We study the natural history, transmission dynamics, and control of infectious diseases in the School of Public Health and the Center for Computational Biology at UC Berkeley.
Our work has centered on pediatric infectious diseases and vaccines against them, in particular pneumococcus (Streptococcus pneumoniae), rotavirus, and group A Streptococcus. We are also interested in statistical methods for vaccine efficacy and effectiveness studies. We have redirected substantial effort to COVID-19 in the ongoing pandemic.
Multiple funded positions are available for PhD students and postdocs. Please contact jlewnard@berkeley.edu with your CV and a description of your background and research interests.
Work by current and former members is indicated in bold text. Work published since July, 2018 is lab output. For more details, see PI Google Scholar.
Snyder RE, Saadeh K, Tang EC, Johnson KA, Holland SN, Qint J, Burghardt NO, Chai SJ, Fernando R, Gonzalez Barrera K, Hernandez C, McManus K, Lorenz K, Maycott J, McGinley J, Lewnard JA. Sexual exposures associated with mpox infection: California, November 2022 to June 2023. J Infect Dis 2023.
Bruxvoort KJ, Fischer H, Lewnard JA, Hong V, Pomichowski M, Grant LR, Jodar L, Gessner BD, Tartof SY. Risk of subsequent lower respiratory tract infection (LRTI) after hospitalization for COVID-19 LRTI and non-COVID-19 LRTI: a retrospective cohort study. Pneumonia 2023.
Lewnard JA, Hong V, Kim JS, Shaw SF, Lewin B, Takhar H, Lipsitch M, Tartof SY. Increased vaccine sensitivity of an emerging SARS-CoV-2 variant. Nature Communications 2023.
Lewnard JA, Mohan BC, Kang G, Laxminarayan R. Attributed causes of excess mortality during the COVID-19 pandemic in a south Indian city. Nature Communications 2023.
Dalto AF, Diallo O, Chard AN, Moulia DL, Fothergill A, Kracalik I, Wegner CW, Markus TM, Pathela P, Still WL, Hawkins S, Mangla AT, Ravi N, Licherdell E, Britton A, Lynfield R, Sutton M, Hansen AP, Betancourt GS, Rowlands JV, Chai SJ, Fisher R, Danza P, Farley M, Zipprich J, Prahl G, Wendel KA, Niccolai L, Castilho JL, Payne DC, Cohn AC, Feldstein LR, CDC Multijurisdictional Mpox Case-Control Study Group. Estimated effectiveness of JYNNEOS vaccine in preventing mpox: a multijurisdictional case-control study, United States, August 19, 2022–March 31, 2023. MMWR 2023.
Lewnard JA, Hong V, Bruxvoort KJ, Grant LR, Jodar L, Cane A, Arguedas A, Pomichowski ME, Gessner BD, Tartof SY. Burden of lower respiratory tract infections preventable by adult immunization with 15- and 20-valent pneumococcal conjugate vaccines in the United States. Clin Infect Dis 2023.
Kumar CK, Sands K, Walsh TR, O’Brien S, Sharland M, Lewnard JA, Hu H, Srikantiah P, Laxminarayan R. Global, regional, and national estimates of the impact of a maternal Klebsiella pneumoniae vaccine: a Bayesian modeling analysis. PLoS Med 2023.
Lewnard JA, Hong V, Kim JS, Shaw SS, Lewin B, Takhar H, Tartof, SY. Asociation of SARS-CoV-2 BA.4/BA.5 Omicron lineages with immune escape and clinical outcome. Nature Communications 2023.
Andrejko KL, Myers JF, Fukui N, Nelson L, Zhao R, Openshaw J, Watt JP, Jain S, Lewnard JA, Pry JM. Real-world uptake of COVID-19 vaccination among individuals expressing vaccine hesitancy: a registry-linkage study. Vaccine 2023.
Andrejko KL, Pry JM*, Myers JF, Mehrotra M, Lambda K, Lim E, Fukui N, DeGuzman JL, Openshaw J, Watt J, Jain S, Lewnard JA. Waning of two-dose BNT162b2 and mRNA-1273 vaccine effectiveness against symptomatic SARS-CoV-2 infection is robust to depletion-of-susceptibles bias. Am J Epidemiol 2022.
Andrejko KL, Myers JM, Openshaw J, Fukui N, Li S, Watt JP, Murray EL, Hoover C, Lewnard JA, Jain S, Pry JM. Receipt of COVID-19 and seasonal influenza vaccines in California (USA) during the 2021–2022 influenza season. Vaccine 2023.
King LM, Lewnard JA, Niccolai LM. Clinical and public health considerations for HPV vaccination in mid-adulthood: a narrative review. Open Forum Infect Dis 2023.
Parker AM, Jackson N, Awasthi S, Kim H, Alwan T, Wyllie AL, Baldwin AB, Brennick NB, Moehle AEA, 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. Clin Infect Dis 2022.
Cheng Q, Collender P, Heaney A, McLoughlin A, Yang Y, Zhang Y, Head J, Dasan R, Liang S, Lv Q, Liu Y, Yang C, Chang H, Waller L, Zelner J, Lewnard JA, Remais J. Optimizing laboratory-based surveillance networks for monitoring multi-genotype or multi-serotype infections. PLoS Comp Biol 2022.
Rogawski McQuade ET, Brennhofer SA, Elwood SE, McMurry TL, Lewnard JA, Mduma E, Shrestha S, Iqbal N, Bessong PO, Kang G, Kosek M, Lima AAM, Amhed T, Liu J, Houpt E, Platts-Mills JA. Frequency of bystander exposure to antibiotics for enteropathogenic bacteria among young children in low-resource settings. Proc Natl Acad Sci U S A 2022.
Adams C, Horton M, Solomon O, Wong MP, Wu SL, Fuller S, Shao X, Fedrigo I, Quach HL, Quach DL, Meas M, Lopez L, Broughton A, Barcellos AL, Shim J, Seymens Y, Hernandez S, Montoya M, Johnsono DM, Beckman KB, Busch MP, Coloma J, Lewnard JA, Harris E, Barcellos LF. Health inequities in SARS-CoV-2 infection, seroprevalence, and COVID-19 vaccination: Results from the East Bay COVID-19 study. PLoS Global Public Health 2022.
Jewell NP, Lewnard JA. On the use of the reproduction number for SARS-CoV-2: Estimation, misinterpretations, and relationships with other ecological measures. J Royal Stat Soc A 2022.
Malden DE, Hong VX, Lewin BJ, Ackerson BK, Lipsitch M, Lewnard JA, Tartof SY. Hospitalization and Emergency Department Encounters for COVID-19 After Paxlovid Treatment — California, December 2021–May 2022. MMWR 2022.
Lewnard JA, Hong VX, Patel MM, Kahn R, Lipsitch M, Tartof SY. Clinical outcomes associated with SARS-CoV-2 Omicron (B.1.1.529) variant and BA.1./BA.1.1 or BA.2 subvariant infection in southern California. Nature Medicine 2022.
Bruxvoort KJ, Lewnard JA, Chen LH, Tseng HF, Chang J, Marrazzo J, Qian L. Prevention of Neisseria gonorrhoeae with meningococcal B vaccine: a matched cohort study in Southern California. Clin Infect Dis 2022.
Lewnard JA, Bruxvoort KJ, Hong VX, Grant LR, Jodar L, Cane A, Gessner BD, Tartof SY. Effectiveness of pneumococccal conjugate vaccination against virus-associated lower respiratory tract infection among adults: a case-control study. J Infect Dis 2022.
Lewnard JA, Fries LF, Cho I, Chen J, Laxminarayan R. Prevention of antimicrobial prescribing among infants following maternal vaccination against respiratory syncytial virus. Proc Natl Acad Sci U S A 2022.
Andrejko K, Head J, Lewnard JA, Remais J. Longitudinal social contact patterns among school-aged children during the COVID-19 pandemic: the Bay Area Contacts among Kids (BACK) study. BMC Infect Dis 2022.
Andrejko KL, Pry JM, Myers JF, Fukui N, DeGuzman JL, Openshaw J, Watt JP, Lewnard JA, Jain S. Effectiveness of face mask or respirator use in indoor public settings for prevention of SARS-CoV-2 infection: California, February-December, 2021. MMWR 2022.
Hitchings MT, Lewnard JA, Dean NE, Ko AI, Ranzani OT, Andrews JR, Cummings DAT. Use of recently vaccinated individuals to detect bias in test-negative case-control studies of COVID-19 vaccine effectiveness. Epidemiology 2022.
Miller AC, Hannah L, Futoma J, Foti NJ, Fox EB, D’Amour A, Sandler M, Saurous RA, Lewnard JA. Statistical deconvolution for inference of infection time series. Epidemiology 2022.
Brennhofer SA, Platts-Mills JA, Lewnard JA, Liu J, Houpt ER, Rogawski McQuade ET. Antibiotic use attributable to specific etiologies of diarrhea in children under two years of age in low-resource settings: a secondary analysis of the MAL-ED birth cohort. BMJ Open 2022.
Lo NC, Andrejko K, Shukla P, Baker T, Sawin VI, Norris SL, Lewnard JA. Contribution and quality of math- ematical modeling evidence in World Health Organization guidelines: a systematic review. Epidemics 2022.
Lewnard JA, Bruxvoort KJ, Fischer H, Hong VX, Grant LR, Jodar L, Cane A, Gessner BD, Tartof SY. Effectiveness of 13-valent pneumococcal conjugate vaccine against medically-attended lower respiratory tract infection and pneumonia among older adults. Clin Infect Dis 2021.
Andrejko K, Pry J, Myers JF, Openshaw J, Watt J, Birkett N, DeGuzman JL, Barbaduomo CM, Dong ZN, Fang AT, Frost PM, Ho T, Javadi MH, Li SS, Tran VH, Wan C, Jain S, Lewnard JA. Predictors of SARS-CoV-2 infection following high-risk exposure. Clin Infect Dis 2021.
Andrejko K, Ratnasiri B, Lewnard JA. Association of pneumococcal serotype with susceptibility to antimicrobial drugs: a systematic review and meta-analysis. Clin Infect Dis 2021.
Andrejko K, Pry JM, Myers JF, Jewell NP, Openshaw J, Watt J, Jain S, Lewnard JA. Prevention of COVID- 19 by mRNA-based vaccines within the general population of California. Clin Infect Dis 2021.
Andrejko K, Whittles LK, Lewnard JA. Health economic value of vaccination against group A Streptococcus in the United States. Clin Infect Dis 2021.
Andrejko K, Ratnasiri B, Hausdorff WP, Laxminarayan R, Lewnard JA. Antimicrobial resistance in pediatric Streptococcus pneumoniae isolates amid global implementation of pneumococcal conjugate vaccines: a systematic review and meta-regression analysis. Lancet Microbe 2021.
Lewnard JA, Patel MM, Jewell NP, Verani JR, Kobayashi M, Tenforde M, Dean NE, Cowling BJ, Lopman BA. Theoretical framework for retrospective studies of the effectiveness of SARS-CoV-2 vaccines. Epidemiology 2021.
Head JR, Andrejko K, Cheng Q, Collender PA, Phillips S, Boser A, Heaney AK, Hoover CM, Wu SL, Northrup G, Clinck K, Harrison R, Lewnard JA, Remais JV . School closures reduced social mixing of children during COVID-19 with implications for transmission risk and school reopening policies. J Royal Soc Interface 2021.
Lewnard JA, Bruxvoort K, Fischer H, Hong V, Grant LR, Jodar L, Gessner BD, Tartof SY. Prevention of COVID- 19 among older adults receiving pneumococcal conjugate vaccine suggests interactions between Streptococcus pneumoniae and SARS-CoV-2 in the respiratory tract. J Infect Dis 2021.
Lewnard JA, Mora AM, Nkwocha O, Kogut K, Rauch SA, Morga N, Hernandez S, Wong MP, Huen K, Andrejko K, Jewell NP, Parra KL, Holland N, Harris E, Cuevas M, Eskenazi B, CHAMACOS-Project-19 Study Team. Prevalence and clinical profile of SARS-CoV-2 infection among farmworkers in California: June–November, 2020. Emerg Infect Dis 2021.
Cheng Q, Collender PA, Heaney AK, Li X, Dasan R, Li C, Lewnard JA, Zelner J, Liang S, Chang HH, Waller LA, Lopman BA, Yang C, Remais JV. Towards a simulation framework for optimizing infectious dis- ease surveillance: an information theoretic approach for surveillance system design. PLoS Comp Biol 2020.
Northrup GR, Qian L, Bruxvoort K, Marx FM, Whittles LK, Lewnard JA. Inference of naturally-acquired immunity using a self-matched negative control design. Epidemiology 2020
Lo NC, Nyathi S, Chapman LAC, Rodriguez-Barraquer I, Kushel M, Bibbins-Domingo K, Lewnard JA. Influenza, mumps, and varicella outbreaks in United States migrant detention centers. JAMA 2020.
Lewnard JA. Uses of pathogen detection data to estimate vaccine direct effects in case-control studies. J Roy Soc Interface 2020.
Lewnard JA, Rogawski McQuade ET, Platts-Mills JA, Kotloff KL, Laxminarayan R. Incidence and etiology of clinically-attended, antibiotic-treated diarrhea among children under five years of age in low- and middle-income countries: evidence from the Global Enteric Multcenter Study. PLoS Negl Trop Dis 2020.
Lewnard JA, Whittles LK, Rick AM, Martin JM. Naturally-acquired protection against upper respiratory symptoms involving group A Streptococcus in a longitudinal cohort study. Clin Infect Dis 2020.
Jewell NP, Lewnard JA, Jewell BL. Predictive mathematical models of the COVID-19 pandemic: Underlying principles and value of projections. JAMA 2020.
Jewell NP, Lewnard JA, Jewell BL. Caution warranted: Using the Institute for Health Metrics and Evaluation (IHME) model for predicting the course of the COVID-19 pandemic. Ann Intern Med 2020.
Lewnard JA, Lo NC. Scientific and ethical basis for contact-reducing interventions against COVID-19. Lancet Infect Dis 2020.
Wohl S, Metsky HC, Schaffner SF, Piantadosi A, Burns M, Lewnard JA, Chak B, Krasilnikova LA, Siddle KJ, Matranga CB, Bankamp B, Hennigan S, Sabina B, Byrne EH, McNall RJ, Shah RR, Qu J, Park DJ, Gharib S, Fitzgerald S, Barreira P, Fleming S, Lett S, Rota PA, Madoff LC, MacInnis BL, Yozwiak NL, Smole S, Grad YH, Sabeti PC. Combining genomics and epidemiology to track mumps virus transmission in the United States. PLoS Biol 2020.
Head JR, Collender PA, Lewnard JA, Skaff NK, Peng Y, Ohringer A, Cheng Q, Baker J, Li C, Liang S, Yang C, Hubbard A, Lopman BA, Remais JV. Early evidence of inactivated enterovirus 71 vaccine impact against hand, foot, and mouth disease in a major center of ongoing transmission in China, 2011–2018: a longitudinal surveillance study. Clin Infect Dis 2020.
Lewnard JA, Givon-Lavi N, Dagan R. Dose-specific effectiveness of 7- and 13-valent pneumococcal conjugate vaccines against vaccine-serotype Streptococcus pneumoniae colonization in children. Clin Infect Dis 2019.
Pitzer VE, Bennett AI, Bar-Zeev N, Jere KC, Lopman BA, Lewnard JA, Parashar UD, Cunliffe NA. Evaluating strategies to improve rotavirus vaccine impact during the second year of life in Malawi. Sci Transl Med 2019.
Lewnard JA, Givon-Lavi N, Dagan R. Interaction with nontypeable Haemophilus influenzae alters progression of Streptococcus pneumonia serotypes from colonization to upper respiratory tract diseases in children in a site-specific manner. J Infect Dis 2019.
Lewnard JA, Lopman BA, Parashar UD, Bennett A, Bar-Zeev N, Cunliffe NA, Samuel P, Guerrero ML, Ruiz-Palacios GM, Kang G, Pitzer VE. Heterogeneous susceptibility to rotavirus infection and gastroenteritis in two birth cohort studies: parameter estimation and epidemiological implications. PLoS Comp Biol 2019.
Lewnard JA, Reingold AL. Emerging challenges and opportunities in infectious disease epidemiology. Am J Epidemiol 2019.
Lewnard JA, Hanage WP. Making sense of differences in pneumococcal serotype replacement. Lancet Infect Dis 2019.
Lewnard JA, Grad Y. Vaccine waning and mumps re-emergence in the United States. Sci Transl Med 2018.
Lewnard JA, Cobey SC. Immune history and influenza vaccine effectiveness. Vaccines 2018.
Phelps MD, Azman AS, Lewnard JA, Antillón M, Simonsen L, Andreasen V, Jensen PKM, Pitzer VE. The importance of thinking beyond the water supply in cholera epidemics: a historical urban case study. PLoS Negl Trop Dis 2017.
Lewnard JA, Givon-Lavi N, Weinberger DM, Lipsitch M, Dagan R. Pan-serotype reduction in progression of Streptococcus pneumoniae to otitis media after rollout of pneumococcal conjugate vaccines. Clin Infect Dis 2017.
Lewnard JA, Lopman BA, Parashar UD, Bar-Zeev N, Samuel P, Guerrero ML, Ruiz-Palacios G, Kang G, Pitzer VE. Naturally-acquired immunity against rotavirus infection and gastroenteritis in children: paired re-analyses of birth-cohort studies. J Infect Dis 2017.
Kunkel A, Lewnard JA, Pitzer VE, Cohen T. Antimicrobial resistance risks of cholera prophylaxis for United Nations peacekeepers. Antimicrob Agents Chemother 2017.
Kürüm E, Warren JL, Schuck-Paim C, Lustig R, Lewnard JA, Fernandes RM, Fuentes R, Bruhn CAW, Taylor RJ, Simonsen L, Weinberger DM. Bayesian model averaging with change points to assess the impact of vaccination and other public health interventions. Epidemiology 2017.
Anwar MY, Lewnard JA, Parikh S, Pitzer VE. Time series analysis of malaria in Afghanistan: using ARIMA models to predict future trends in incidence. Malaria J 2016.
Lewnard JA, Townsend JP. Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India. Proc Natl Acad Sci U S A 2016.
Pham TTH, Apparicio P, Landry S, Lewnard JA. Disentangling the effects of urban form and socio-demographic context on street tree cover: A multi-level analysis from Montreal. Landscape Urban Plan 2017.
Lewnard JA, Huppert A, Givon-Lavi N, Pettigrew MM, Regev-Yochay G, Dagan R, Weinberger DM. Density, serotype diversity, and fitness of Streptococcus pneumoniae in upper respiratory co-colonization with nontypeable Haemophilus influenzae. J Infect Dis 2016.
Lewnard JA, Gonsalves G, Ko AI. Low risk of international Zika virus spread due to the 2016 Olympics in Brazil. Ann Intern Med 2016.
Lewnard JA, Antillón M, Gonsalves G, Miller AC, Ko AI, Pitzer VE. Strategies to prevent cholera introduction during international personnel deployments: a computational modeling analysis based on the 2010 Haiti outbreak. PLoS Med 2016.
Lewnard JA, Jirmanus L, Júnior NN, Machado PR, Glesby MJ, Ko AI, Carvallho EM, Schriefer A, Weinberger DM. Forecasting temporal dynamics of cutaneous leishmaniasis in Northeast Brazil. PLoS Negl Trop Dis 2014.
Rivers C, Alexander K, Bellan S, Del Valle S, Drake JM, Eisenberg JN, Eubank S, Ferrari M, Halloran ME, Galvani AP, Lewis BL, Lewnard JA, Lofgren E, Macal M, Marathe M, Ndeffo Mbah ML, Meyers LA, Meza R, Park A, Porco T, Scarpino SV, Shaman J, Vespignani A, Yang W. Ebola: models do more than forecast. Nature 2014.
Lewnard JA, Berrang-Ford L, Lwasa S, Bambaiha Namanya D, Patterson KA, Donnelly B, Kulkarni MA, Harper SL, Ogden NH, Carcamo CP, IHACC Research Team. Relative undernourishment and food insecurity associations with Plasmodium falciparum among Batwa pygmies in Uganda: evidence from a cross-sectional survey. Am J Trop Med Hyg 2014.