Anne Wyllie, PhD

• Akiko Iwasaki
• Albert C Shaw
• Albert Ko
• Benjamin Goldman-Israelow
• Carlos R Oliveira
• Craig B. Wilen
• Dana Small
• Daniel Weinberger
• David A. Hafler
• David van Dijk
• Dennis G Moledina
• Ellen F Foxman
• Gregg Gonsalves
• Harlan Krumholz
• Jeffrey Testani
• Malini Harigopal
• Marie-Louise Landry
• Naftali Kaminski
• Nathan Grubaugh
• Richard A Martinello
• Roy S. Herbst
• Ruth R Montgomery
• Serena Spudich
• Shelli Farhadian
• Steven Kleinstein
• Tomokazu S Sumida
• Xiting Yan

Aged; Carrier State; Epidemiology; Microbiology; Pneumococcal Infections; Pneumonia, Pneumococcal; Public Health; Respiratory Tract Infections; Saliva; Streptococcus pneumoniae; Coronavirus Infections; Pneumococcal Vaccines; Molecular Diagnostic Techniques; Real-Time Polymerase Chain Reaction; Microbiota

Community Health; Infectious Diseases; Maternal & Child Health; Respiratory Disease/Infections; Microbiome; COVID-19

• Magnetic bead-based separation of pneumococcal serotypesYork A, Huynh E, Mbodj S, Yolda-Carr D, Hislop M, Echlin H, Rosch J, Weinberger D, Wyllie A. Magnetic bead-based separation of pneumococcal serotypes Cell Reports Methods 2023, 3: 100410. PMID: 36936076, PMCID: PMC10014298, DOI: 10.1016/j.crmeth.2023.100410.
• Routine saliva testing for SARS-CoV-2 in children: Methods for partnering with community childcare centersRayack E, Askari H, Zirinsky E, Lapidus S, Sheikha H, Peno C, Kazemi Y, Yolda-Carr D, Liu C, Grubaugh N, Ko A, Wyllie A, Spatz E, Oliveira C, Bei A. Routine saliva testing for SARS-CoV-2 in children: Methods for partnering with community childcare centers Frontiers In Public Health 2023, 11: 1003158. PMID: 36817891, PMCID: PMC9936085, DOI: 10.3389/fpubh.2023.1003158.
• Magnetic bead-based separation of pneumococcal serotypesYork A, Huynh E, Mbodj S, Yolda-Carr D, Hislop M, Echlin H, Rosch J, Weinberger D, Wyllie A. Magnetic bead-based separation of pneumococcal serotypes Cell Reports Methods 2023, 3: 100410. DOI: 10.1016/j.crmeth.2023.100410.
• Saliva-based methods for SARS-CoV-2 testing in low- and middle-income countriesTan 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.
• Impact of Temporary Storage Conditions on the Viability of Streptococcus pneumoniae in SalivaAllicock 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.
• Association of upper respiratory Streptococcus pneumoniae colonization with SARS-CoV-2 infection among adults.Parker A, Jackson N, Awasthi S, Kim H, Alwan T, Wyllie A, Baldwin A, Brennick N, Moehle E, Giannikopoulos P, Kogut K, Holland N, Mora-Wyrobek A, Eskenazi B, Riley L, Lewnard J. Association of upper respiratory Streptococcus pneumoniae colonization with SARS-CoV-2 infection among adults. Clinical Infectious Diseases 2022 PMID: 36401872, DOI: 10.1093/cid/ciac907.
• Detection of pneumococcus during hospitalization for SARS-CoV-2Stahlfeld A, Glick L, Ott I, Craft S, Yolda-Carr D, Harden C, Nakahata M, Farhadian S, Grant L, Alexander-Parrish R, Arguedas A, Gessner B, Weinberger D, Wyllie A. Detection of pneumococcus during hospitalization for SARS-CoV-2 FEMS Microbes 2022, 3 DOI: 10.1093/femsmc/xtac026.
• Association of upper respiratory Streptococcus pneumoniae colonization with SARS-CoV-2 infection among adults.Parker AM, Jackson N, Awasthi S, Kim H, Alwan T, Wyllie AL, Baldwin AB, Brennick NB, Moehle EA, Giannikopoulos P, Kogut K, Holland N, Mora-Wyrobek A, Eskenazi B, Riley LW, Lewnard JA. Association of upper respiratory Streptococcus pneumoniae colonization with SARS-CoV-2 infection among adults. MedRxiv : The Preprint Server For Health Sciences 2022 PMID: 36238718, PMCID: PMC9558443, DOI: 10.1101/2022.10.04.22280709.
• Saliva as an alternative to nasopharyngeal swabs for detection of respiratory syncytial virus (RSV) in childrenLangedijk 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.
• Pneumococcal genetic variability in age-dependent bacterial carriageKremer P, Ferwerda B, Bootsma HJ, Rots NY, Wijmenga-Monsuur AJ, Sanders E, Trzciński K, Wyllie AL, Turner P, van der Ende A, Brouwer MC, Bentley SD, van de Beek D, Lees JA. Pneumococcal genetic variability in age-dependent bacterial carriage ELife 2022, 11: e69244. PMID: 35881438, PMCID: PMC9395192, DOI: 10.7554/elife.69244.
• Saliva as a sample type for SARS-CoV-2 detection: implementation successes and opportunities around the globeTobik 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.
• Evaluation of saliva self-collection devices for SARS-CoV-2 diagnosticsAllicock 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.
• Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C, Deng W, Chen M, Raredon MSB, Hoehn KB, Wang G, Wang Z, DeIuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Stein Y, Minasyan M, Mohanty S, Ruff WE, Cohen I, Raddassi K, Niklason L, Ko A, Montgomery R, Farhadian S, Iwasaki A, Shaw A, van Dijk D, Zhao H, Kleinstein S, Hafler D, Kaminski N, Dela Cruz C. Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19 Nature Communications 2022, 13: 440. PMID: 35064122, PMCID: PMC8782894, DOI: 10.1038/s41467-021-27716-4.
• Evaluation of the Liberty16 Mobile Real Time PCR Device for Use With the SalivaDirect Assay for SARS-CoV-2 TestingYolda-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.
• Saliva RT-PCR Sensitivity Over the Course of SARS-CoV-2 InfectionWyllie AL, Premsrirut PK. Saliva RT-PCR Sensitivity Over the Course of SARS-CoV-2 Infection JAMA 2022, 327: 182-183. PMID: 35015044, DOI: 10.1001/jama.2021.21703.
• Sequencing SARS-CoV-2 Genomes from SalivaAlpert T, Vogels CBF, Breban MI, Petrone ME, Team Y, Wyllie A, Grubaugh N, Fauver J. Sequencing SARS-CoV-2 Genomes from Saliva Virus Evolution 2022, 8: veab098-. PMID: 35542310, PMCID: PMC9074962, DOI: 10.1093/ve/veab098.
• Persistence of pneumococcal carriage among older adults in the community despite COVID-19 mitigation measuresAnne L. Wyllie, Sidiya Mbodj, Darani A. Thammavongsa, Maikel S. Hislop, Devyn Yolda-Carr, Pari Waghela, Maura Nakahata, Anne E. Watkins, Noel J. Vega, Anna York, Orchid M. Allicock, Geisa Wilkins, Andrea Ouyang, Laura Siqueiros, Yvette Strong, Kelly Anastasio, Ronika Alexander-Parrish, Adriano Arguedas, Bradford D. Gessner, Daniel M. Weinberger medRxiv 2022.06.28.22276654; doi: https://doi.org/10.1101/2022.06.28.22276654
• 301. Detection of Pneumococcal Pneumonia During SARS-CoV-2 InfectionWatkins A, Yolda-Carr D, Ott I, Nakahata M, Moore A, Muenker M, Tokuyama M, Vogels C, Campbell M, Datta R, Cruz C, Farhadian S, Iwasaki A, Ko A, Grubaugh N, Alexander-Parrish R, Arguedas A, Gessner B, Weinberger D, Wyllie A. 301. Detection of Pneumococcal Pneumonia During SARS-CoV-2 Infection Open Forum Infectious Diseases 2021, 8: s257-s257. PMCID: PMC8644655, DOI: 10.1093/ofid/ofab466.503.
• 1321. Acquisition and Transmission of Streptococcus pneumoniae in Individuals Over the Age of 60 Years Residing in New Haven, CT, USAWyllie 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: s749-s749. PMCID: PMC8689704, DOI: 10.1093/ofid/ofab466.1513.
• 362. Saliva as a Reliable Sample Type for Mass SARS-CoV-2 Testing StrategiesWyllie 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: s284-s284. PMCID: PMC8644416, DOI: 10.1093/ofid/ofab466.563.
• Longitudinal Immune Profiling of a Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection in a Solid Organ Transplant RecipientKlein J, Brito AF, Trubin P, Lu P, Wong P, Alpert T, Peña-Hernández MA, Haynes W, Kamath K, Liu F, Vogels CBF, Fauver JR, Lucas C, Oh J, Mao T, Silva J, Wyllie AL, Muenker MC, Casanovas-Massana A, Moore AJ, Petrone ME, Kalinich CC, Dela Cruz C, Farhadian S, Ring A, Shon J, Ko AI, Grubaugh ND, Israelow B, Iwasaki A, Azar MM, Team F. Longitudinal Immune Profiling of a Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection in a Solid Organ Transplant Recipient The Journal Of Infectious Diseases 2021, 225: 374-384. PMID: 34718647, PMCID: PMC8807168, DOI: 10.1093/infdis/jiab553.
• Reply to: A finding of sex similarities rather than differences in COVID-19 outcomesTakahashi 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.
• 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.
• Understanding the Barriers to Pooled SARS-CoV-2 Testing in the United StatesFenichel 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.
• Implementation of a pooled surveillance testing program for asymptomatic SARS-CoV-2 infections in K-12 schools and universitiesMendoza RP, Bi C, Cheng HT, Gabutan E, Pagapas G, Khan N, Hoxie H, Hanna S, Holmes K, Gao N, Lewis R, Wang H, Neumann D, Chan A, Takizawa M, Lowe J, Chen X, Kelly B, Asif A, Barnes K, Khan N, May B, Chowdhury T, Pollonini G, Gouda N, Guy C, Gordon C, Ayoluwa N, Colon E, Miller-Medzon N, Jones S, Hossain R, Dodson A, Weng M, McGaskey M, Vasileva A, Lincoln AE, Sikka R, Wyllie AL, Berke EM, Libien J, Pincus M, Premsrirut PK. Implementation of a pooled surveillance testing program for asymptomatic SARS-CoV-2 infections in K-12 schools and universities EClinicalMedicine 2021, 38: 101028. PMID: 34308321, PMCID: PMC8286123, DOI: 10.1016/j.eclinm.2021.101028.
• Testing Saliva to Reveal the Submerged Cases of the COVID-19 IcebergBorghi E, Massa V, Zuccotti G, Wyllie AL. Testing Saliva to Reveal the Submerged Cases of the COVID-19 Iceberg Frontiers In Microbiology 2021, 12: 721635. PMID: 34322114, PMCID: PMC8312273, DOI: 10.3389/fmicb.2021.721635.
• Evidence for SARS-CoV-2 Spike Protein in the Urine of COVID-19 Patients.George S, Pal AC, Gagnon J, Timalsina S, Singh P, Vydyam P, Munshi M, Chiu JE, Renard I, Harden CA, Ott IM, Watkins AE, Vogels CBF, Lu P, Tokuyama M, Venkataraman A, Casanovas-Massana A, Wyllie AL, Rao V, Campbell M, Farhadian SF, Grubaugh ND, Dela Cruz CS, Ko AI, Berna Perez AZ, Akaho EH, Moledina DG, Testani J, John AR, Ledizet M, Mamoun CB. Evidence for SARS-CoV-2 Spike Protein in the Urine of COVID-19 Patients. Kidney360 2021, 2: 924-936. PMID: 35373072, PMCID: PMC8791366, DOI: 10.34067/kid.0002172021.
• Diverse functional autoantibodies in patients with COVID-19Wang EY, Mao T, Klein J, Dai Y, Huck JD, Jaycox JR, Liu F, Zhou T, Israelow B, Wong P, Coppi A, Lucas C, Silva J, Oh JE, Song E, Perotti ES, Zheng NS, Fischer S, Campbell M, Fournier JB, Wyllie AL, Vogels CBF, Ott IM, Kalinich CC, Petrone ME, Watkins AE, Dela Cruz C, Farhadian S, Schulz W, Ma S, Grubaugh N, Ko A, Iwasaki A, Ring A. Diverse functional autoantibodies in patients with COVID-19 Nature 2021, 595: 283-288. PMID: 34010947, DOI: 10.1038/s41586-021-03631-y.
• Saliva as a gold-standard sample for SARS-CoV-2 detectionTan 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.
• Stability of SARS-CoV-2 RNA in Nonsupplemented Saliva - Volume 27, Number 4—April 2021 - Emerging Infectious Diseases journal - CDCOtt 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.
• Increased SARS-CoV-2 Testing Capacity with Pooled Saliva Samples - Volume 27, Number 4—April 2021 - Emerging Infectious Diseases journal - CDCWatkins AE, Fenichel EP, Weinberger DM, Vogels CBF, Brackney DE, Casanovas-Massana A, Campbell M, Fournier J, Bermejo S, Datta R, Dela Cruz CS, Farhadian SF, Iwasaki A, Ko AI, Grubaugh ND, Wyllie AL, . Increased SARS-CoV-2 Testing Capacity with Pooled Saliva Samples - Volume 27, Number 4—April 2021 - Emerging Infectious Diseases journal - CDC Emerging Infectious Diseases 2021, 27: 1184-1187. PMID: 33755009, PMCID: PMC8007323, DOI: 10.3201/eid2704.204200.
• Tracking smell loss to identify healthcare workers with SARS-CoV-2 infectionWeiss JJ, Attuquayefio TN, White EB, Li F, Herz RS, White TL, Campbell M, Geng B, Datta R, Wyllie AL, Grubaugh ND, Casanovas-Massana A, Muenker MC, Moore AJ, Handoko R, Iwasaki A, Martinello RA, Ko AI, Small DM, Farhadian SF, . Tracking smell loss to identify healthcare workers with SARS-CoV-2 infection PLOS ONE 2021, 16: e0248025. PMID: 33657167, PMCID: PMC7928484, DOI: 10.1371/journal.pone.0248025.
• Saliva for Detection of SARS-CoV-2. Reply.Wyllie AL, Vogels CBF, Grubaugh ND. Saliva for Detection of SARS-CoV-2. Reply. New England Journal Of Medicine 2021, 384: e31. PMID: 33534974, DOI: 10.1056/nejmc2032165.
• Saliva viral load is a dynamic unifying correlate of COVID-19 severity and mortality.Silva J, Lucas C, Sundaram M, Israelow B, Wong P, Klein J, Tokuyama M, Lu P, Venkataraman A, Liu F, Mao T, Oh JE, Park A, Casanovas-Massana A, Vogels CBF, Muenker CM, Zell J, Fournier JB, Campbell M, Chiorazzi M, Ruiz Fuentes E, Petrone M, Kalinich CC, Ott IM, Watkins A, Moore AJ, Nakahata MI, Grubaugh ND, Farhadian S, Dela Cruz C, Ko A, Schulz WL, Ring AM, Ma S, Omer S, Wyllie AL, Iwasaki A. Saliva viral load is a dynamic unifying correlate of COVID-19 severity and mortality. MedRxiv : The Preprint Server For Health Sciences 2021 PMID: 33442706, PMCID: PMC7805468, DOI: 10.1101/2021.01.04.21249236.
• 68. Active Monitoring of a Healthcare Worker Cohort During the COVID-19 EpidemicDatta R, Campbell M, Wyllie A, Casanovas-Massana A, Handoko R, Sewanan L, Naushad N, Simonov M, White E, Valdez J, Liu F, Omer S, Dela Cruz C, Farhadian S, Ring A, Iwasaki A, Grubaugh N, Martinello R, Ko A. 68. Active Monitoring of a Healthcare Worker Cohort During the COVID-19 Epidemic Open Forum Infectious Diseases 2020, 7: s165-s165. PMCID: PMC7778054, DOI: 10.1093/ofid/ofaa439.378.
• 493. Clinical and Epidemiological Features of Healthcare Workers Detected with Coronavirus DiseaseCampbell M, Datta R, Wyllie A, Casanovas-Massana A, Handoko R, Sewanan L, Ko A, Martinello R. 493. Clinical and Epidemiological Features of Healthcare Workers Detected with Coronavirus Disease Open Forum Infectious Diseases 2020, 7: s313-s313. PMCID: PMC7777234, DOI: 10.1093/ofid/ofaa439.686.
• SalivaDirect: A simplified and flexible platform to enhance SARS-CoV-2 testing capacityVogels CBF, Watkins AE, Harden CA, Brackney DE, Shafer J, Wang J, Caraballo C, Kalinich CC, Ott IM, Fauver JR, Kudo E, Lu P, Venkataraman A, Tokuyama M, Moore AJ, Muenker MC, Casanovas-Massana A, Fournier J, Bermejo S, Campbell M, Datta R, Nelson A, Team Y, Anastasio K, Askenase M, Batsu M, Bickerton S, Brower K, Bucklin M, Cahill S, Cao Y, Courchaine E, DeIuliis G, Earnest R, Geng B, Goldman-Israelow B, Handoko R, Khoury-Hanold W, Kim D, Knaggs L, Kuang M, Lapidus S, Lim J, Linehan M, Lu-Culligan A, Martin A, Matos I, McDonald D, Minasyan M, Nakahata M, Naushad N, Nouws J, Obaid A, Odio C, Oh J, Omer S, Park A, Park H, Peng X, Petrone M, Prophet S, Rice T, Rose K, Sewanan L, Sharma L, Shaw A, Shepard D, Smolgovsky M, Sonnert N, Strong Y, Todeasa C, Valdez J, Velazquez S, Vijayakumar P, White E, Yang Y, Dela Cruz C, Ko A, Iwasaki A, Krumholz H, Matheus J, Hui P, Liu C, Farhadian S, Sikka R, Wyllie A, Grubaugh N. SalivaDirect: A simplified and flexible platform to enhance SARS-CoV-2 testing capacity Med 2020, 2: 263-280.e6. PMID: 33521748, PMCID: PMC7836249, DOI: 10.1016/j.medj.2020.12.010.
• Kinetics of antibody responses dictate COVID-19 outcome.Lucas C, Klein J, Sundaram M, Liu F, Wong P, Silva J, Mao T, Oh JE, Tokuyama M, Lu P, Venkataraman A, Park A, Israelow B, Wyllie AL, Vogels CBF, Muenker MC, Casanovas-Massana A, Schulz WL, Zell J, Campbell M, Fournier JB, Grubaugh ND, Farhadian S, Wisnewski AV, Cruz CD, Omer S, Ko AI, Ring A, Iwasaki A. Kinetics of antibody responses dictate COVID-19 outcome. MedRxiv : The Preprint Server For Health Sciences 2020 PMID: 33398304, PMCID: PMC7781347, DOI: 10.1101/2020.12.18.20248331.
• Detection of SARS-CoV-2 RNA by multiplex RT-qPCRKudo 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, , 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.
• Serotype Patterns of Pneumococcal Disease in Adults Are Correlated With Carriage Patterns in Older Children.Wyllie AL, Warren JL, Regev-Yochay G, Givon-Lavi N, Dagan R, Weinberger DM. Serotype Patterns of Pneumococcal Disease in Adults Are Correlated With Carriage Patterns in Older Children. Clinical Infectious Diseases 2020, 72: e768-e775. PMID: 32989457, PMCID: PMC8315131, DOI: 10.1093/cid/ciaa1480.
• Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2Wyllie 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.
• Sex differences in immune responses that underlie COVID-19 disease outcomesTakahashi 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.
• Real-time public health communication of local SARS-CoV-2 genomic epidemiologyKalinich CC, Jensen CG, Neugebauer P, Petrone ME, Peña-Hernández M, Ott IM, Wyllie AL, Alpert T, Vogels CBF, Fauver JR, Grubaugh ND, Brito AF. Real-time public health communication of local SARS-CoV-2 genomic epidemiology PLOS Biology 2020, 18: e3000869. PMID: 32822393, PMCID: PMC7467297, DOI: 10.1371/journal.pbio.3000869.
• The COVID-19 XPRIZE and the need for scalable, fast, and widespread testingMacKay MJ, Hooker AC, Afshinnekoo E, Salit M, Kelly J, Feldstein JV, Haft N, Schenkel D, Nambi S, Cai Y, Zhang F, Church G, Dai J, Wang CL, Levy S, Huber J, Ji HP, Kriegel A, Wyllie AL, Mason CE. The COVID-19 XPRIZE and the need for scalable, fast, and widespread testing Nature Biotechnology 2020, 38: 1021-1024. PMID: 32820257, PMCID: PMC7543743, DOI: 10.1038/s41587-020-0655-4.
• SARS-CoV-2 infection of the placentaHosier 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.
• Longitudinal analyses reveal immunological misfiring in severe COVID-19Lucas 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.
• Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe setsVogels 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.
• The Sensitivity of Respiratory Tract Specimens for the Detection of SARS-CoV-2: A Protocol for a Living Systematic Review and Meta-Analysis.Moore AJ, Nakahata MI, Kalinich CC, Nyhan K, Bromberg DJ, Shi X, Ko AI, Grubaugh ND, Casanovas-Massana A, Wyllie AL. The Sensitivity of Respiratory Tract Specimens for the Detection of SARS-CoV-2: A Protocol for a Living Systematic Review and Meta-Analysis. MedRxiv : The Preprint Server For Health Sciences 2020 PMID: 32637978, PMCID: PMC7340204, DOI: 10.1101/2020.07.02.20144543.
• Acute encephalopathy with elevated CSF inflammatory markers as the initial presentation of COVID-19Farhadian S, Glick LR, Vogels CBF, Thomas J, Chiarella J, Casanovas-Massana A, Zhou J, Odio C, Vijayakumar P, Geng B, Fournier J, Bermejo S, Fauver JR, Alpert T, Wyllie AL, Turcotte C, Steinle M, Paczkowski P, Dela Cruz C, Wilen C, Ko AI, MacKay S, Grubaugh ND, Spudich S, Barakat LA. Acute encephalopathy with elevated CSF inflammatory markers as the initial presentation of COVID-19 BMC Neurology 2020, 20: 248. PMID: 32552792, PMCID: PMC7301053, DOI: 10.1186/s12883-020-01812-2.
• Acute encephalopathy with elevated CSF inflammatory markers as the initial presentation of COVID-19.Farhadian S, Glick LR, Vogels CBF, Thomas J, Chiarella J, Casanovas-Massana A, Zhou J, Odio C, Vijayakumar P, Geng B, Fournier J, Bermejo S, Fauver JR, Alpert T, Wyllie AL, Turcotte C, Steinle M, Paczkowski P, Cruz CD, Wilen C, Ko AI, MacKay S, Grubaugh ND, Spudich S, Aoun Barakat L. Acute encephalopathy with elevated CSF inflammatory markers as the initial presentation of COVID-19. Research Square 2020 PMID: 32702723, PMCID: PMC7336693, DOI: 10.21203/rs.3.rs-28583/v1.
• Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United StatesFauver JR, Petrone ME, Hodcroft EB, Shioda K, Ehrlich HY, Watts AG, Vogels CBF, Brito AF, Alpert T, Muyombwe A, Razeq J, Downing R, Cheemarla NR, Wyllie AL, Kalinich CC, Ott IM, Quick J, Loman NJ, Neugebauer KM, Greninger AL, Jerome KR, Roychoudhury P, Xie H, Shrestha L, Huang ML, Pitzer VE, Iwasaki A, Omer SB, Khan K, Bogoch II, Martinello RA, Foxman EF, Landry ML, Neher RA, Ko AI, Grubaugh ND. Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States Cell 2020, 181: 990-996.e5. PMID: 32386545, PMCID: PMC7204677, DOI: 10.1016/j.cell.2020.04.021.
• Upper respiratory tract colonization with Streptococcus pneumoniae in adultsArguedas A, Trzciński K, O’Brien K, Ferreira DM, Wyllie AL, Weinberger D, Danon L, Pelton SI, Azzari C, Hammitt LL, Sá-Leão R, Brandileone MC, Saha S, Suaya J, Isturiz R, Jodar L, Gessner BD. Upper respiratory tract colonization with Streptococcus pneumoniae in adults Expert Review Of Vaccines 2020, 19: 353-366. PMID: 32237926, DOI: 10.1080/14760584.2020.1750378.
• Variation of growth characteristics of pneumococcus with environmental conditionsTóthpál A, Desobry K, Joshi SS, Wyllie AL, Weinberger DM. Variation of growth characteristics of pneumococcus with environmental conditions BMC Microbiology 2019, 19: 304. PMID: 31878880, PMCID: PMC6933730, DOI: 10.1186/s12866-019-1671-8.
• Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitisLees JA, Ferwerda B, Kremer PHC, Wheeler NE, Serón MV, Croucher NJ, Gladstone RA, Bootsma HJ, Rots NY, Wijmega-Monsuur AJ, Sanders EAM, Trzciński K, Wyllie AL, Zwinderman AH, van den Berg LH, van Rheenen W, Veldink JH, Harboe ZB, Lundbo LF, de Groot LCPGM, van Schoor NM, van der Velde N, Ängquist LH, Sørensen TIA, Nohr EA, Mentzer AJ, Mills TC, Knight JC, du Plessis M, Nzenze S, Weiser JN, Parkhill J, Madhi S, Benfield T, von Gottberg A, van der Ende A, Brouwer MC, Barrett JC, Bentley SD, van de Beek D. Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis Nature Communications 2019, 10: 2176. PMID: 31092817, PMCID: PMC6520353, DOI: 10.1038/s41467-019-09976-3.
• Exploring Immune Development in Infants With Moderate to Severe Atopic DermatitisHulshof L, Overbeek SA, Wyllie AL, Chu MLJN, Bogaert D, de Jager W, Knippels LMJ, Sanders EAM, van Aalderen WMC, Garssen J, Land B, Sprikkelman AB, Group T, Blauw A, Dontje B, Duijvestein Y, de Boom W, Groot I, Boks M, van Kooyk Y, Fandri D, Hijnen D, Middelkamp-Hup M, Papi B, Roelofs M, Rijnierse A, Veening D, Support C, Prakken B, Tusscher G, Tupker R, Willemsen L. Exploring Immune Development in Infants With Moderate to Severe Atopic Dermatitis Frontiers In Immunology 2018, 9: 630. PMID: 29966024, PMCID: PMC5884950, DOI: 10.3389/fimmu.2018.00630.
• Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal speciesWyllie AL, Pannekoek Y, Bovenkerk S, van Engelsdorp Gastelaars J, Ferwerda B, van de Beek D, Sanders EAM, Trzciński K, van der Ende A. Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species Open Biology 2017, 7: 170074. PMID: 28931649, PMCID: PMC5627049, DOI: 10.1098/rsob.170074.
• Molecular surveillance on Streptococcus pneumoniae carriage in non-elderly adults; little evidence for pneumococcal circulation independent from the reservoir in childrenWyllie AL, Rümke LW, Arp K, Bosch AA, Bruin JP, Rots NY, Wijmenga-Monsuur AJ, Sanders EA, Trzciński K. Molecular surveillance on Streptococcus pneumoniae carriage in non-elderly adults; little evidence for pneumococcal circulation independent from the reservoir in children Scientific Reports 2016, 6: 34888. PMID: 27713565, PMCID: PMC5054371, DOI: 10.1038/srep34888.
• Molecular surveillance of nasopharyngeal carriage of Streptococcus pneumoniae in children vaccinated with conjugated polysaccharide pneumococcal vaccinesWyllie AL, Wijmenga-Monsuur AJ, van Houten MA, Bosch AATM, Groot JA, van Engelsdorp Gastelaars J, Bruin JP, Bogaert D, Rots NY, Sanders EAM, Trzciński K. Molecular surveillance of nasopharyngeal carriage of Streptococcus pneumoniae in children vaccinated with conjugated polysaccharide pneumococcal vaccines Scientific Reports 2016, 6: 23809. PMID: 27046258, PMCID: PMC4820691, DOI: 10.1038/srep23809.
• Development of the Nasopharyngeal Microbiota in Infants with Cystic FibrosisPrevaes SM, de Winter-de Groot KM, Janssens HM, de Steenhuijsen Piters WA, Tramper-Stranders GA, Wyllie AL, Hasrat R, Tiddens HA, van Westreenen M, van der Ent CK, Sanders EA, Bogaert D. Development of the Nasopharyngeal Microbiota in Infants with Cystic Fibrosis American Journal Of Respiratory And Critical Care Medicine 2016, 193: 504-515. PMID: 26492486, DOI: 10.1164/rccm.201509-1759oc.
• Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patientsde Steenhuijsen Piters WA, Huijskens EG, Wyllie AL, Biesbroek G, van den Bergh MR, Veenhoven RH, Wang X, Trzciński K, Bonten MJ, Rossen JW, Sanders EA, Bogaert D. Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients The ISME Journal: Multidisciplinary Journal Of Microbial Ecology 2015, 10: 97-108. PMID: 26151645, PMCID: PMC4681870, DOI: 10.1038/ismej.2015.99.
• Carriage of Streptococcus pneumoniae in Aged Adults with Influenza-Like-IllnessKrone CL, Wyllie AL, van Beek J, Rots NY, Oja AE, Chu ML, Bruin JP, Bogaert D, Sanders EA, Trzciński K. Carriage of Streptococcus pneumoniae in Aged Adults with Influenza-Like-Illness PLOS ONE 2015, 10: e0119875. PMID: 25789854, PMCID: PMC4366201, DOI: 10.1371/journal.pone.0119875.
• Streptococcus pneumoniae in Saliva of Dutch Primary School ChildrenWyllie AL, Chu ML, Schellens MH, van Engelsdorp Gastelaars J, Jansen MD, van der Ende A, Bogaert D, Sanders EA, Trzciński K. Streptococcus pneumoniae in Saliva of Dutch Primary School Children PLOS ONE 2014, 9: e102045. PMID: 25013895, PMCID: PMC4094488, DOI: 10.1371/journal.pone.0102045.
• WS1.3 Respiratory microbiota dynamics in newborns with cystic fibrosis and healthy controls: A longitudinal studyPrevaes S, de Winter-de Groot K, Tramper-Stranders G, Tiddens H, van Westreenen M, Janssens H, Wyllie A, van der Ent C, Sanders E, Bogaert D. WS1.3 Respiratory microbiota dynamics in newborns with cystic fibrosis and healthy controls: A longitudinal study Journal Of Cystic Fibrosis 2013, 12: s1. DOI: 10.1016/s1569-1993(13)60004-1.
• Superiority of Trans-Oral over Trans-Nasal Sampling in Detecting Streptococcus pneumoniae Colonization in AdultsTrzciński K, Bogaert D, Wyllie A, Chu ML, van der Ende A, Bruin JP, van den Dobbelsteen G, Veenhoven RH, Sanders EA. Superiority of Trans-Oral over Trans-Nasal Sampling in Detecting Streptococcus pneumoniae Colonization in Adults PLOS ONE 2013, 8: e60520. PMID: 23555985, PMCID: PMC3610877, DOI: 10.1371/journal.pone.0060520.