2023
Method versatility in RNA extraction-free PCR detection of SARS-CoV-2 in saliva samples
Allicock O, Yolda-Carr D, Earnest R, Breban M, Vega N, Ott I, Kalinich C, Alpert T, Petrone M, Wyllie A. Method versatility in RNA extraction-free PCR detection of SARS-CoV-2 in saliva samples. Progress In Biophysics And Molecular Biology 2023, 182: 103-108. PMID: 37369293, PMCID: PMC10290768, DOI: 10.1016/j.pbiomolbio.2023.06.004.Peer-Reviewed Original Research
2022
Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons
Chaguza C, Coppi A, Earnest R, Ferguson D, Kerantzas N, Warner F, Young HP, Breban MI, Billig K, Koch RT, Pham K, Kalinich CC, Ott IM, Fauver JR, Hahn AM, Tikhonova IR, Castaldi C, De Kumar B, Pettker CM, Warren JL, Weinberger DM, Landry ML, Peaper DR, Schulz W, Vogels CBF, Grubaugh ND. Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons. Med 2022, 3: 325-334.e4. PMID: 35399324, PMCID: PMC8983481, DOI: 10.1016/j.medj.2022.03.010.Peer-Reviewed Original ResearchConceptsSpike gene target failureSARS-CoV-2 Omicron variantPositivity rateOmicron variantOmicron infectionVaccine dosesVaccine-induced immunityNumber of dosesTest positivity rateOdds of infectionSARS-CoV-2Significant reductionDominant Delta variantUnvaccinated personsVaccination statusHigher oddsDelta variantInfectionVaccine manufacturersDisease controlVirus copiesDosesPCR testOddsTarget failure
2021
Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2
Vogels CBF, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, Kalinich CC, Earnest R, Rothman JE, de Jesus J, Claro I, Ferreira G, Crispim MAE, Network B, Singh L, Tegally H, Anyaneji UJ, Africa N, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, Grubaugh ND. Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. PLOS Biology 2021, 19: e3001236. PMID: 33961632, PMCID: PMC8133773, DOI: 10.1371/journal.pbio.3001236.Peer-Reviewed Original Research
2020
Detection of SARS-CoV-2 RNA by multiplex RT-qPCR
Kudo E, Israelow B, Vogels CBF, Lu P, Wyllie AL, Tokuyama M, Venkataraman A, Brackney DE, Ott IM, Petrone ME, Earnest R, Lapidus S, Muenker MC, Moore AJ, Casanovas-Massana A, Team Y, Omer SB, Dela Cruz CS, Farhadian SF, Ko AI, Grubaugh ND, Iwasaki A. Detection of SARS-CoV-2 RNA by multiplex RT-qPCR. PLOS Biology 2020, 18: e3000867. PMID: 33027248, PMCID: PMC7571696, DOI: 10.1371/journal.pbio.3000867.Peer-Reviewed Original ResearchMeSH KeywordsBetacoronavirusCase-Control StudiesClinical Laboratory TechniquesCoronavirus InfectionsCOVID-19COVID-19 TestingDNA PrimersHEK293 CellsHumansLimit of DetectionMultiplex Polymerase Chain ReactionNasopharynxPandemicsPneumonia, ViralReagent Kits, DiagnosticReverse Transcriptase Polymerase Chain ReactionRNA, ViralSARS-CoV-2United StatesConceptsSARS-CoV-2 RNAMultiplex RT-qPCRRT-qPCRSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testingSARS-CoV-2Quantitative reverse transcription PCRCycle threshold valuesReverse transcription-PCRRT-qPCR assaysDisease controlMultiplex RT-qPCR assayTranscription-PCRAssaysSingle assayLow copy numberSaliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2
Wyllie AL, Fournier J, Casanovas-Massana A, Campbell M, Tokuyama M, Vijayakumar P, Warren JL, Geng B, Muenker MC, Moore AJ, Vogels CBF, Petrone ME, Ott IM, Lu P, Venkataraman A, Lu-Culligan A, Klein J, Earnest R, Simonov M, Datta R, Handoko R, Naushad N, Sewanan LR, Valdez J, White EB, Lapidus S, Kalinich CC, Jiang X, Kim DJ, Kudo E, Linehan M, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Weizman OE, Wong P, Yang Y, Bermejo S, Odio CD, Omer SB, Dela Cruz CS, Farhadian S, Martinello RA, Iwasaki A, Grubaugh ND, Ko AI. Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2. New England Journal Of Medicine 2020, 383: 1283-1286. PMID: 32857487, PMCID: PMC7484747, DOI: 10.1056/nejmc2016359.Peer-Reviewed Original ResearchAnalytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets
Vogels CBF, Brito AF, Wyllie AL, Fauver JR, Ott IM, Kalinich CC, Petrone ME, Casanovas-Massana A, Catherine Muenker M, Moore AJ, Klein J, Lu P, Lu-Culligan A, Jiang X, Kim DJ, Kudo E, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Tokuyama M, Venkataraman A, Weizman OE, Wong P, Yang Y, Cheemarla NR, White EB, Lapidus S, Earnest R, Geng B, Vijayakumar P, Odio C, Fournier J, Bermejo S, Farhadian S, Dela Cruz CS, Iwasaki A, Ko AI, Landry ML, Foxman EF, Grubaugh ND. Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets. Nature Microbiology 2020, 5: 1299-1305. PMID: 32651556, PMCID: PMC9241364, DOI: 10.1038/s41564-020-0761-6.Peer-Reviewed Original ResearchConceptsSARS-CoV-2SARS-CoV-2 RTSevere acute respiratory syndrome coronavirusAcute respiratory syndrome coronavirusViral RNA copiesPublic health laboratoriesPublic health interventionsReverse transcription-PCR assaySARS-CoV-2 diagnostic testingDiagnostic assaysTranscription-PCR assaySARS-CoV-2 evolutionQuantitative reverse transcription-PCR assaysRapid diagnostic assaysHealth laboratoriesHealth interventionsDiagnostic testingRNA copiesPrimer-probe setsAssaysLow sensitivityCritical needAnalytical sensitivity