from the Kemayoran COVID Emergency Hospital Laboratory and the West Java Provincial Health Laboratory from April to October 2022. Data analysis was carried out to determine conformity and validity values. Results. Analysis using Cohen’s kappa coefficient test showed high conformity between SNP and WGS (p value <0.001; kappa coefficient = 0.948). SNP showed great validity values on omicron BA.1 (90% sensitivity; 100% specificity), omicron BA.2 (100% sensitivity; 99% specificity), and omicron BA.4/5 (99.2% sensitivity; 100% specificity). Conclusion. The SNP method can be a more time-efficient alternative to detect omicron variants of SARS-CoV-2 and distinguish their sublineages (BA.1, BA.2, and BA.4/5) by two different specific gene mutations in combination analysis (ΔH69/V70 and Q493R mutations). |
| format | Article |
| id | doaj-art-5946fa56e70640d1a7bbf889d2f66855 |
| institution | Kabale University |
| issn | 1687-8647 |
| language | English |
| publishDate | 2023-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Advances in Virology |
| spelling | doaj-art-5946fa56e70640d1a7bbf889d2f668552025-02-03T01:31:52ZengWileyAdvances in Virology1687-86472023-01-01202310.1155/2023/6618710The Single-Nucleotide Polymorphism (SNP) Validity to Detect Omicron VariantsLia Gardenia Partakusuma0Luhung Budiailmiawan1null Budiman2Ida Parwati3null Aryati4Basti Andriyoko5Louisa Markus6Corine Niswara7Cut Nur Cinthia Alamanda8Faculty of Medicine and Post Graduate ProgrammePalabuhanratu HospitalCOVID Emergency HospitalDepartment of Clinical PathologyDepartment of Clinical PathologyDepartment of Clinical PathologyCengkareng HospitalCOVID Emergency HospitalWest Java Provincial Health LaboratoryIntroduction. Mutation of SARS-CoV-2 has generated several variants of concern (VOC) which spread promptly worldwide. These emerging variants affected global strategies to overcome COVID-19. Variants of SARS-CoV-2 are determined by the whole genome sequencing (WGS) assay, which is time-consuming, with limited availability (only in several laboratories). Hence, a faster and more accessible examination is needed. The single-nucleotide polymorphism (SNP) method is one of the options for genomic variation surveillance that can help provide an answer to this challenge. This study aims to determine the validity of the SNP method with PCR to detect omicron variants of SARS-CoV-2 compared with the gold standard, WGS. Methods. This is a diagnostic analysis of 140 confirmed COVID-19 nasopharyngeal samples taken from the Kemayoran COVID Emergency Hospital Laboratory and the West Java Provincial Health Laboratory from April to October 2022. Data analysis was carried out to determine conformity and validity values. Results. Analysis using Cohen’s kappa coefficient test showed high conformity between SNP and WGS (p value <0.001; kappa coefficient = 0.948). SNP showed great validity values on omicron BA.1 (90% sensitivity; 100% specificity), omicron BA.2 (100% sensitivity; 99% specificity), and omicron BA.4/5 (99.2% sensitivity; 100% specificity). Conclusion. The SNP method can be a more time-efficient alternative to detect omicron variants of SARS-CoV-2 and distinguish their sublineages (BA.1, BA.2, and BA.4/5) by two different specific gene mutations in combination analysis (ΔH69/V70 and Q493R mutations).http://dx.doi.org/10.1155/2023/6618710 |
| spellingShingle | Lia Gardenia Partakusuma Luhung Budiailmiawan null Budiman Ida Parwati null Aryati Basti Andriyoko Louisa Markus Corine Niswara Cut Nur Cinthia Alamanda The Single-Nucleotide Polymorphism (SNP) Validity to Detect Omicron Variants Advances in Virology |
| title | The Single-Nucleotide Polymorphism (SNP) Validity to Detect Omicron Variants |
| title_full | The Single-Nucleotide Polymorphism (SNP) Validity to Detect Omicron Variants |
| title_fullStr | The Single-Nucleotide Polymorphism (SNP) Validity to Detect Omicron Variants |
| title_full_unstemmed | The Single-Nucleotide Polymorphism (SNP) Validity to Detect Omicron Variants |
| title_short | The Single-Nucleotide Polymorphism (SNP) Validity to Detect Omicron Variants |
| title_sort | single nucleotide polymorphism snp validity to detect omicron variants |
| url | http://dx.doi.org/10.1155/2023/6618710 |
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