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
Daily Rapid Antigen Exit Testing to Tailor University COVID-19 Isolation Policy - Volume 28, Number 12—December 2022 - Emerging Infectious Diseases journal - CDC
Earnest R, Chen C, Chaguza C, Hahn A, Grubaugh N, Wilson M, . Daily Rapid Antigen Exit Testing to Tailor University COVID-19 Isolation Policy - Volume 28, Number 12—December 2022 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2022, 28: 2455-2462. PMID: 36417936, PMCID: PMC9707582, DOI: 10.3201/eid2812.220969.Peer-Reviewed Original ResearchSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Outbreak at a College With High Coronavirus Disease 2019 (COVID-19) Vaccination Coverage—Connecticut, August 2021–September 2021
Bart S, Curtiss CC, Earnest R, Lobe-Costonis R, Peterson H, McWilliams C, Billig K, Hadler JL, Grubaugh ND, Arcelus VJ, Sosa LE. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Outbreak at a College With High Coronavirus Disease 2019 (COVID-19) Vaccination Coverage—Connecticut, August 2021–September 2021. Clinical Infectious Diseases 2022, 75: s243-s250. PMID: 35675696, PMCID: PMC9214140, DOI: 10.1093/cid/ciac422.Peer-Reviewed Original ResearchMeSH KeywordsConnecticutCOVID-19Disease OutbreaksHumansPhylogenySARS-CoV-2Vaccination CoverageVaccinesConceptsSARS-CoV-2 infectionLaboratory-confirmed SARS-CoV-2 infectionSARS-CoV-2 casesHigh vaccination coverageMultivariate logistic regressionDelta variant outbreakSARS-CoV-2 outbreakVaccine seriesVaccination historyVaccination coverageUnvaccinated studentsViral testsVariant outbreakInfected studentsUninfected studentsInfectionWeekly testingLogistic regressionAttack rateConnecticut DepartmentPublic healthViral sourcesViral genome sequencesOutbreakSocial gatheringsCombining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota
Petrone ME, Rothman JE, Breban MI, Ott IM, Russell A, Lasek-Nesselquist E, Badr H, Kelly K, Omerza G, Renzette N, Watkins AE, Kalinich CC, Alpert T, Brito AF, Earnest R, Tikhonova IR, Castaldi C, Kelly JP, Shudt M, Plitnick J, Schneider E, Murphy S, Neal C, Laszlo E, Altajar A, Pearson C, Muyombwe A, Downing R, Razeq J, Niccolai L, Wilson MS, Anderson ML, Wang J, Liu C, Hui P, Mane S, Taylor BP, Hanage WP, Landry ML, Peaper DR, Bilguvar K, Fauver JR, Vogels CBF, Gardner LM, Pitzer VE, St. George K, Adams MD, Grubaugh ND. Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota. Communications Biology 2022, 5: 439. PMID: 35545661, PMCID: PMC9095641, DOI: 10.1038/s42003-022-03347-3.Peer-Reviewed Original ResearchRapid 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 failureComparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA
Earnest R, Uddin R, Matluk N, Renzette N, Turbett SE, Siddle KJ, Loreth C, Adams G, Tomkins-Tinch CH, Petrone ME, Rothman JE, Breban MI, Koch RT, Billig K, Fauver JR, Vogels CBF, Bilguvar K, De Kumar B, Landry ML, Peaper DR, Kelly K, Omerza G, Grieser H, Meak S, Martha J, Dewey HB, Kales S, Berenzy D, Carpenter-Azevedo K, King E, Huard RC, Novitsky V, Howison M, Darpolor J, Manne A, Kantor R, Smole SC, Brown CM, Fink T, Lang AS, Gallagher GR, Pitzer VE, Sabeti PC, Gabriel S, MacInnis BL, Team N, Altajar A, DeJesus A, Brito A, Watkins A, Muyombwe A, Blumenstiel B, Neal C, Kalinich C, Liu C, Loreth C, Castaldi C, Pearson C, Bernard C, Nolet C, Ferguson D, Buzby E, Laszlo E, Reagan F, Vicente G, Rooke H, Munger H, Johnson H, Tikhonova I, Ott I, Razeq J, Meldrim J, Brown J, Wang J, Vostok J, Beauchamp J, Grimsby J, Hall J, Messer K, Larkin K, Vernest K, Madoff L, Green L, Webber L, Gagne L, Ulcena M, Ray M, Fisher M, Barter M, Lee M, DeFelice M, Cipicchio M, Smith N, Lennon N, Fitzgerald N, Kerantzas N, Hui P, Harrington R, Downing R, Haye R, Lynch R, Anderson S, Hennigan S, English S, Cofsky S, Clancy S, Mane S, Ash S, Baez S, Fleming S, Murphy S, Chaluvadi S, Alpert T, Rivard T, Schulz W, Mandese Z, Tewhey R, Adams M, Park D, Lemieux J, Grubaugh N. Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA. Cell Reports Medicine 2022, 3: 100583. PMID: 35480627, PMCID: PMC8913280, DOI: 10.1016/j.xcrm.2022.100583.Peer-Reviewed Original ResearchConceptsEnhanced transmissibilitySARS-CoV-2 variant DeltaSARS-CoV-2 Delta variantViral RNA copiesPublic health programsAlpha infectionDelta infectionEffective reproductive numberDelta variantHealth programsVariant DeltaRNA copiesInfectionAlphaReproductive numberTransmissibilityEpidemiological dynamics
2021
Reply to: A finding of sex similarities rather than differences in COVID-19 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 JB, Odio CD, Farhadian S, Dela Cruz C, Grubaugh ND, Schulz WL, Ring AM, Ko AI, Omer SB, Iwasaki A. Reply to: A finding of sex similarities rather than differences in COVID-19 outcomes. Nature 2021, 597: e10-e11. PMID: 34552250, DOI: 10.1038/s41586-021-03645-6.Peer-Reviewed Original ResearchMultiplex 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 ResearchMultiple Transmission Chains within COVID-19 Cluster, Connecticut, USA, 2020 - Volume 27, Number 10—October 2021 - Emerging Infectious Diseases journal - CDC
Bart S, Flaherty E, Alpert T, Carlson S, Fasulo L, Earnest R, White EB, Dickens N, Brito AF, Grubaugh ND, Hadler JL, Sosa LE. Multiple Transmission Chains within COVID-19 Cluster, Connecticut, USA, 2020 - Volume 27, Number 10—October 2021 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2021, 27: 2669-2672. PMID: 34545794, PMCID: PMC8462310, DOI: 10.3201/eid2710.211196.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 ResearchSex 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 cytokinesLongitudinal analyses reveal immunological misfiring in severe COVID-19
Lucas C, Wong P, Klein J, Castro TBR, Silva J, Sundaram M, Ellingson MK, Mao T, Oh JE, Israelow B, Takahashi T, Tokuyama M, Lu P, Venkataraman A, Park A, Mohanty S, Wang H, Wyllie AL, Vogels CBF, Earnest R, Lapidus S, Ott IM, Moore AJ, Muenker MC, Fournier JB, Campbell M, Odio CD, Casanovas-Massana A, Herbst R, Shaw A, Medzhitov R, Schulz W, Grubaugh N, Dela Cruz C, Farhadian S, Ko A, Omer S, Iwasaki A. Longitudinal analyses reveal immunological misfiring in severe COVID-19. Nature 2020, 584: 463-469. PMID: 32717743, PMCID: PMC7477538, DOI: 10.1038/s41586-020-2588-y.Peer-Reviewed Original ResearchConceptsSevere COVID-19Moderate COVID-19Immune signaturesDisease outcomeCOVID-19Disease trajectoriesInterleukin-5Early immune signaturesInnate cell lineagesType 2 effectorsT cell numbersPoor clinical outcomeWorse disease outcomesImmune response profileCoronavirus disease 2019Distinct disease trajectoriesCytokine levelsImmunological correlatesImmune profileClinical outcomesEarly elevationImmune profilingIL-13Immunoglobulin EDisease 2019Analytical 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