2024
A low-cost culture- and DNA extraction-free method for the molecular detection of pneumococcal carriage in saliva
Peno C, Lin T, Hislop M, Yolda-Carr D, Farjado K, York A, Pitzer V, Weinberger D, Bei A, Allicock O, Wyllie A. A low-cost culture- and DNA extraction-free method for the molecular detection of pneumococcal carriage in saliva. Microbiology Spectrum 2024, 12: e00591-24. PMID: 39028185, PMCID: PMC11370248, DOI: 10.1128/spectrum.00591-24.Peer-Reviewed Original ResearchDetection of pneumococciDetection of pneumococcal carriagePneumococcal carriageCarriage surveillanceLow-resource settingsChildren attending childcare centersCarriage of pneumococciDNA extractionSaliva samplesMolecular methodsCultural enrichmentImprove surveillance effortsQPCR-based protocolPneumococcal vaccineExtraction-free methodMolecular detectionNucleic acid extractionVaccination strategiesPneumococciCulture-enrichment methodExtraction-free protocolPurified DNASalivaPaired samplesCarriage
2023
649. Expansion Of A Low-Cost, Open-Source, Saliva-Based PCR Test For The Detection Of Mpox Virus
Thomas R, Yolda-Carr D, Steel S, Tobik E, Zepeda T, Brownlee M, Saladi S, Parkin J, Fajardo K, Allicock O, Wyllie A. 649. Expansion Of A Low-Cost, Open-Source, Saliva-Based PCR Test For The Detection Of Mpox Virus. Open Forum Infectious Diseases 2023, 10: ofad500.712. PMCID: PMC10677374, DOI: 10.1093/ofid/ofad500.712.Peer-Reviewed Original Research881. Saliva-Based, Extraction-Free PCR Testing For The Detection Of Key Respiratory Pathogens
Allicock O, Lin T, Fajardo K, Yolda-Carr D, Hislop M, Wang J, Zuniga D, Platt W, Tuohy B, Peno C, Wyllie A. 881. Saliva-Based, Extraction-Free PCR Testing For The Detection Of Key Respiratory Pathogens. Open Forum Infectious Diseases 2023, 10: ofad500.926. PMCID: PMC10677551, DOI: 10.1093/ofid/ofad500.926.Peer-Reviewed Original ResearchSARS-CoV-2Saliva samplesRespiratory virusesRespiratory pathogensSARS-CoV-2 PCR testInfluenza A/BSARS-CoV-2 testingUpper respiratory tract pathogensAdditional respiratory virusesDetection of hMPVMass testing strategyPCR testCommon respiratory virusesCommon respiratory pathogensRespiratory tract pathogensKey respiratory pathogensYears of ageSARS-CoV-2 detectionGrant/research supportTransmissible infectious diseasesUse of salivaYale HealthRespiratory symptomsInfluenza B.Nasopharyngeal swabsThe potential of saliva as an accessible and sensitive sample type for the detection of respiratory pathogens and host immunity
Laxton C, Peno C, Hahn A, Allicock O, Perniciaro S, Wyllie A. The potential of saliva as an accessible and sensitive sample type for the detection of respiratory pathogens and host immunity. The Lancet Microbe 2023, 4: e837-e850. PMID: 37516121, DOI: 10.1016/s2666-5247(23)00135-0.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsSARS-CoV-2Respiratory pathogensPotential of salivaUsefulness of salivaUse of salivaRespiratory specimenRespiratory secretionsDisease burdenImmunological componentsImmunity surveillanceClinical utilityHost immunityClinical useDiagnostic testsNon-invasive natureSalivaCOVID-19 pandemicSample typesMethodological factorsPathogensImmunitySecretionMethod 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 ResearchPooled 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 protocolHigh Levels of Detection of Nonpneumococcal Species of Streptococcus in Saliva from Adults in the United States
Hislop M, Allicock O, Thammavongsa D, Mbodj S, Nelson A, Shaw A, Weinberger D, Wyllie A. High Levels of Detection of Nonpneumococcal Species of Streptococcus in Saliva from Adults in the United States. Microbiology Spectrum 2023, 11: e05207-22. PMID: 37067447, PMCID: PMC10269540, DOI: 10.1128/spectrum.05207-22.Peer-Reviewed Original ResearchPersistence of Pneumococcal Carriage among Older Adults in the Community despite COVID-19 Mitigation Measures
Wyllie A, Mbodj S, Thammavongsa D, Hislop M, Yolda-Carr D, Waghela P, Nakahata M, Stahlfeld A, Vega N, York A, Allicock O, Wilkins G, Ouyang A, Siqueiros L, Strong Y, Anastasio K, Alexander-Parrish R, Arguedas A, Gessner B, Weinberger D. Persistence of Pneumococcal Carriage among Older Adults in the Community despite COVID-19 Mitigation Measures. Microbiology Spectrum 2023, 11: e04879-22. PMID: 37036377, PMCID: PMC10269788, DOI: 10.1128/spectrum.04879-22.Peer-Reviewed Original ResearchConceptsInvasive pneumococcal diseasePneumococcal diseaseSchool-aged childrenOlder adultsPneumococcal carriageSaliva samplesCOVID-19 pandemicRate of carriageCOVID-19-related disruptionsUpper respiratory tractRegular contactNew Haven areaFirst yearCarriage prevalencePre-pandemic levelsMedical historyRespiratory tractHigh prevalenceStreptococcus pneumoniaeCOVID-19 mitigation measuresStudy participantsPneumococciPrevalenceDiseaseCarriageDeficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS
Guo C, Che X, Briese T, Ranjan A, Allicock O, Yates R, Cheng A, March D, Hornig M, Komaroff A, Levine S, Bateman L, Vernon S, Klimas N, Montoya J, Peterson D, Lipkin W, Williams B. Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS. Cell Host & Microbe 2023, 31: 288-304.e8. PMID: 36758522, PMCID: PMC10183837, DOI: 10.1016/j.chom.2023.01.004.Peer-Reviewed Original ResearchConceptsME/CFSFaecalibacterium prausnitziiMyalgic encephalomyelitis/chronic fatigue syndromeFecal short-chain fatty acidsChronic fatigue syndromeShort-chain fatty acidsGut microbiome diversityGut dysbiosisGastrointestinal disturbancesTherapeutic trialsFatigue severityFatigue syndromeOrthostatic intoleranceValidation cohortHealthy controlsCognitive dysfunctionFatigue symptomsGut microbiomeDiverse cohortButyrate producersHuman gutPossible targetsEubacterium rectaleCohortMulti-omics analysis
2022
Saliva-based methods for SARS-CoV-2 testing in low- and middle-income countries
Tan S, Allicock O, Katamba A, Carrington C, Wyllie A, Armstrong-Hough M. Saliva-based methods for SARS-CoV-2 testing in low- and middle-income countries. Bulletin Of The World Health Organization 2022, 100: 808-814. PMID: 36466209, PMCID: PMC9706358, DOI: 10.2471/blt.22.288526.Peer-Reviewed Original ResearchImpact of Temporary Storage Conditions on the Viability of Streptococcus pneumoniae in Saliva
Allicock O, York A, Waghela P, Yolda-Carr D, Weinberger D, Wyllie A. Impact of Temporary Storage Conditions on the Viability of Streptococcus pneumoniae in Saliva. MSphere 2022, 7: e00331-22. PMID: 36409104, PMCID: PMC9769876, DOI: 10.1128/msphere.00331-22.Peer-Reviewed Original ResearchSaliva as an alternative to nasopharyngeal swabs for detection of respiratory syncytial virus (RSV) in children
Langedijk A, Allicock O, Van Wijk M, Yolda-Carr D, Weinberger D, Wyllie A, Bont L. Saliva as an alternative to nasopharyngeal swabs for detection of respiratory syncytial virus (RSV) in children. 2022, 4519. DOI: 10.1183/13993003.congress-2022.4519.Peer-Reviewed Original ResearchSaliva as a sample type for SARS-CoV-2 detection: implementation successes and opportunities around the globe
Tobik ER, Kitfield-Vernon LB, Thomas RJ, Steel SA, Tan SH, Allicock OM, Choate BL, Akbarzada S, Wyllie AL. Saliva as a sample type for SARS-CoV-2 detection: implementation successes and opportunities around the globe. Expert Review Of Molecular Diagnostics 2022, 22: 519-535. PMID: 35763281, DOI: 10.1080/14737159.2022.2094250.Peer-Reviewed Original ResearchEvaluation of saliva self-collection devices for SARS-CoV-2 diagnostics
Allicock OM, Petrone ME, Yolda-Carr D, Breban M, Walsh H, Watkins AE, Rothman JE, Farhadian SF, Grubaugh ND, Wyllie AL. Evaluation of saliva self-collection devices for SARS-CoV-2 diagnostics. BMC Infectious Diseases 2022, 22: 284. PMID: 35337266, PMCID: PMC8953967, DOI: 10.1186/s12879-022-07285-7.Peer-Reviewed Original Research
2021
362. Saliva as a Reliable Sample Type for Mass SARS-CoV-2 Testing Strategies
Wyllie A, Vogels C, Allicock O, Watkins A, Petrone M, Yolda-Carr D, Harden C, Brackney D, Kalinich C, Breban M, Ott I, Sikka R, Kadiri L, Grubaugh N. 362. Saliva as a Reliable Sample Type for Mass SARS-CoV-2 Testing Strategies. Open Forum Infectious Diseases 2021, 8: 284-284. PMCID: PMC8644416, DOI: 10.1093/ofid/ofab466.563.Peer-Reviewed Original Research1321. Acquisition and Transmission of Streptococcus pneumoniae in Individuals Over the Age of 60 Years Residing in New Haven, CT, USA
Wyllie A, Mbodj S, Yolda-Carr D, Thammavongsa D, Waghela P, Nakahata M, Vega N, York A, Allicock O, Alexander-Parrish R, Arguedas A, Gessner B, Weinberger D, Hislop M. 1321. Acquisition and Transmission of Streptococcus pneumoniae in Individuals Over the Age of 60 Years Residing in New Haven, CT, USA. Open Forum Infectious Diseases 2021, 8: 749-749. PMCID: PMC8689704, DOI: 10.1093/ofid/ofab466.1513.Peer-Reviewed Original ResearchPneumococcal carriageSaliva samplesOlder adultsPreventative public health measuresPneumococcal conjugate vaccineNew Haven areaPublic health measuresPneumococcal acquisitionPneumococcal diseaseConjugate vaccinePneumococcal transmissionStudy enrollmentMedical historyImportant burdenDemonstrate evidenceStreptococcus pneumoniaeHealth measuresMultiple timepointsTime pointsWeeksAdultsCOVID-19 pandemicAgeHigh ratePneumococciSaliva as a gold-standard sample for SARS-CoV-2 detection
Tan SH, Allicock O, Armstrong-Hough M, Wyllie AL. Saliva as a gold-standard sample for SARS-CoV-2 detection. The Lancet Respiratory Medicine 2021, 9: 562-564. PMID: 33887248, PMCID: PMC8055204, DOI: 10.1016/s2213-2600(21)00178-8.Peer-Reviewed Original ResearchNovel murine models for studying Cache Valley virus pathogenesis and in utero transmission
López K, Wilson S, Coutermash-Ott S, Tanelus M, Stone W, Porier D, Auguste D, Muller J, Allicock O, Paulson S, Erasmus J, Auguste A. Novel murine models for studying Cache Valley virus pathogenesis and in utero transmission. Emerging Microbes & Infections 2021, 10: 1649-1659. PMID: 34353229, PMCID: PMC8381923, DOI: 10.1080/22221751.2021.1965497.Peer-Reviewed Original ResearchConceptsCache Valley virusMurine modelLong-term therapeutic studiesTissue tropismImmune-competent miceNovel murine modelHighest seropositivity rateInnate immune responseType I interferonCompetent mosquito vectorsSmall animal modelsWide tissue tropismAge-dependent mannerAge-dependent pathogenesisIFN-αβRUtero transmissionSeropositivity rateSpontaneous abortionLethal infectionDisease outcomeVirus pathogenesisImmune responseTherapeutic studiesCongenital malformationsAnimal models
2020
Determinants of dengue virus dispersal in the Americas
Allicock O, Sahadeo N, Lemey P, Auguste A, Suchard M, Rambaut A, Carrington C. Determinants of dengue virus dispersal in the Americas. Virus Evolution 2020, 6: veaa074. PMID: 33408877, PMCID: PMC7772473, DOI: 10.1093/ve/veaa074.Peer-Reviewed Original Research
2019
Phylogenetic analysis of Theileria equi and Babesia caballi sequences from thoroughbred mares and foals in Trinidad
Sant C, Allicock O, d’Abadie R, Charles R, Georges K. Phylogenetic analysis of Theileria equi and Babesia caballi sequences from thoroughbred mares and foals in Trinidad. Parasitology Research 2019, 118: 1171-1177. PMID: 30761425, DOI: 10.1007/s00436-019-06240-x.Peer-Reviewed Original ResearchConceptsT. equi sequencesT. equiTheileria equiB. caballiMovement of horsesEquine piroplasmosisBabesia caballiEquine populationIxodid ticksNew genotypesEquid populationsCaballiSame genotypeThoroughbred maresHorsesEquiDifferent geographical regionsGenotypesSaint KittsTransplacental transmissionAdult horsesFoalsGeographical regionsRRNA geneFoetal loss