1
|
Ealand CS, Gordhan BG, Machowski EE, Kana BD. Development of primer-probe sets to rapidly distinguish single nucleotide polymorphisms in SARS-CoV-2 lineages. Front Cell Infect Microbiol 2023; 13:1283328. [PMID: 38130775 PMCID: PMC10733533 DOI: 10.3389/fcimb.2023.1283328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023] Open
Abstract
Ongoing SARS-CoV-2 infections are driven by the emergence of various variants, with differential propensities to escape immune containment. Single nucleotide polymorphisms (SNPs) in the RNA genome result in altered protein structures and when these changes occur in the S-gene, encoding the spike protein, the ability of the virus to penetrate host cells to initiate an infection can be significantly altered. As a result, vaccine efficacy and prior immunity may be diminished, potentially leading to new waves of infection. Early detection of SARS-CoV-2 variants using a rapid and scalable approach will be paramount for continued monitoring of new infections. In this study, we developed minor groove-binding (MGB) probe-based qPCR assays targeted to specific SNPs in the S-gene, which are present in variants of concern (VOC), namely the E484K, N501Y, G446S and D405N mutations. A total of 95 archived SARS-CoV-2 positive clinical specimens collected in Johannesburg, South Africa between February 2021 and March 2022 were assessed using these qPCR assays. To independently confirm SNP detection, Sanger sequencing of the relevant region in the S-gene were performed. Where a PCR product could be generated and sequenced, qPCR assays were 100% concordant highlighting the robustness of the approach. These assays, and the approach described, offer the opportunity for easy detection and scaling of targeted detection of variant-defining SNPs in the clinical setting.
Collapse
Affiliation(s)
| | | | | | - Bavesh D. Kana
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical Tuberculosis (TB) Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and The National Health Laboratory Service, Johannesburg, South Africa
| |
Collapse
|
2
|
Gordhan BG, Herrera C, Pillay AD, Seiphetlo T, Ealand CS, Machowski E, Singh N, Seatholo N, Otwombe K, Lebina L, Frise R, Scarlatti G, Chiodi F, Martinson N, Fox J, Kana BD. Evaluation of a human mucosal tissue explant model for SARS-CoV-2 replication. PLoS One 2023; 18:e0291146. [PMID: 37769001 PMCID: PMC10538748 DOI: 10.1371/journal.pone.0291146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/23/2023] [Indexed: 09/30/2023] Open
Abstract
With the onset of COVID-19, the development of ex vivo laboratory models became an urgent priority to study host-pathogen interactions in response to the pandemic. In this study, we aimed to establish an ex vivo mucosal tissue explant challenge model for studying SARS-CoV-2 infection and replication. Nasal or oral tissue samples were collected from eligible participants and explants generated from the tissue were infected with various SARS-CoV-2 strains, including IC19 (lineage B.1.13), Beta (lineage B.1.351) and Delta (lineage B.1.617.2). A qRT-PCR assay used to measure viral replication in the tissue explants over a 15-day period, demonstrated no replication for any viral strains tested. Based on this, the ex vivo challenge protocol was modified by reducing the viral infection time and duration of sampling. Despite these changes, viral infectivity of the nasal and oral mucosa was not improved. Since 67% of the enrolled participants were already vaccinated against SARS-CoV-2, it is possible that neutralizing antibodies in explant tissue may have prevented the establishment of infection. However, we were unable to optimize plaque assays aimed at titrating the virus in supernatants from both infected and uninfected tissue, due to limited volume of culture supernatant available at the various collection time points. Currently, the reasons for the inability of these mucosal tissue samples to support replication of SARS-CoV-2 ex vivo remains unclear and requires further investigation.
Collapse
Affiliation(s)
- Bhavna Gowan Gordhan
- Faculty of Health Sciences, Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Carolina Herrera
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Azure-Dee Pillay
- Faculty of Health Sciences, Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
| | - Thabiso Seiphetlo
- Faculty of Health Sciences, Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
| | - Christopher Shawn Ealand
- Faculty of Health Sciences, Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Edith Machowski
- Faculty of Health Sciences, Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Natasha Singh
- Faculty of Health Sciences, Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
| | - Ntombexolo Seatholo
- Faculty of Health Sciences, Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
| | - Kennedy Otwombe
- Faculty of Health Sciences, Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
- Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Limakatso Lebina
- Faculty of Health Sciences, Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
| | - Rebecca Frise
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Gabriella Scarlatti
- Viral Evolution and Transmission Unit, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Francesca Chiodi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Neil Martinson
- Faculty of Health Sciences, Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University Center for TB Research, Baltimore, MD, United States of America
| | - Julie Fox
- Guys and St. Thomas’ NHS Foundation Trust and King’s College London, London, United Kingdom
| | - Bavesh Davandra Kana
- Faculty of Health Sciences, Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| |
Collapse
|