Application of a high-resolution melt assay for monitoring SARS-CoV-2 variants in Burkina Faso and Kenya
ABSTRACT The rapid emergence and global dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlighted a need for robust, adaptable surveillance systems. However, financial and infrastructure requirements for whole-genome sequencing mean most surveillance data have come fr...
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American Society for Microbiology
2025-06-01
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| Online Access: | https://journals.asm.org/doi/10.1128/msphere.00027-25 |
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| author | Caitlin Greenland-Bews Sonal Shah Morine Achieng Emilie S. Badoum Yaya Bah Hellen C. Barsosio Helena Brazal-Monzó Jennifer Canizales Anna Drabko Alice J. Fraser Luke Hannan Sheikh Jarju Jean-Moise Kaboré Mariama A. Kujabi Cristina Leggio Maia Lesosky Jarra Manneh Tegwen Marlais Julian Matthewman Issa Nebié Eric Onyango Alphonse Ouedraogo Kephas Otieno Samuel S. Serme Sodiomon Sirima Ben Soulama Brian Tangara Alfred Tiono William Wu Emily R. Adams Abdul Karim Sesay Chris Drakeley Feiko O. ter Kuile Issiaka Soulama Simon Kariuki David J. Allen Thomas Edwards |
| author_facet | Caitlin Greenland-Bews Sonal Shah Morine Achieng Emilie S. Badoum Yaya Bah Hellen C. Barsosio Helena Brazal-Monzó Jennifer Canizales Anna Drabko Alice J. Fraser Luke Hannan Sheikh Jarju Jean-Moise Kaboré Mariama A. Kujabi Cristina Leggio Maia Lesosky Jarra Manneh Tegwen Marlais Julian Matthewman Issa Nebié Eric Onyango Alphonse Ouedraogo Kephas Otieno Samuel S. Serme Sodiomon Sirima Ben Soulama Brian Tangara Alfred Tiono William Wu Emily R. Adams Abdul Karim Sesay Chris Drakeley Feiko O. ter Kuile Issiaka Soulama Simon Kariuki David J. Allen Thomas Edwards |
| author_sort | Caitlin Greenland-Bews |
| collection | DOAJ |
| description | ABSTRACT The rapid emergence and global dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlighted a need for robust, adaptable surveillance systems. However, financial and infrastructure requirements for whole-genome sequencing mean most surveillance data have come from higher-resource geographies, despite unprecedented investment in sequencing in low- and middle-income countries (LMICs). Consequently, the molecular epidemiology of SARS-CoV-2 in some LMICs is limited, and there is a need for more cost-accessible technologies to help close data gaps for surveillance of SARS-CoV-2 variants. To address this, we have developed two high-resolution melt (HRM) curve assays that target variant-defining mutations in the SARS-CoV-2 genome, which give unique signature profiles that define different SARS-CoV-2 variants of concern (VOCs). Extracted RNA from SARS-CoV-2-positive samples collected from 205 participants (112 in Burkina Faso, 93 in Kenya) enrolled in the MALCOV study (Malaria as a Risk Factor for COVID-19) between February 2021 and February 2022 were analyzed using our optimized HRM assays. With next-generation sequencing on Oxford Nanopore MinION as a reference, two HRM assays, HRM-VOC-1 and HRM-VOC-2, demonstrated sensitivity/specificity of 100%/99.29% and 92.86%/99.39%, respectively, for detecting Alpha, 90.08%/100% and 92.31%/100% for Delta, and 93.75%/100% and 100%/99.38% for Omicron BA.1. The assays described here provide a lower-cost approach to conducting molecular epidemiology, capable of high-throughput testing. We successfully scaled up the HRM-VOC-2 assay to screen a total of 506 samples from which we were able to show the replacement of Alpha with the introduction of Delta and the replacement of Delta by the Omicron variant in this community in Kisumu, Kenya.IMPORTANCEThe rapid evolution of the severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) demonstrated the need for accessible surveillance tools so all communities can conduct viral surveillance. Sequencing, the gold standard, is still a largely inaccessible methodology in low-resource settings. Here, we present a quick, low-cost tool to screen for the common VOCs, designed to support surveillance efforts in low-resource settings. This tool was used to screen samples from Burkina Faso and Western Kenya throughout the pandemic. We show through comparison to sequencing that our assay can generate highly similar data on the different variants circulating in a population, therefore showing the effectiveness of our tool. While not a replacement for sequencing, we present a method of screening and prioritizing samples for further investigation and reduce overburdening sequencing capacity. Our findings provide insight into one potential tool that could be further applied to pathogen screening in the absence of robust sequencing infrastructure. |
| format | Article |
| id | doaj-art-f1fe9ddbce7b40aeba3af929e74a37f2 |
| institution | Matheson Library |
| issn | 2379-5042 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSphere |
| spelling | doaj-art-f1fe9ddbce7b40aeba3af929e74a37f22025-06-25T13:00:36ZengAmerican Society for MicrobiologymSphere2379-50422025-06-0110610.1128/msphere.00027-25Application of a high-resolution melt assay for monitoring SARS-CoV-2 variants in Burkina Faso and KenyaCaitlin Greenland-Bews0Sonal Shah1Morine Achieng2Emilie S. Badoum3Yaya Bah4Hellen C. Barsosio5Helena Brazal-Monzó6Jennifer Canizales7Anna Drabko8Alice J. Fraser9Luke Hannan10Sheikh Jarju11Jean-Moise Kaboré12Mariama A. Kujabi13Cristina Leggio14Maia Lesosky15Jarra Manneh16Tegwen Marlais17Julian Matthewman18Issa Nebié19Eric Onyango20Alphonse Ouedraogo21Kephas Otieno22Samuel S. Serme23Sodiomon Sirima24Ben Soulama25Brian Tangara26Alfred Tiono27William Wu28Emily R. Adams29Abdul Karim Sesay30Chris Drakeley31Feiko O. ter Kuile32Issiaka Soulama33Simon Kariuki34David J. Allen35Thomas Edwards36The Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United KingdomDepartment of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United KingdomCentre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kisumu County, KenyaGroupe de Recherche Action en Santé (GRAS), Ouagadougou, Burkina FasoMedical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, GambiaThe Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United KingdomDepartment of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United KingdomNational Heart and Lung Institute, Imperial College London, London, United KingdomQuantitative Engineering Design (QED), Sheridan, Wyoming, USAThe Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United KingdomDepartment of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United KingdomMedical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, GambiaGroupe de Recherche Action en Santé (GRAS), Ouagadougou, Burkina FasoMedical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, GambiaUK-Public Health Rapid Support Team (UK-PHRST), UK Health Security Agency (UKHSA), London, United KingdomNational Heart and Lung Institute, Imperial College London, London, United KingdomMedical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, GambiaDepartment of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United KingdomFaculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United KingdomGroupe de Recherche Action en Santé (GRAS), Ouagadougou, Burkina FasoCentre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kisumu County, KenyaGroupe de Recherche Action en Santé (GRAS), Ouagadougou, Burkina FasoThe Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United KingdomGroupe de Recherche Action en Santé (GRAS), Ouagadougou, Burkina FasoGroupe de Recherche Action en Santé (GRAS), Ouagadougou, Burkina FasoGroupe de Recherche Action en Santé (GRAS), Ouagadougou, Burkina FasoThe Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United KingdomGroupe de Recherche Action en Santé (GRAS), Ouagadougou, Burkina FasoQuantitative Engineering Design (QED), Sheridan, Wyoming, USADepartment of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United KingdomMedical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, GambiaDepartment of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United KingdomCentre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kisumu County, KenyaGroupe de Recherche Action en Santé (GRAS), Ouagadougou, Burkina FasoThe Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United KingdomDepartment of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United KingdomThe Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United KingdomABSTRACT The rapid emergence and global dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlighted a need for robust, adaptable surveillance systems. However, financial and infrastructure requirements for whole-genome sequencing mean most surveillance data have come from higher-resource geographies, despite unprecedented investment in sequencing in low- and middle-income countries (LMICs). Consequently, the molecular epidemiology of SARS-CoV-2 in some LMICs is limited, and there is a need for more cost-accessible technologies to help close data gaps for surveillance of SARS-CoV-2 variants. To address this, we have developed two high-resolution melt (HRM) curve assays that target variant-defining mutations in the SARS-CoV-2 genome, which give unique signature profiles that define different SARS-CoV-2 variants of concern (VOCs). Extracted RNA from SARS-CoV-2-positive samples collected from 205 participants (112 in Burkina Faso, 93 in Kenya) enrolled in the MALCOV study (Malaria as a Risk Factor for COVID-19) between February 2021 and February 2022 were analyzed using our optimized HRM assays. With next-generation sequencing on Oxford Nanopore MinION as a reference, two HRM assays, HRM-VOC-1 and HRM-VOC-2, demonstrated sensitivity/specificity of 100%/99.29% and 92.86%/99.39%, respectively, for detecting Alpha, 90.08%/100% and 92.31%/100% for Delta, and 93.75%/100% and 100%/99.38% for Omicron BA.1. The assays described here provide a lower-cost approach to conducting molecular epidemiology, capable of high-throughput testing. We successfully scaled up the HRM-VOC-2 assay to screen a total of 506 samples from which we were able to show the replacement of Alpha with the introduction of Delta and the replacement of Delta by the Omicron variant in this community in Kisumu, Kenya.IMPORTANCEThe rapid evolution of the severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) demonstrated the need for accessible surveillance tools so all communities can conduct viral surveillance. Sequencing, the gold standard, is still a largely inaccessible methodology in low-resource settings. Here, we present a quick, low-cost tool to screen for the common VOCs, designed to support surveillance efforts in low-resource settings. This tool was used to screen samples from Burkina Faso and Western Kenya throughout the pandemic. We show through comparison to sequencing that our assay can generate highly similar data on the different variants circulating in a population, therefore showing the effectiveness of our tool. While not a replacement for sequencing, we present a method of screening and prioritizing samples for further investigation and reduce overburdening sequencing capacity. Our findings provide insight into one potential tool that could be further applied to pathogen screening in the absence of robust sequencing infrastructure.https://journals.asm.org/doi/10.1128/msphere.00027-25SARS-CoV-2variants of concernHRMdiagnosticssurveillanceBurkina Faso |
| spellingShingle | Caitlin Greenland-Bews Sonal Shah Morine Achieng Emilie S. Badoum Yaya Bah Hellen C. Barsosio Helena Brazal-Monzó Jennifer Canizales Anna Drabko Alice J. Fraser Luke Hannan Sheikh Jarju Jean-Moise Kaboré Mariama A. Kujabi Cristina Leggio Maia Lesosky Jarra Manneh Tegwen Marlais Julian Matthewman Issa Nebié Eric Onyango Alphonse Ouedraogo Kephas Otieno Samuel S. Serme Sodiomon Sirima Ben Soulama Brian Tangara Alfred Tiono William Wu Emily R. Adams Abdul Karim Sesay Chris Drakeley Feiko O. ter Kuile Issiaka Soulama Simon Kariuki David J. Allen Thomas Edwards Application of a high-resolution melt assay for monitoring SARS-CoV-2 variants in Burkina Faso and Kenya mSphere SARS-CoV-2 variants of concern HRM diagnostics surveillance Burkina Faso |
| title | Application of a high-resolution melt assay for monitoring SARS-CoV-2 variants in Burkina Faso and Kenya |
| title_full | Application of a high-resolution melt assay for monitoring SARS-CoV-2 variants in Burkina Faso and Kenya |
| title_fullStr | Application of a high-resolution melt assay for monitoring SARS-CoV-2 variants in Burkina Faso and Kenya |
| title_full_unstemmed | Application of a high-resolution melt assay for monitoring SARS-CoV-2 variants in Burkina Faso and Kenya |
| title_short | Application of a high-resolution melt assay for monitoring SARS-CoV-2 variants in Burkina Faso and Kenya |
| title_sort | application of a high resolution melt assay for monitoring sars cov 2 variants in burkina faso and kenya |
| topic | SARS-CoV-2 variants of concern HRM diagnostics surveillance Burkina Faso |
| url | https://journals.asm.org/doi/10.1128/msphere.00027-25 |
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