2023
Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients
Diray-Arce J, Fourati S, Jayavelu N, Patel R, Maguire C, Chang A, Dandekar R, Qi J, Lee B, van Zalm P, Schroeder A, Chen E, Konstorum A, Brito A, Gygi J, Kho A, Chen J, Pawar S, Gonzalez-Reiche A, Hoch A, Milliren C, Overton J, Westendorf K, Network I, Abraham J, Adkisson M, Albert M, Torres L, Alvarenga B, Anderson M, Anderson E, Arnett A, Asashima H, Atkinson M, Baden L, Barton B, Beach K, Beagle E, Becker P, Bell M, Bernui M, Bime C, Kumar A, Booth L, Borresen B, Brakenridge S, Bristow L, Bryant R, Calfee C, Manuel J, Carrillo S, Chak S, Chang I, Connors J, Conway M, Corry D, Cowan D, Croen B, Dela Cruz C, Cusimano G, Eaker L, Edwards C, Ehrlich L, Elashoff D, Erickson H, Erle D, Farhadian S, Farrugia K, Fatou B, Fernandes A, Fernandez-Sesma A, Fragiadakis G, Furukawa S, Geltman J, Ghale R, Bermúdez M, Goonewardene M, Sanchez E, Guirgis F, Hafler D, Hamilton S, Harris P, Nemati A, Hendrickson C, Agudelo N, Hodder T, Holland S, Hough C, Huerta C, Hurley K, Hutton S, Iwasaki A, Jauregui A, Jha M, Johnson B, Joyner D, Kangelaris K, Kelly G, Khalil Z, Khan Z, Kheradmand F, Kim J, Kimura H, Ko A, Kohr B, Kraft M, Krummel M, Kutzler M, Lasky-Su J, Lee S, Lee D, Leipold M, Lentucci C, Leroux C, Lin E, Liu S, Love C, Lu Z, Maliskova L, Roth B, Manohar M, Martens M, McComsey G, McEnaney K, McLin R, Melamed E, Melnyk N, Mendez K, Messer W, Metcalf J, Michelotti G, Mick E, Mohanty S, Mosier J, Mulder L, Murphy M, Nadeau K, Nelson E, Nelson A, Nguyen V, Oberhaus J, Panganiban B, Pellegrini K, Pickering H, Powell D, Presnell S, Pulendran B, Rahman A, Sadeed A, Raskin A, Reed E, Pereira S, Rivera A, Rogers J, Rogers A, Rogowski B, Rooks R, Rosenberg-Hasson Y, Rothman J, Rousseau J, Salehi-Rad R, Saluvan M, Samaha H, Schaenman J, Schunk R, Semenza N, Sen S, Sevransky J, Seyfert-Margolis V, Shaheen T, Shaw A, Sieg S, Siegel S, Sigal N, Siles N, Simmons B, Simon V, Singh G, Sinko L, Smith C, Smolen K, Song L, Srivastava K, Sullivan P, Syphurs C, Tcheou J, Tegos G, Tharp G, Ally A, Tsitsiklis A, Ungaro R, Vaysman T, Viode A, Vita R, Wang X, Ward A, Ward D, Willmore A, Woloszczuk K, Wong K, Woodruff P, Xu L, van Haren S, van de Guchte A, Zhao Y, Cairns C, Rouphael N, Bosinger S, Kim-Schulze S, Krammer F, Rosen L, Grubaugh N, van Bakel H, Wilson M, Rajan J, Steen H, Eckalbar W, Cotsapas C, Langelier C, Levy O, Altman M, Maecker H, Montgomery R, Haddad E, Sekaly R, Esserman D, Ozonoff A, Becker P, Augustine A, Guan L, Peters B, Kleinstein S. Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients. Cell Reports Medicine 2023, 4: 101079. PMID: 37327781, PMCID: PMC10203880, DOI: 10.1016/j.xcrm.2023.101079.Peer-Reviewed Original ResearchConceptsDisease courseFatal COVID-19 diseaseHospitalized COVID-19 patientsSevere disease courseCOVID-19 participantsCOVID-19 patientsTrajectory groupsHost immune responseCOVID-19 diseaseImmune correlatesAcute infectionClinical courseHospital admissionClinical outcomesFatal outcomeClinical prognosisImmune responseSevere diseaseLongitudinal bloodNasal samplesBiologic stateLongitudinal studyDistinct assaysCohortMolecular signatures
2022
Change in covid-19 risk over time following vaccination with CoronaVac: test negative case-control study
Hitchings MDT, Ranzani OT, Lind ML, Dorion M, D'Agostini TL, de Paula RC, de Paula OFP, de Moura Villela EF, Scaramuzzini Torres MS, de Oliveira SB, Schulz W, Almiron M, Said R, de Oliveira RD, Vieira da Silva P, de Araújo WN, Gorinchteyn JC, Dean NE, Andrews JR, Cummings DAT, Ko AI, Croda J. Change in covid-19 risk over time following vaccination with CoronaVac: test negative case-control study. The BMJ 2022, 377: e070102. PMID: 35697361, PMCID: PMC9189440, DOI: 10.1136/bmj-2022-070102.Peer-Reviewed Original ResearchConceptsSymptomatic COVID-19Negative case-control studyCase-control studyHospital admissionOdds ratioCOVID-19Series completionCovid-19 related hospital admissionReverse transcription polymerase chain reaction testingTranscription polymerase chain reaction testingSevere COVID-19 outcomesSARS-CoV-2 infectionPolymerase chain reaction testingInactivated whole virus vaccineDoses of CoronaVacAcute respiratory illnessTest-negative controlsWhole virus vaccineRelated hospital admissionsHealthcare worker statusConditional logistic regressionCOVID-19 outcomesCOVID-19 symptomsMunicipality of residenceSARS-CoV-2
2021
Effectiveness of the CoronaVac vaccine in older adults during a gamma variant associated epidemic of covid-19 in Brazil: test negative case-control study
Ranzani OT, Hitchings MDT, Dorion M, D'Agostini TL, de Paula RC, de Paula OFP, Villela EFM, Torres MSS, de Oliveira SB, Schulz W, Almiron M, Said R, de Oliveira RD, Vieira da Silva P, de Araújo WN, Gorinchteyn JC, Andrews JR, Cummings DAT, Ko AI, Croda J. Effectiveness of the CoronaVac vaccine in older adults during a gamma variant associated epidemic of covid-19 in Brazil: test negative case-control study. The BMJ 2021, 374: n2015. PMID: 34417194, PMCID: PMC8377801, DOI: 10.1136/bmj.n2015.Peer-Reviewed Original ResearchConceptsSymptomatic COVID-19Negative case-control studyCase-control studyHospital admissionVaccine effectivenessSecond doseDose regimenElderly populationCOVID-19Reverse transcription polymerase chain reaction testingTranscription polymerase chain reaction testingPolymerase chain reaction testingGamma variantInactivated whole virus vaccineAdjusted vaccine effectivenessTest-negative controlsWhole virus vaccineCOVID-19 statusCOVID-19 symptomsYounger age groupsMunicipality of residenceSARS-CoV-2RT-PCR testSelf-reported raceCoronaVac vaccine
2020
Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics
Peccia J, Zulli A, Brackney DE, Grubaugh ND, Kaplan EH, Casanovas-Massana A, Ko AI, Malik AA, Wang D, Wang M, Warren JL, Weinberger DM, Arnold W, Omer SB. Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics. Nature Biotechnology 2020, 38: 1164-1167. PMID: 32948856, PMCID: PMC8325066, DOI: 10.1038/s41587-020-0684-z.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 positive test resultsSARS-CoV-2 RNAPositive test resultsHospital admissionSpecimen collectionCOVID-19 hospital admissionsLocal hospital admissionsSARS-CoV-2 RNA concentrationsCoronavirus disease 2019 (COVID-19) outbreakRNA concentrationDisease 2019 outbreakClinical test resultsInfection surveillanceInfection dynamicsPositive testPopulation-wide levelCommunity infection dynamicsAdmissionNew Haven