2023
Pooled RNA-extraction-free testing of saliva for the detection of SARS-CoV-2
Allicock O, Yolda-Carr D, Todd J, Wyllie A. Pooled RNA-extraction-free testing of saliva for the detection of SARS-CoV-2. Scientific Reports 2023, 13: 7426. PMID: 37156888, PMCID: PMC10165292, DOI: 10.1038/s41598-023-34662-2.Peer-Reviewed Original ResearchConceptsSARS-CoV-2RT-qPCR assaysSARS-CoV-2 testingVirus-infected individualsAged care facilitiesSelf-collected salivaSARS-CoV-2 spreadActionable time frameAsymptomatic individualsTest turnaround timeHealthcare workersGeneral populationCare facilitiesTest availabilityWeekly testingFree testingClinical salivaPositive agreementClinical laboratoriesSalivaCT valuesSuch testingTesting workflowIndividual testingTesting protocol
2022
Evaluation of the Liberty16 Mobile Real Time PCR Device for Use With the SalivaDirect Assay for SARS-CoV-2 Testing
Yolda-Carr D, Thammavongsa DA, Vega N, Turner SJ, Pickering PJ, Wyllie AL. Evaluation of the Liberty16 Mobile Real Time PCR Device for Use With the SalivaDirect Assay for SARS-CoV-2 Testing. Frontiers In Cellular And Infection Microbiology 2022, 11: 808773. PMID: 35118013, PMCID: PMC8804088, DOI: 10.3389/fcimb.2021.808773.Peer-Reviewed Original ResearchConceptsLimit of detectionReal-time PCR deviceSARS-CoV-2 testingSmall portable devicesPCR devicePortable devicesSARS-CoV-2 detectionHigh sensitivitySARS-CoV-2 RNADevicesInfectious respiratory diseaseSARS-CoV-2Low-resource settingsRespiratory diseaseImplementation of testingFurther optimizationSaliva samplesProtocolGold standardRT-qPCRTimely accessCOVID-19 pandemicDetectionLOD rangeSensitivity
2021
Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications.
Moore KJM, Cahill J, Aidelberg G, Aronoff R, Bektaş A, Bezdan D, Butler DJ, Chittur SV, Codyre M, Federici F, Tanner NA, Tighe SW, True R, Ware SB, Wyllie AL, Afshin EE, Bendesky A, Chang CB, Dela Rosa R, Elhaik E, Erickson D, Goldsborough AS, Grills G, Hadasch K, Hayden A, Her SY, Karl JA, Kim CH, Kriegel AJ, Kunstman T, Landau Z, Land K, Langhorst BW, Lindner AB, Mayer BE, McLaughlin LA, McLaughlin MT, Molloy J, Mozsary C, Nadler JL, D'Silva M, Ng D, O'Connor DH, Ongerth JE, Osuolale O, Pinharanda A, Plenker D, Ranjan R, Rosbash M, Rotem A, Segarra J, Schürer S, Sherrill-Mix S, Solo-Gabriele H, To S, Vogt MC, Yu AD, Mason CE. Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications. Journal Of Biomolecular Techniques 2021, 32: 228-275. PMID: 35136384, PMCID: PMC8802757, DOI: 10.7171/jbt.21-3203-017.Peer-Reviewed Original ResearchUnderstanding the Barriers to Pooled SARS-CoV-2 Testing in the United States
Fenichel EP, Koch RT, Gilbert A, Gonsalves G, Wyllie AL. Understanding the Barriers to Pooled SARS-CoV-2 Testing in the United States. Microbiology Spectrum 2021, 9: e00312-21. PMID: 34378949, PMCID: PMC8552767, DOI: 10.1128/spectrum.00312-21.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 testingSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detectionPooled testingPooled testing strategyClinical Laboratory Improvement AmendmentsTraditional diagnostic testingEmergence of variantsTesting strategiesDiagnostic testingVirus resurgenceEarly detectionClear protocolsTest capacityTesting capacityUnited StatesTest priceSurveillance measuresTest reportingMajor barrierUptakeAdequate resourcesResponseTestingTesting programU.S. laboratoriesStability of SARS-CoV-2 RNA in Nonsupplemented Saliva - Volume 27, Number 4—April 2021 - Emerging Infectious Diseases journal - CDC
Ott IM, Strine MS, Watkins AE, Boot M, Kalinich CC, Harden CA, Vogels CBF, Casanovas-Massana A, Moore AJ, Muenker MC, Nakahata M, Tokuyama M, Nelson A, Fournier J, Bermejo S, Campbell M, Datta R, Dela Cruz CS, Farhadian SF, Ko AI, Iwasaki A, Grubaugh ND, Wilen CB, Wyllie AL, . Stability of SARS-CoV-2 RNA in Nonsupplemented Saliva - Volume 27, Number 4—April 2021 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2021, 27: 1146-1150. PMID: 33754989, PMCID: PMC8007305, DOI: 10.3201/eid2704.204199.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 numberSex differences in immune responses that underlie COVID-19 disease outcomes
Takahashi T, Ellingson MK, Wong P, Israelow B, Lucas C, Klein J, Silva J, Mao T, Oh JE, Tokuyama M, Lu P, Venkataraman A, Park A, Liu F, Meir A, Sun J, Wang EY, Casanovas-Massana A, Wyllie AL, Vogels CBF, Earnest R, Lapidus S, Ott IM, Moore AJ, Shaw A, Fournier J, Odio C, Farhadian S, Dela Cruz C, Grubaugh N, Schulz W, Ring A, Ko A, Omer S, Iwasaki A. Sex differences in immune responses that underlie COVID-19 disease outcomes. Nature 2020, 588: 315-320. PMID: 32846427, PMCID: PMC7725931, DOI: 10.1038/s41586-020-2700-3.Peer-Reviewed Original ResearchConceptsInnate immune cytokinesFemale patientsMale patientsImmune cytokinesDisease outcomeImmune responseCOVID-19COVID-19 disease outcomesPoor T cell responsesSARS-CoV-2 infectionSevere acute respiratory syndrome coronavirusAcute respiratory syndrome coronavirusSex-based approachModerate COVID-19Sex differencesRobust T cell activationT cell responsesWorse disease progressionWorse disease outcomesHigher plasma levelsNon-classical monocytesCoronavirus disease 2019T cell activationImmunomodulatory medicationsPlasma cytokinesSARS-CoV-2 infection of the placenta
Hosier H, Farhadian SF, Morotti RA, Deshmukh U, Lu-Culligan A, Campbell KH, Yasumoto Y, Vogels C, Casanovas-Massana A, Vijayakumar P, Geng B, Odio CD, Fournier J, Brito AF, Fauver JR, Liu F, Alpert T, Tal R, Szigeti-Buck K, Perincheri S, Larsen C, Gariepy AM, Aguilar G, Fardelmann KL, Harigopal M, Taylor HS, Pettker CM, Wyllie AL, Dela Cruz CS, Ring AM, Grubaugh ND, Ko AI, Horvath TL, Iwasaki A, Reddy UM, Lipkind HS. SARS-CoV-2 infection of the placenta. Journal Of Clinical Investigation 2020, 130: 4947-4953. PMID: 32573498, PMCID: PMC7456249, DOI: 10.1172/jci139569.Peer-Reviewed Case Reports and Technical NotesMeSH KeywordsAbortion, TherapeuticAbruptio PlacentaeAdultBetacoronavirusCoronavirus InfectionsCOVID-19FemaleHumansMicroscopy, Electron, TransmissionPandemicsPhylogenyPlacentaPneumonia, ViralPre-EclampsiaPregnancyPregnancy Complications, InfectiousPregnancy Trimester, SecondRNA, ViralSARS-CoV-2Viral LoadConceptsSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2SARS-CoV-2 infectionRespiratory syndrome coronavirus 2SARS-CoV-2 invasionMaternal antibody responseSymptomatic COVID-19Second trimester pregnancySyndrome coronavirus 2Coronavirus disease 2019Materno-fetal interfaceDense macrophage infiltratesPlacental abruptionSevere preeclampsiaMacrophage infiltratesSevere morbidityTrimester pregnancyPregnant womenCoronavirus 2Antibody responseBackgroundThe effectsDisease 2019Histological examinationImmunohistochemical assaysPlacentaAnalytical 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