1
|
Emmen IE, Vuyk WC, Lail AJ, Wolf S, O'Connor EJ, Dalvie R, Bhasin M, Virdi A, White C, Hassan NR, Richardson A, VanSleet G, Weiler A, Rounds-Dunn S, Van Horn K, Gartler M, Jorgenson J, Spelman M, Ottosen S, Minor NR, Wilson N, Friedrich TC, O'Connor DH. SARS-CoV-2 Genomic Surveillance from Community-Distributed Rapid Antigen Tests, Wisconsin, USA. Emerg Infect Dis 2025; 31:61-69. [PMID: 40359069 PMCID: PMC12078534 DOI: 10.3201/eid3113.241192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2025] Open
Abstract
In the United States, SARS-CoV-2 genomic surveillance initially relied almost entirely on residual diagnostic specimens from nucleic acid amplification-based tests. However, use of those tests waned after the end of the COVID-19 Public Health Emergency on May 11, 2023. In Dane County, Wisconsin, we partnered with local- and state-level public health agencies and the South Central Library System to continue genomic surveillance by obtaining SARS-CoV-2 genome sequences from freely available community rapid antigen tests (RATs). During August 15, 2023-February 29, 2024, we received 227 RAT samples, from which we generated 127 sequences with >10× depth of coverage for >90% of the SARS-CoV-2 genome. In a subset of tests, lower cycle threshold values correlated with sequence success. Our results demonstrated that collecting and sequencing results from RATs in partnership with community sites is a practical approach for sustaining SARS-CoV-2 genomic surveillance.
Collapse
|
2
|
Anasir MI, Kamel K, Adypatti NMG, Jamaluddin MS, Ahmad FA, Norhisham SN, Sukri MZM, Rosli NR, Saif SN, Basarudin NI, Azzam-Sayuti M, Karim AHA, Puat MK, Thayan R, Zain RM. Whole-genome sequencing of SARS-CoV-2 from residual viral RNA present on positive rapid antigen test kits for genomic surveillance. Western Pac Surveill Response J 2025; 16:1-6. [PMID: 40171102 PMCID: PMC11957951 DOI: 10.5365/wpsar.2025.16.1.1140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2025] Open
Affiliation(s)
- Mohd Ishtiaq Anasir
- Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
| | - Khayri Kamel
- Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
| | - Nor Malizza G Adypatti
- Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
| | - Mohammad Syafiq Jamaluddin
- Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
| | - Farah Amira Ahmad
- Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
| | - Siti Nurhidayah Norhisham
- Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
| | - Muhammad Zulfazli Mohamad Sukri
- Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
| | - Nur Rafiqah Rosli
- Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
| | - Siti Norazrina Saif
- Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
| | - Nurul Izzati Basarudin
- Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
| | - Mohamad Azzam-Sayuti
- Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
| | | | - Mahirah Kamil Puat
- Pathology Department, Hospital Tengku Ampuan Rahimah, Selangor, Malaysia
| | - Ravindran Thayan
- Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
| | - Rozainanee Mohd Zain
- Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
| |
Collapse
|
3
|
Moso MA, Taiaroa G, Steinig E, Zhanduisenov M, Butel-Simoes G, Savic I, Taouk ML, Chea S, Moselen J, O'Keefe J, Prestedge J, Pollock GL, Khan M, Soloczynskyj K, Fernando J, Martin GE, Caly L, Barr IG, Tran T, Druce J, Lim CK, Williamson DA. Non-SARS-CoV-2 respiratory viral detection and whole genome sequencing from COVID-19 rapid antigen test devices: a laboratory evaluation study. THE LANCET. MICROBE 2024; 5:e317-e325. [PMID: 38359857 DOI: 10.1016/s2666-5247(23)00375-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 11/01/2023] [Accepted: 11/15/2023] [Indexed: 02/17/2024]
Abstract
BACKGROUND There has been high uptake of rapid antigen test device use for point-of-care COVID-19 diagnosis. Individuals who are symptomatic but test negative on COVID-19 rapid antigen test devices might have a different respiratory viral infection. We aimed to detect and sequence non-SARS-CoV-2 respiratory viruses from rapid antigen test devices, which could assist in the characterisation and surveillance of circulating respiratory viruses in the community. METHODS We applied archival clinical nose and throat swabs collected between Jan 1, 2015, and Dec 31, 2022, that previously tested positive for a common respiratory virus (adenovirus, influenza, metapneumovirus, parainfluenza, rhinovirus, respiratory syncytial virus [RSV], or seasonal coronavirus; 132 swabs and 140 viral targets) on PCR to two commercially available COVID-19 rapid antigen test devices, the Panbio COVID-19 Ag Rapid Test Device and Roche SARS-CoV-2 Antigen Self-Test. In addition, we collected 31 COVID-19 rapid antigen test devices used to test patients who were symptomatic at The Royal Melbourne Hospital emergency department in Melbourne, Australia. We extracted total nucleic acid from the device paper test strips and assessed viral recovery using multiplex real-time PCR (rtPCR) and capture-based whole genome sequencing. Sequence and genome data were analysed through custom computational pipelines, including subtyping. FINDINGS Of the 140 respiratory viral targets from archival samples, 89 (64%) and 88 (63%) were positive on rtPCR for the relevant taxa following extraction from Panbio or Roche rapid antigen test devices, respectively. Recovery was variable across taxa: we detected influenza A in nine of 18 samples from Panbio and seven of 18 from Roche devices; parainfluenza in 11 of 20 samples from Panbio and 12 of 20 from Roche devices; human metapneumovirus in 11 of 16 from Panbio and 14 of 16 from Roche devices; seasonal coronavirus in eight of 19 from Panbio and two of 19 from Roche devices; rhinovirus in 24 of 28 from Panbio and 27 of 28 from Roche devices; influenza B in four of 15 in both devices; and RSV in 16 of 18 in both devices. Of the 31 COVID-19 devices collected from The Royal Melbourne Hospital emergency department, 11 tested positive for a respiratory virus on rtPCR, including one device positive for influenza A virus, one positive for RSV, four positive for rhinovirus, and five positive for SARS-CoV-2. Sequences of target respiratory viruses from archival samples were detected in 55 (98·2%) of 56 samples from Panbio and 48 (85·7%) of 56 from Roche rapid antigen test devices. 98 (87·5%) of 112 viral genomes were completely assembled from these data, enabling subtyping for RSV and influenza viruses. All 11 samples collected from the emergency department had viral sequences detected, with near-complete genomes assembled for influenza A and RSV. INTERPRETATION Non-SARS-CoV-2 respiratory viruses can be detected and sequenced from COVID-19 rapid antigen devices. Recovery of near full-length viral sequences from these devices provides a valuable opportunity to expand genomic surveillance programmes for public health monitoring of circulating respiratory viruses. FUNDING Australian Government Medical Research Future Fund and Australian National Health and Medical Research Council.
Collapse
Affiliation(s)
- Michael A Moso
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - George Taiaroa
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Eike Steinig
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Madiyar Zhanduisenov
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Grace Butel-Simoes
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ivana Savic
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mona L Taouk
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Socheata Chea
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jean Moselen
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jacinta O'Keefe
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jacqueline Prestedge
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Georgina L Pollock
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mohammad Khan
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Katherine Soloczynskyj
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Janath Fernando
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Genevieve E Martin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, VIC, Australia
| | - Thomas Tran
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Julian Druce
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Chuan K Lim
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.
| |
Collapse
|
4
|
Cucina A, Contino F, Brunacci G, Orlando V, La Rocca M, Indelicato S, Di Gaudio F. The Suitability of RNA from Positive SARS-CoV-2 Rapid Antigen Tests for Whole Virus Genome Sequencing and Variant Identification to Maintain Genomic Surveillance. Diagnostics (Basel) 2023; 13:3618. [PMID: 38132202 PMCID: PMC10742923 DOI: 10.3390/diagnostics13243618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/24/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
The COVID-19 pandemic has transformed laboratory management, with a surge in demand for diagnostic tests prompting the adoption of new diagnostic assays and the spread of variant surveillance tools. Rapid antigen tests (RATs) were initially used only for screening and later as suitable infection assessment tools. This study explores the feasibility of sequencing the SARS-CoV-2 genome from the residue of the nasopharyngeal swab extraction buffers of rapid antigen tests (RATs) to identify different COVID-19 lineages and sub-lineages. METHODS Viral RNA was extracted from the residue of the nasopharyngeal swab extraction buffers of RATs and, after a confirmation of positivity through a reaction of RT-PCR, viral genome sequencing was performed. RESULTS Overall, the quality of the sequences obtained from the RNA extracted from the residue of the nasopharyngeal swab extraction buffers of RATs was adequate and allowed us to identify the SARS-CoV-2 variants' circulation and distribution in a period when the use of molecular swabs had been drastically reduced. CONCLUSIONS This study demonstrates the potential for genomic surveillance by sequencing SARS-CoV-2 from the residue of the nasopharyngeal swab extraction buffers of RATs, highlighting alternative possibilities for tracking variants.
Collapse
Affiliation(s)
- Annamaria Cucina
- Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Chromatography and Mass Spectrometry Section, Quality Control and Chemical Risk (CQRC), Via del Vespro, 133, 90127 Palermo, Italy; (A.C.); (F.C.); (G.B.); (V.O.)
| | - Flavia Contino
- Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Chromatography and Mass Spectrometry Section, Quality Control and Chemical Risk (CQRC), Via del Vespro, 133, 90127 Palermo, Italy; (A.C.); (F.C.); (G.B.); (V.O.)
| | - Giuseppina Brunacci
- Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Chromatography and Mass Spectrometry Section, Quality Control and Chemical Risk (CQRC), Via del Vespro, 133, 90127 Palermo, Italy; (A.C.); (F.C.); (G.B.); (V.O.)
| | - Valentina Orlando
- Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Chromatography and Mass Spectrometry Section, Quality Control and Chemical Risk (CQRC), Via del Vespro, 133, 90127 Palermo, Italy; (A.C.); (F.C.); (G.B.); (V.O.)
| | - Mario La Rocca
- Regional Health Department, Department of Strategic Planning, Piazza Ottavio Ziino, 24, 90145 Palermo, Italy;
| | - Sergio Indelicato
- Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Chromatography and Mass Spectrometry Section, Quality Control and Chemical Risk (CQRC), Via del Vespro, 133, 90127 Palermo, Italy; (A.C.); (F.C.); (G.B.); (V.O.)
| | - Francesca Di Gaudio
- Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Chromatography and Mass Spectrometry Section, Quality Control and Chemical Risk (CQRC), Via del Vespro, 133, 90127 Palermo, Italy; (A.C.); (F.C.); (G.B.); (V.O.)
- PROMISE-Promotion of Health, Maternal-Childhood, Internal and Specialized Medicine of Excellence “G. D’Alessandro”, University of Palermo, Piazza delle Cliniche, 2, 90127 Palermo, Italy
| |
Collapse
|
5
|
Pérez-Rodríguez FJ, Laubscher F, Chudzinski V, Kaiser L, Cordey S. Direct Dengue Virus Genome Sequencing from Antigen NS1 Rapid Diagnostic Tests: A Proof-of-Concept with the Standard Q Dengue Duo Assay. Viruses 2023; 15:2167. [PMID: 38005845 PMCID: PMC10674465 DOI: 10.3390/v15112167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
With nearly half of the world's population being at risk of infection, dengue virus represents a major global health issue. The use of dengue antigen rapid diagnostic tests (Ag-RDTs) represents an alternative to PCR methods for the diagnosis of acute infections since they display excellent sensitivities and specificities and can be performed outside the laboratory. The high genetic diversity of the dengue virus genome represents a challenge for vaccine development, and the progressive expansion of this virus into previously nonendemic regions justifies the implementation of a genomic surveillance program. In this proof-of-concept study, we show the feasibility of sequencing dengue virus genomes directly from positive Ag-RDT (Standard Q Dengue Duo Test assay, n = 7) cassettes stored up to 31 days at room temperature after testing. For 5 of the 7 samples, a high number of reads were obtained allowing phylogenetic analyses to be carried out to determine not only the serotypes (dengue 1, 2, 3 and 4 were detected) but also the genotypes. Furthermore, in one sample, our unbiased metagenomic next-generation sequencing approach made it possible to detect epizootic hemorrhagic disease virus sequences, an arthropod-transmitted virus in ruminants. To conclude, as such an approach requires no cold storage or freezing of samples, dengue Ag-RDTs represent a very pragmatic and robust alternative for the genomic surveillance of dengue virus.
Collapse
Affiliation(s)
- Francisco-Javier Pérez-Rodríguez
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.-J.P.-R.); (F.L.); (V.C.); (L.K.)
- Swiss Reference Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Florian Laubscher
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.-J.P.-R.); (F.L.); (V.C.); (L.K.)
| | - Valentin Chudzinski
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.-J.P.-R.); (F.L.); (V.C.); (L.K.)
| | - Laurent Kaiser
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.-J.P.-R.); (F.L.); (V.C.); (L.K.)
- Swiss Reference Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.-J.P.-R.); (F.L.); (V.C.); (L.K.)
| |
Collapse
|
6
|
Nguyen PV, Carmola LR, Wang E, Bassit L, Rao A, Greenleaf M, Sullivan JA, Martin GS, Lam WA, Waggoner JJ, Piantadosi A. SARS-CoV-2 molecular testing and whole genome sequencing following RNA recovery from used BinaxNOW COVID-19 antigen self tests. J Clin Virol 2023; 162:105426. [PMID: 37028004 PMCID: PMC10036152 DOI: 10.1016/j.jcv.2023.105426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/14/2023] [Accepted: 03/19/2023] [Indexed: 03/25/2023]
Abstract
Widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has led to a decrease in availability of clinical samples for viral genomic surveillance. As an alternative sample source, we evaluated RNA isolated from BinaxNOW swabs stored at ambient temperature for SARS-CoV-2 rRT-PCR and full viral genome sequencing. 81 of 103 samples (78.6%) yielded detectable RNA, and 46 of 57 samples (80.7 %) yielded complete genome sequences. Our results illustrate that SARS-CoV-2 RNA extracted from used Binax test swabs provides an important opportunity for improving SARS-CoV-2 genomic surveillance, evaluating transmission clusters, and monitoring within-patient evolution.
Collapse
Affiliation(s)
- Phuong-Vi Nguyen
- Emory University Department of Medicine, Atlanta, GA, USA; Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
| | | | - Ethan Wang
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA; Emory University Department of Pathology and Laboratory Medicine, Atlanta, GA, USA
| | - Leda Bassit
- Emory University Department of Pathology and Laboratory Medicine, Atlanta, GA, USA; Laboratory of Biochemical Pharmacology, Emory University, Atlanta, GA, USA
| | - Anuradha Rao
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA; Emory University Department of Pediatrics, Atlanta, GA, USA
| | - Morgan Greenleaf
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
| | - Julie A Sullivan
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
| | - Greg S Martin
- Emory University Department of Medicine, Atlanta, GA, USA; Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA
| | - Wilbur A Lam
- Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA; Emory University Department of Pediatrics, Atlanta, GA, USA; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jesse J Waggoner
- Emory University Department of Medicine, Atlanta, GA, USA; Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA.
| | - Anne Piantadosi
- Emory University Department of Medicine, Atlanta, GA, USA; Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, USA; Emory University Department of Pathology and Laboratory Medicine, Atlanta, GA, USA
| |
Collapse
|
7
|
Rector A, Bloemen M, Schiettekatte G, Maes P, Van Ranst M, Wollants E. Sequencing directly from antigen-detection rapid diagnostic tests in Belgium, 2022: a gamechanger in genomic surveillance? Euro Surveill 2023; 28:2200618. [PMID: 36862099 PMCID: PMC9983067 DOI: 10.2807/1560-7917.es.2023.28.9.2200618] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
BackgroundLateral flow antigen-detection rapid diagnostic tests (Ag-RDTs) for viral infections constitute a fast, cheap and reliable alternative to nucleic acid amplification tests (NAATs). Whereas leftover material from NAATs can be employed for genomic analysis of positive samples, there is a paucity of information on whether viral genetic characterisation can be achieved from archived Ag-RDTs.AimTo evaluate the possibility of retrieving leftover material of several viruses from a range of Ag-RDTs, for molecular genetic analysis.MethodsArchived Ag-RDTs which had been stored for up to 3 months at room temperature were used to extract viral nucleic acids for subsequent RT-qPCR, Sanger sequencing and Nanopore whole genome sequencing. The effects of brands of Ag-RDT and of various ways to prepare Ag-RDT material were evaluated.ResultsSARS-CoV-2 nucleic acids were successfully extracted and sequenced from nine different brands of Ag-RDTs for SARS-CoV-2, and for five of these, after storage for 3 months at room temperature. The approach also worked for Ag-RDTs for influenza virus (n = 3 brands), as well as for rotavirus and adenovirus 40/41 (n = 1 brand). The buffer of the Ag-RDT had an important influence on viral RNA yield from the test strip and the efficiency of subsequent sequencing.ConclusionOur finding that the test strip in Ag-RDTs is suited to preserve viral genomic material, even for several months at room temperature, and therefore can serve as source material for genetic characterisation could help improve global coverage of genomic surveillance for SARS-CoV-2 as well as for other viruses.
Collapse
Affiliation(s)
- Annabel Rector
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Mandy Bloemen
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Gilberte Schiettekatte
- Center for Medical Analysis, Department of Molecular Biology and Immunology, Herentals, Belgium
| | - Piet Maes
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Marc Van Ranst
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium,University Hospitals Leuven, Department of Laboratory Medicine, National Reference Center for Respiratory Pathogens, Leuven, Belgium
| | - Elke Wollants
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| |
Collapse
|
8
|
Nguyen PV, Carmola LR, Wang E, Bassit L, Rao A, Greenleaf M, Sullivan JA, Martin GS, Lam WA, Waggoner JJ, Piantadosi A. SARS-CoV-2 molecular testing and whole genome sequencing following RNA recovery from used BinaxNOW COVID-19 Antigen Self Tests. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.09.23284337. [PMID: 36712132 PMCID: PMC9882431 DOI: 10.1101/2023.01.09.23284337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has led to a decrease in availability of clinical samples for viral genomic surveillance. As an alternative sample source, we evaluated RNA isolated from BinaxNOW swabs stored at ambient temperature for SARS-CoV-2 rRT-PCR and full viral genome sequencing. 81 of 103 samples (78.6%) yielded detectable RNA, and 46 of 57 samples (80.7 %) yielded complete genome sequences. Our results illustrate that SARS-CoV-2 RNA extracted from used Binax test swabs provides an important opportunity for improving SARS-CoV-2 genomic surveillance, evaluating transmission clusters, and monitoring within-patient evolution.
Collapse
|
9
|
Han AX, Toporowski A, Sacks JA, Perkins MD, Briand S, van Kerkhove M, Hannay E, Carmona S, Rodriguez B, Parker E, Nichols BE, Russell CA. SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs. Nat Genet 2023; 55:26-33. [PMID: 36624344 PMCID: PMC9839449 DOI: 10.1038/s41588-022-01267-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/11/2022] [Indexed: 01/11/2023]
Abstract
The first step in SARS-CoV-2 genomic surveillance is testing to identify people who are infected. However, global testing rates are falling as we emerge from the acute health emergency and remain low in many low- and middle-income countries (mean = 27 tests per 100,000 people per day). We simulated COVID-19 epidemics in a prototypical low- and middle-income country to investigate how testing rates, sampling strategies and sequencing proportions jointly impact surveillance outcomes, and showed that low testing rates and spatiotemporal biases delay time to detection of new variants by weeks to months and can lead to unreliable estimates of variant prevalence, even when the proportion of samples sequenced is increased. Accordingly, investments in wider access to diagnostics to support testing rates of approximately 100 tests per 100,000 people per day could enable more timely detection of new variants and reliable estimates of variant prevalence. The performance of global SARS-CoV-2 genomic surveillance programs is fundamentally limited by access to diagnostic testing.
Collapse
Affiliation(s)
- Alvin X Han
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
| | - Amy Toporowski
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Jilian A Sacks
- Department of Epidemic and Pandemic Preparedness and Prevention, Emergency Preparedness Programme, World Health Organization, Geneva, Switzerland
| | - Mark D Perkins
- Department of Epidemic and Pandemic Preparedness and Prevention, Emergency Preparedness Programme, World Health Organization, Geneva, Switzerland
| | - Sylvie Briand
- Department of Epidemic and Pandemic Preparedness and Prevention, Emergency Preparedness Programme, World Health Organization, Geneva, Switzerland
| | - Maria van Kerkhove
- Department of Epidemic and Pandemic Preparedness and Prevention, Emergency Preparedness Programme, World Health Organization, Geneva, Switzerland
| | - Emma Hannay
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Sergio Carmona
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Bill Rodriguez
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Brooke E Nichols
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
- Department of Global Health, School of Public Health, Boston University, Boston, MA, USA
| | - Colin A Russell
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
- Department of Global Health, School of Public Health, Boston University, Boston, MA, USA.
| |
Collapse
|
10
|
Martin GE, Taiaroa G, Taouk ML, Savic I, O'Keefe J, Quach R, Prestedge J, Krysiak M, Caly L, Williamson DA. Maintaining genomic surveillance using whole-genome sequencing of SARS-CoV-2 from rapid antigen test devices. THE LANCET. INFECTIOUS DISEASES 2022; 22:1417-1418. [PMID: 35934015 PMCID: PMC9352270 DOI: 10.1016/s1473-3099(22)00512-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 12/24/2022]
Affiliation(s)
- Genevieve E Martin
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - George Taiaroa
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mona L Taouk
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ivana Savic
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jacinta O'Keefe
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Robert Quach
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jacqueline Prestedge
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Marcelina Krysiak
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.
| |
Collapse
|