Multiplex qPCR Discriminates Variants of Concern to Enhance Global Surveillance of SARS-CoV-2

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Tipo de produção
bookPart
Data de publicação
2023
DOI
Scopus
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Título do Volume
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JENNY STANFORD PUBLISHING
Autores
VOGELS, C. B. F.
BREBAN, M. I.
OTT, I. M.
ALPERT, T.
PETRONE, M. E.
WATKINS, A. E.
KALINICH, C. C.
EARNEST, R.
ROTHMAN, J. E.
Citação
Vogels, C. B. F.; Breban, M. I.; Ott, I. M.; Alpert, T.; Petrone, M. E.; Watkins, A. E.; Kalinich, C. C.; Earnest, R.; Rothman, J. E.; de Jesus, J. G.; Claro, I. M.; Ferreir, G. M.; Crispim, M. A. E.; Singh, L.; Tegally, H.; Anyaneji, U. J.; Hodcrof, E. B.; Mason, C. E.; Khullar, G.; Metti, J.; Dudley, J. T.; MacKay, M. J.; Nash, M.; Wang, J.; Liu, C.; Hui, P.; Murphy, S.; Neal, C.; Laszlo, E.; Landry, M. L.; Muyombwe, A.; Downing, R.; Razeq, J.; de Oliveira, T.; Faria, N. R.; Sabino, E. C.; Neher, R. A.; Fauver, J. R.; Grubaugh, N. D.. Multiplex qPCR Discriminates Variants of Concern to Enhance Global Surveillance of SARS-CoV-2. In: . Advances in Medical Imaging, Detection, and Diagnosis: JENNY STANFORD PUBLISHING, 2023. p.891-905.
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Resumo
Broadly accessible and inexpensive surveillance methods are needed to track Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOC) around the world. While sequencing is the gold standard to identify circulating SARS-CoV-2 variants, routine genomic surveillance is not available in many locations primarily due to a lack of resources and expertise. The Institutional Review Board from the Yale University Human Research Protection Program determined that the RT-qPCR testing and sequencing of de-identified remnant COVID-19 clinical samples conducted in this study is not research involving human patients. Multiplex-PCR products were purified by using AmpureXP beads, and quantification was carried out using the Qubit dsDNA High Sensitivity assay on the Qubit 3.0. © 2023 Jenny Stanford Publishing Pte. Ltd.
Palavras-chave
complementary DNA (cDNA), Coronavirus Disease 2019 (COVID-19), cycle threshold (Ct), global initiative on sharing avian influenza data (GISAID), Institutional Review Board (IRB), open reading frame (ORF), reverse transcriptase quantitative PCR (RT-qPCR), Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), spike gene target failure (SGTF), variants of concern (VOC), variants of interest (VOI)
URI
https://observatorio.fm.usp.br/handle/OPI/57196
Referências
  1. Davies N.G., Barnard R.C., Jarvis C.I., Kucharski A.J., Munday J., Pearson C.A.B., Et al., Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England
  2. Rambaut A., Loman N., Pybus O.B.W., Barrett J., Carabelli A., Connor T., Et al., Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations, (2020)
  3. Lauring A.S., Hodcroft E.B., Genetic variants of SARS-CoV-2-What do they mean?, JAMA, 325, 6, pp. 529-531, (2021)
  4. Borges V., Sousa C., Menezes L., Aaoa M.G., Picao M., Almeida J.P., Et al., Tracking SARS-CoV-2 VOC 202012/01 (lineage B.1.1.7) dissemination in Portugal: Insights from nationwide RT-PCR Spike gene drop out data, (2021)
  5. Volz E., Mishra S., Chand M., Barrett J.C., Johnson R., Geidelberg L., Et al., Transmission of SARS-CoV-2 lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data, (2021)
  6. Solutions for surveillance of the S gene mutation in the B.1.1.7 (501Y.V1) SARS-CoV-2 strain lineage, (2020)
  7. Kidd M., Richter A., Best A., Mirza J., Percival B., Mayhew M., Et al., S-variant SARS-CoV-2 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-QPCR, (2020)
  8. Galloway S.E., Paul P., MacCannell D.R., Johansson M.A., Brooks J.T., MacNeil A., Et al., Emergence of SARS-CoV-2 B.1.1.7 lineage-United States, December 29, 2020-January 12, 2021, MMWR Morb Mortal Wkly Rep, 70, pp. 95-99, (2021)
  9. Moreno G., Braun K., Larsen B.B., Alpert T., Worobey M., Grubaugh N., Et al., Detection of non-B.1.1.7 spike Δ69/70 sequences (B.1.375) in the United States, (2021)
  10. Larsen B.B., Worobey M., Identification of a novel SARS-CoV-2 Spike 69-70 deletion lineage circulating in the United States, (2020)
  11. Tegally H., Wilkinson E., Giovanetti M., Iranzadeh A., Fonseca V., Giandhari J., Et al., Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa, (2020)
  12. Faria N.R., Iaoa M.C., Candido D., La M.F., Andrade P.S., Coletti T.M., Et al., Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: Preliminary findings, (2021)
  13. Greaney A.J., Loes A.N., Crawford K.H.D., Starr T.N., Malone K.D., Chu H.Y., Et al., Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies, Cell Host Microbe, 29, 3, pp. 463-476.e6, (2021)
  14. Hadfield J., Megill C., Bell S.M., Huddleston J., Potter B., Callender C., Et al., Nextstrain: Real-time tracking of pathogen evolution, Bioinformatics, 34, pp. 4121-4123, (2018)
  15. Lu X., Wang L., Sakthivel S.K., Whitaker B., Murray J., Kamili S., Et al., US CDC real-time reverse transcription PCR panel for detection of severe acute respiratory syndrome coronavirus 2, Emerg Infect Dis, 26, 8, (2020)
  16. Kudo E., Israelow B., Vogels C.B.F., Lu P., Wyllie A.L., Tokuyama M., Et al., Detection of SARS-CoV-2 RNA by multiplex RT-qPCR, (2020)
  17. Vogels C., Fauver J., Grubaugh N., Multiplexed RT-qPCR to screen for SARS-COV-2 B.1.1.7, B.1.351, and P.1 variants of concern v3. protocols.io, (2021)
  18. Lasek-Nesselquist E., Lapierre P., Schneider E., St George K., Pata J., The localized rise of a B.1.526 variant containing an E484K mutation in New York State, (2021)
  19. Deng X., Garcia-Knight M.A., Khalid M.M., Servellita V., Wang C., Morris M.K., Et al., Trans-mission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation
  20. Quick J., nCoV-2019 sequencing protocol v3, (2020)
  21. Quick J., Grubaugh N.D., Pullan S.T., Claro I.M., Smith A.D., Gangavarapu K., Et al., Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples, Nat Protoc, 12, pp. 1261-2176, (2017)
  22. Artic Network, (2020)
  23. Artic Network, (2020)
  24. Rambaut A., Holmes E.C., O'Toole A., Hill V., McCrone J.T., Ruis C., Et al., A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology, Nat Microbiol, 5, pp. 1403-1407, (2020)
  25. Tyson J.R., Phillip J., Stoddart D., Sparks N., Wickenhagen A., Hall G., Et al., Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore, (2020)

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Livros e Capítulos de Livros - FM/MIP
Livros e Capítulos de Livros - LIM/46
Livros e Capítulos de Livros - ODS/03