Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 Variants
The prolonged course of the COVID-19 pandemic necessitates sustained surveillance of emerging variants. This study aimed to develop a multiplex real-time polymerase chain reaction (rt-PCR) suitable for the real-time tracking of Omicron subvariants in clinical and wastewater samples. Plasmids contain...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-12-01
|
| Series: | Viruses |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4915/15/12/2397 |
| _version_ | 1797379087160836096 |
|---|---|
| author | Ting Yan Rongrong Zheng Yinghui Li Siyang Sun Xiaohong Zeng Zhijiao Yue Yiqun Liao Qinghua Hu Ye Xu Qingge Li |
| author_facet | Ting Yan Rongrong Zheng Yinghui Li Siyang Sun Xiaohong Zeng Zhijiao Yue Yiqun Liao Qinghua Hu Ye Xu Qingge Li |
| author_sort | Ting Yan |
| collection | DOAJ |
| description | The prolonged course of the COVID-19 pandemic necessitates sustained surveillance of emerging variants. This study aimed to develop a multiplex real-time polymerase chain reaction (rt-PCR) suitable for the real-time tracking of Omicron subvariants in clinical and wastewater samples. Plasmids containing variant-specific mutations were used to develop a MeltArray assay. After a comprehensive evaluation of both analytical and clinical performance, the established assay was used to detect Omicron variants in clinical and wastewater samples, and the results were compared with those of next-generation sequencing (NGS) and droplet digital PCR (ddPCR). The MeltArray assay identified 14 variant-specific mutations, enabling the detection of five Omicron sublineages (BA.2*, BA.5.2*, BA.2.75*, BQ.1*, and XBB.1*) and eight subvariants (BF.7, BN.1, BR.2, BQ.1.1, XBB.1.5, XBB.1.16, XBB.1.9, and BA.4.6). The limit of detection (LOD) of the assay was 50 copies/reaction, and no cross-reactivity was observed with 15 other respiratory viruses. Using NGS as the reference method, the clinical evaluation of 232 swab samples exhibited a clinical sensitivity of > 95.12% (95% CI 89.77–97.75%) and a specificity of > 95.21% (95% CI, 91.15–97.46%). When used to evaluate the Omicron outbreak from late 2022 to early 2023, the MeltArray assay performed on 1408 samples revealed that the epidemic was driven by BA.5.2* (883, 62.71%) and BF.7 (525, 37.29%). Additionally, the MeltArray assay demonstrated potential for estimating variant abundance in wastewater samples. The MeltArray assay is a rapid and scalable method for identifying SARS-CoV-2 variants. Integrating this approach with NGS and ddPCR will improve variant surveillance capabilities and ensure preparedness for future variants. |
| first_indexed | 2024-03-08T20:17:02Z |
| format | Article |
| id | doaj.art-58c75f982d9e46eca54aa0ddb81c10b4 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-08T20:17:02Z |
| publishDate | 2023-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-58c75f982d9e46eca54aa0ddb81c10b42023-12-22T14:49:19ZengMDPI AGViruses1999-49152023-12-011512239710.3390/v15122397Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 VariantsTing Yan0Rongrong Zheng1Yinghui Li2Siyang Sun3Xiaohong Zeng4Zhijiao Yue5Yiqun Liao6Qinghua Hu7Ye Xu8Qingge Li9Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, ChinaXiamen Centre for Disease Control and Prevention, Xiamen 361021, ChinaShenzhen Centre for Disease Control and Prevention, Shenzhen 518055, ChinaEngineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, ChinaXiamen Centre for Disease Control and Prevention, Xiamen 361021, ChinaShenzhen Centre for Disease Control and Prevention, Shenzhen 518055, ChinaEngineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, ChinaShenzhen Centre for Disease Control and Prevention, Shenzhen 518055, ChinaEngineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, ChinaEngineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, ChinaThe prolonged course of the COVID-19 pandemic necessitates sustained surveillance of emerging variants. This study aimed to develop a multiplex real-time polymerase chain reaction (rt-PCR) suitable for the real-time tracking of Omicron subvariants in clinical and wastewater samples. Plasmids containing variant-specific mutations were used to develop a MeltArray assay. After a comprehensive evaluation of both analytical and clinical performance, the established assay was used to detect Omicron variants in clinical and wastewater samples, and the results were compared with those of next-generation sequencing (NGS) and droplet digital PCR (ddPCR). The MeltArray assay identified 14 variant-specific mutations, enabling the detection of five Omicron sublineages (BA.2*, BA.5.2*, BA.2.75*, BQ.1*, and XBB.1*) and eight subvariants (BF.7, BN.1, BR.2, BQ.1.1, XBB.1.5, XBB.1.16, XBB.1.9, and BA.4.6). The limit of detection (LOD) of the assay was 50 copies/reaction, and no cross-reactivity was observed with 15 other respiratory viruses. Using NGS as the reference method, the clinical evaluation of 232 swab samples exhibited a clinical sensitivity of > 95.12% (95% CI 89.77–97.75%) and a specificity of > 95.21% (95% CI, 91.15–97.46%). When used to evaluate the Omicron outbreak from late 2022 to early 2023, the MeltArray assay performed on 1408 samples revealed that the epidemic was driven by BA.5.2* (883, 62.71%) and BF.7 (525, 37.29%). Additionally, the MeltArray assay demonstrated potential for estimating variant abundance in wastewater samples. The MeltArray assay is a rapid and scalable method for identifying SARS-CoV-2 variants. Integrating this approach with NGS and ddPCR will improve variant surveillance capabilities and ensure preparedness for future variants.https://www.mdpi.com/1999-4915/15/12/2397COVID-19omicron subvariantsmultiplex PCRwastewater surveillanceSARS-CoV-2 |
| spellingShingle | Ting Yan Rongrong Zheng Yinghui Li Siyang Sun Xiaohong Zeng Zhijiao Yue Yiqun Liao Qinghua Hu Ye Xu Qingge Li Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 Variants Viruses COVID-19 omicron subvariants multiplex PCR wastewater surveillance SARS-CoV-2 |
| title | Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 Variants |
| title_full | Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 Variants |
| title_fullStr | Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 Variants |
| title_full_unstemmed | Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 Variants |
| title_short | Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 Variants |
| title_sort | epidemiological insights into the omicron outbreak via meltarray assisted real time tracking of sars cov 2 variants |
| topic | COVID-19 omicron subvariants multiplex PCR wastewater surveillance SARS-CoV-2 |
| url | https://www.mdpi.com/1999-4915/15/12/2397 |
| work_keys_str_mv | AT tingyan epidemiologicalinsightsintotheomicronoutbreakviameltarrayassistedrealtimetrackingofsarscov2variants AT rongrongzheng epidemiologicalinsightsintotheomicronoutbreakviameltarrayassistedrealtimetrackingofsarscov2variants AT yinghuili epidemiologicalinsightsintotheomicronoutbreakviameltarrayassistedrealtimetrackingofsarscov2variants AT siyangsun epidemiologicalinsightsintotheomicronoutbreakviameltarrayassistedrealtimetrackingofsarscov2variants AT xiaohongzeng epidemiologicalinsightsintotheomicronoutbreakviameltarrayassistedrealtimetrackingofsarscov2variants AT zhijiaoyue epidemiologicalinsightsintotheomicronoutbreakviameltarrayassistedrealtimetrackingofsarscov2variants AT yiqunliao epidemiologicalinsightsintotheomicronoutbreakviameltarrayassistedrealtimetrackingofsarscov2variants AT qinghuahu epidemiologicalinsightsintotheomicronoutbreakviameltarrayassistedrealtimetrackingofsarscov2variants AT yexu epidemiologicalinsightsintotheomicronoutbreakviameltarrayassistedrealtimetrackingofsarscov2variants AT qinggeli epidemiologicalinsightsintotheomicronoutbreakviameltarrayassistedrealtimetrackingofsarscov2variants |