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Sarah E. Cobey

Associate Professor
cobey@uchicago.edu
Websites
Research Summary
Broadly, my group investigates the coevolution of pathogens and hosts’ adaptive immunity. We use computational and mathematical tools to test hypotheses and to advance theory. Our earlier work focused on the evolutionary consequences of immune-mediated competition between different pathogen strains, including pneumococcus, human papillomavirus, and especially influenza. More recently, our focus has expanded to include the related dynamics of the host immune response. We are investigating the evolution of antibody repertoires within hosts over time, in particular to identify the roles of infection history, chance, vaccination, and host genetics in generating the diversity of B cell responses. This research involves linking epidemiological and immunological observations of B cells to the antigenic and genetic evolution of influenza viruses. Consequently, it makes extensive use of longitudinal dynamical models of individuals and birth cohorts as well as techniques from molecular evolution to investigate coevolution across scales. Understanding the dynamics of vaccination is another area of focus. We have investigated the actual and expected impacts of vaccines against pneumococcus, human papillomavirus, and influenza. With influenza, we have been investigating the impact of the vaccine on viral transmission and local evolution and how immune history might reduce the vaccine’s effectiveness and alter selective pressures. Improving vaccination strategies given hosts’ diverse immune histories and the potential for rapid evolution by the pathogen is a long-term aim of our work. Ultimately, we want to explain coevolution sufficiently well to enable prediction, or at least to determine when prediction is not feasible.
Keywords
coevolution, infectious disease dynamics, influenza, mathematical modeling, vaccination, B cells
Education
  • Princeton University, AB Ecology & Evolution 2002
  • University of Michigan, Ann Arbor, PhD Ecology & Evolution 2009
  • Harvard School of Public Health, Postdoctoral Infectious disease dynamics 2013
Biosciences Graduate Program Association
Awards & Honors
  • 2002 - Phi Beta Kappa Princeton University
  • 2002 - Senior Book Prize, Ecology & Evolution Princeton University
  • 2002 - Sigma Xi Society Princeton University
  • 2005 - NSF Graduate Research Fellowship University of Michigan
  • 2011 - NIH Kirchstein National Research Service Award Harvard School of Public Health
  • 2014 - James S. McDonnell Foundation Complex Systems Scholar Award University of Chicago
  • 2014 - NIH New Innovator Award University of Chicago
  • 2016 - Neubauer Faculty Development Fellowship University of Chicago
Publications

  1. Simon V, Kota V, Bloomquist RF, Hanley HB, Forgacs D, Pahwa S, Pallikkuth S, Miller LG, Schaenman J, Yeaman MR, Manthei D, Wolf J, Gaur AH, Estepp JH, Srivastava K, Carreño JM, Cuevas F. PARIS and SPARTA: Finding the Achilles' Heel of SARS-CoV-2. mSphere. 2022 May 19; e0017922. View in: PubMed

  2. Goyal S, Gerardin J, Cobey S, Son C, McCarthy O, Dror A, Lightner S, Ezike NO, Duffus WA, Bennett AC. SARS-CoV-2 Infection Among Pregnant People at Labor and Delivery and Changes in Infection Rates in the General Population: Lessons Learned From Illinois. Public Health Rep. 2022 May 05; 333549221091826. View in: PubMed

  3. Lin Y, Yang B, Cobey S, Lau EHY, Adam DC, Wong JY, Bond HS, Cheung JK, Ho F, Gao H, Ali ST, Leung NHL, Tsang TK, Wu P, Leung GM, Cowling BJ. Incorporating temporal distribution of population-level viral load enables real-time estimation of COVID-19 transmission. Nat Commun. 2022 03 03; 13(1):1155. View in: PubMed

  4. Du Z, Wang L, Pandey A, Lim WW, Chinazzi M, Piontti APY, Lau EHY, Wu P, Malani A, Cobey S, Cowling BJ. Modeling comparative cost-effectiveness of SARS-CoV-2 vaccine dose fractionation in India. Nat Med. 2022 05; 28(5):934-938. View in: PubMed

  5. Wen FT, Malani A, Cobey S. The Potential Beneficial Effects of Vaccination on Antigenically Evolving Pathogens. Am Nat. 2022 02; 199(2):223-237. View in: PubMed

  6. Grubaugh ND, Cobey S. Of variants and vaccines. Cell. 2021 12 22; 184(26):6222-6223. View in: PubMed

  7. Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday JD, Bosse NI, Sherrat K, Thompson RN, White LF, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S. Correction: Practical considerations for measuring the effective reproductive number, Rt. PLoS Comput Biol. 2021 Dec; 17(12):e1009679. View in: PubMed

  8. Clipman SJ, Wesolowski A, Mehta SH, Cobey S, Cummings DAT, Solomon SS. Improvements in Severe Acute Respiratory Syndrome Coronavirus 2 Testing Cascade in the United States: Data From Serial Cross-sectional Assessments. Clin Infect Dis. 2022 05 03; 74(9):1534-1542. View in: PubMed

  9. Vieira MC, Donato CM, Arevalo P, Rimmelzwaan GF, Wood T, Lopez L, Huang QS, Dhanasekaran V, Koelle K, Cobey S. Lineage-specific protection and immune imprinting shape the age distributions of influenza B cases. Nat Commun. 2021 07 14; 12(1):4313. View in: PubMed

  10. Cowling BJ, Lim WW, Cobey S. Fractionation of COVID-19 vaccine doses could extend limited supplies and reduce mortality. Nat Med. 2021 08; 27(8):1321-1323. View in: PubMed

  11. Guthmiller JJ, Utset HA, Henry C, Li L, Zheng NY, Sun W, Costa Vieira M, Zost S, Huang M, Hensley SE, Cobey S, Palese P, Wilson PC. An Egg-Derived Sulfated N-Acetyllactosamine Glycan Is an Antigenic Decoy of Influenza Virus Vaccines. mBio. 2021 06 29; 12(3):e0083821. View in: PubMed

  12. Holden TM, Richardson RAK, Arevalo P, Duffus WA, Runge M, Whitney E, Wise L, Ezike NO, Patrick S, Cobey S, Gerardin J. Geographic and demographic heterogeneity of SARS-CoV-2 diagnostic testing in Illinois, USA, March to December 2020. BMC Public Health. 2021 06 10; 21(1):1105. View in: PubMed

  13. Lutrick K, Ellingson KD, Baccam Z, Rivers P, Beitel S, Parker J, Hollister J, Sun X, Gerald JK, Komatsu K, Kim E, LaFleur B, Grant L, Yoo YM, Kumar A, Mayo Lamberte J, Cowling BJ, Cobey S, Thornburg NJ, Meece JK, Kutty P, Nikolich-Zugich J, Thompson MG, Burgess JL. COVID-19 Infection, Reinfection, and Vaccine Effectiveness in a Prospective Cohort of Arizona Frontline/Essential Workers: The AZ HEROES Research Protocol. JMIR Res Protoc. 2021 May 26. View in: PubMed

  14. Bloom JD, Chan YA, Baric RS, Bjorkman PJ, Cobey S, Deverman BE, Fisman DN, Gupta R, Iwasaki A, Lipsitch M, Medzhitov R, Neher RA, Nielsen R, Patterson N, Stearns T, van Nimwegen E, Worobey M, Relman DA. Investigate the origins of COVID-19. Science. 2021 05 14; 372(6543):694. View in: PubMed

  15. Holden TM, Richardson RAK, Arevalo P, Duffus WA, Runge M, Whitney E, Wise L, Ezike NO, Patrick S, Cobey S, Gerardin J. Geographic and demographic heterogeneity of SARS-CoV-2 diagnostic testing in Illinois, USA, March to December 2020. medRxiv. 2021 Apr 20. View in: PubMed

  16. Cobey S, Larremore DB, Grad YH, Lipsitch M. Concerns about SARS-CoV-2 evolution should not hold back efforts to expand vaccination. Nat Rev Immunol. 2021 05; 21(5):330-335. View in: PubMed

  17. Bubar KM, Reinholt K, Kissler SM, Lipsitch M, Cobey S, Grad YH, Larremore DB. Model-informed COVID-19 vaccine prioritization strategies by age and serostatus. Science. 2021 02 26; 371(6532):916-921. View in: PubMed

  18. Clipman SJ, Wesolowski A, Mehta SH, Agarwal S, Cobey SE, Cummings DAT, Gibson DG, Labrique AB, Kirk GD, Solomon SS. SARS-CoV-2 Testing in Florida, Illinois, and Maryland: Access and Barriers. medRxiv. 2020 Dec 24. View in: PubMed

  19. Bubar KM, Reinholt K, Kissler SM, Lipsitch M, Cobey S, Grad YH, Larremore DB. Model-informed COVID-19 vaccine prioritization strategies by age and serostatus. medRxiv. 2021 Jan 08. View in: PubMed

  20. Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday JD, Bosse NI, Sherrat K, Thompson RN, White LF, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S. Practical considerations for measuring the effective reproductive number, Rt. PLoS Comput Biol. 2020 12; 16(12):e1008409. View in: PubMed

  21. Dugan HL, Guthmiller JJ, Arevalo P, Huang M, Chen YQ, Neu KE, Henry C, Zheng NY, Lan LY, Tepora ME, Stovicek O, Bitar D, Palm AE, Stamper CT, Changrob S, Utset HA, Coughlan L, Krammer F, Cobey S, Wilson PC. Preexisting immunity shapes distinct antibody landscapes after influenza virus infection and vaccination in humans. Sci Transl Med. 2020 12 09; 12(573). View in: PubMed

  22. Gouma S, Kim K, Weirick ME, Gumina ME, Branche A, Topham DJ, Martin ET, Monto AS, Cobey S, Hensley SE. Middle-aged individuals may be in a perpetual state of H3N2 influenza virus susceptibility. Nat Commun. 2020 09 11; 11(1):4566. View in: PubMed

  23. Arevalo P, McLean HQ, Belongia EA, Cobey S. Earliest infections predict the age distribution of seasonal influenza A cases. Elife. 2020 07 07; 9. View in: PubMed

  24. Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay J, De Salazar PM, Hellewell J, Meakin S, Munday J, Bosse NI, Sherrat K, Thompson RN, White LF, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S. Practical considerations for measuring the effective reproductive number, Rt. medRxiv. 2020 Aug 28. View in: PubMed

  25. Caudill VR, Qin S, Winstead R, Kaur J, Tisthammer K, Pineda EG, Solis C, Cobey S, Bedford T, Carja O, Eggo RM, Koelle K, Lythgoe K, Regoes R, Roy S, Allen N, Aviles M, Baker BA, Bauer W, Bermudez S, Carlson C, Castellanos E, Catalan FL, Chemel AK, Elliot J, Evans D, Fiutek N, Fryer E, Goodfellow SM, Hecht M, Hopp K, Hopson ED, Jaberi A, Kinney C, Lao D, Le A, Lo J, Lopez AG, López A, Lorenzo FG, Luu GT, Mahoney AR, Melton RL, Nascimento GD, Pradhananga A, Rodrigues NS, Shieh A, Sims J, Singh R, Sulaeman H, Thu R, Tran K, Tran L, Winters EJ, Wong A, Pennings PS. CpG-creating mutations are costly in many human viruses. Evol Ecol. 2020; 34(3):339-359. View in: PubMed

  26. Cobey S. Modeling infectious disease dynamics. Science. 2020 May 15; 368(6492):713-714. View in: PubMed

  27. Gouma S, Zost SJ, Parkhouse K, Branche A, Topham DJ, Cobey S, Hensley SE. Comparison of Human H3N2 Antibody Responses Elicited by Egg-Based, Cell-Based, and Recombinant Protein-Based Influenza Vaccines During the 2017-2018 Season. Clin Infect Dis. 2020 09 12; 71(6):1447-1453. View in: PubMed

  28. Ranjeva S, Subramanian R, Fang VJ, Leung GM, Ip DKM, Perera RAPM, Peiris JSM, Cowling BJ, Cobey S. Age-specific differences in the dynamics of protective immunity to influenza. Nat Commun. 2019 04 10; 10(1):1660. View in: PubMed

  29. Henry C, Zheng NY, Huang M, Cabanov A, Rojas KT, Kaur K, Andrews SF, Palm AE, Chen YQ, Li Y, Hoskova K, Utset HA, Vieira MC, Wrammert J, Ahmed R, Holden-Wiltse J, Topham DJ, Treanor JJ, Ertl HC, Schmader KE, Cobey S, Krammer F, Hensley SE, Greenberg H, He XS, Wilson PC. Influenza Virus Vaccination Elicits Poorly Adapted B Cell Responses in Elderly Individuals. Cell Host Microbe. 2019 03 13; 25(3):357-366.e6. View in: PubMed

  30. Cobey S. Repeated Vaccination May Protect Children From Influenza Infection. JAMA Netw Open. 2018 10 05; 1(6):e183730. View in: PubMed

  31. Neu KE, Guthmiller JJ, Huang M, La J, Vieira MC, Kim K, Zheng NY, Cortese M, Tepora ME, Hamel NJ, Rojas KT, Henry C, Shaw D, Dulberger CL, Pulendran B, Cobey S, Khan AA, Wilson PC. Spec-seq unveils transcriptional subpopulations of antibody-secreting cells following influenza vaccination. J Clin Invest. 2019 01 02; 129(1):93-105. View in: PubMed

  32. Cai FY, Fussell T, Cobey S, Lipsitch M. Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine. PLoS Comput Biol. 2018 10; 14(10):e1006333. View in: PubMed

  33. Wen FT, Bell SM, Bedford T, Cobey S. Estimating Vaccine-Driven Selection in Seasonal Influenza. Viruses. 2018 09 18; 10(9). View in: PubMed

  34. Wilson PC, Cobey S. Characterization of the immunologic repertoire: A quick start guide. Immunol Rev. 2018 07; 284(1):5-8. View in: PubMed

  35. Lewnard JA, Cobey S. Immune History and Influenza Vaccine Effectiveness. Vaccines (Basel). 2018 May 21; 6(2). View in: PubMed

  36. Vieira MC, Zinder D, Cobey S. Selection and Neutral Mutations Drive Pervasive Mutability Losses in Long-Lived Anti-HIV B-Cell Lineages. Mol Biol Evol. 2018 05 01; 35(5):1135-1146. View in: PubMed

  37. Cobey S, Grad YH. Response to Skowronski and De Serres. Clin Infect Dis. 2018 10 15; 67(9):1476. View in: PubMed

  38. Cobey S, Gouma S, Parkhouse K, Chambers BS, Ertl HC, Schmader KE, Halpin RA, Lin X, Stockwell TB, Das SR, Landon E, Tesic V, Youngster I, Pinsky BA, Wentworth DE, Hensley SE, Grad YH. Poor Immunogenicity, Not Vaccine Strain Egg Adaptation, May Explain the Low H3N2 Influenza Vaccine Effectiveness in 2012-2013. Clin Infect Dis. 2018 07 18; 67(3):327-333. View in: PubMed

  39. Ranjeva SL, Baskerville EB, Dukic V, Villa LL, Lazcano-Ponce E, Giuliano AR, Dwyer G, Cobey S. Recurring infection with ecologically distinct HPV types can explain high prevalence and diversity. Proc Natl Acad Sci U S A. 2017 12 19; 114(51):13573-13578. View in: PubMed

  40. Zost SJ, Parkhouse K, Gumina ME, Kim K, Diaz Perez S, Wilson PC, Treanor JJ, Sant AJ, Cobey S, Hensley SE. Contemporary H3N2 influenza viruses have a glycosylation site that alters binding of antibodies elicited by egg-adapted vaccine strains. Proc Natl Acad Sci U S A. 2017 11 21; 114(47):12578-12583. View in: PubMed

  41. Cobey S. Sick if you do, sick if you don't. Nat Ecol Evol. 2017 11; 1(11):1602-1603. View in: PubMed

  42. Cobey S, Baskerville EB, Colijn C, Hanage W, Fraser C, Lipsitch M. Host population structure and treatment frequency maintain balancing selection on drug resistance. J R Soc Interface. 2017 08; 14(133). View in: PubMed

  43. Pessia A, Grad Y, Cobey S, Puranen JS, Corander J. K-Pax2: Bayesian identification of cluster-defining amino acid positions in large sequence datasets. Microb Genom. 2015 Jul; 1(1):e000025. View in: PubMed

  44. Baskerville EB, Cobey S. Does influenza drive absolute humidity? Proc Natl Acad Sci U S A. 2017 03 21; 114(12):E2270-E2271. View in: PubMed

  45. Cobey S, Hensley SE. Immune history and influenza virus susceptibility. Curr Opin Virol. 2017 02; 22:105-111. View in: PubMed

  46. Cobey S, Baskerville EB. Limits to Causal Inference with State-Space Reconstruction for Infectious Disease. PLoS One. 2016; 11(12):e0169050. View in: PubMed

  47. Lipsitch M, Barclay W, Raman R, Russell CJ, Belser JA, Cobey S, Kasson PM, Lloyd-Smith JO, Maurer-Stroh S, Riley S, Beauchemin CA, Bedford T, Friedrich TC, Handel A, Herfst S, Murcia PR, Roche B, Wilke CO, Russell CA. Viral factors in influenza pandemic risk assessment. Elife. 2016 11 11; 5. View in: PubMed

  48. Wen F, Bedford T, Cobey S. Explaining the geographical origins of seasonal influenza A (H3N2). Proc Biol Sci. 2016 09 14; 283(1838). View in: PubMed

  49. Childs LM, Baskerville EB, Cobey S. Trade-offs in antibody repertoires to complex antigens. Philos Trans R Soc Lond B Biol Sci. 2015 Sep 05; 370(1676). View in: PubMed

  50. Cobey S, Wilson P, Matsen FA. The evolution within us. Philos Trans R Soc Lond B Biol Sci. 2015 Sep 05; 370(1676). View in: PubMed

  51. Perron GG, Inglis RF, Pennings PS, Cobey S. Fighting microbial drug resistance: a primer on the role of evolutionary biology in public health. Evol Appl. 2015 Mar; 8(3):211-22. View in: PubMed

  52. Cobey S. Pathogen evolution and the immunological niche. Ann N Y Acad Sci. 2014 Jul; 1320:1-15. View in: PubMed

  53. Shogan BD, Smith DP, Packman AI, Kelley ST, Landon EM, Bhangar S, Vora GJ, Jones RM, Keegan K, Stephens B, Ramos T, Kirkup BC, Levin H, Rosenthal M, Foxman B, Chang EB, Siegel J, Cobey S, An G, Alverdy JC, Olsiewski PJ, Martin MO, Marrs R, Hernandez M, Christley S, Morowitz M, Weber S, Gilbert J. The Hospital Microbiome Project: Meeting report for the 2nd Hospital Microbiome Project, Chicago, USA, January 15(th), 2013. Stand Genomic Sci. 2013 Jul 30; 8(3):571-9. View in: PubMed

  54. Ampofo WK, Baylor N, Cobey S, Cox NJ, Daves S, Edwards S, Ferguson N, Grohmann G, Hay A, Katz J, Kullabutr K, Lambert L, Levandowski R, Mishra AC, Monto A, Siqueira M, Tashiro M, Waddell AL, Wairagkar N, Wood J, Zambon M, Zhang W. Improving influenza vaccine virus selection: report of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14-16 June 2010. Influenza Other Respir Viruses. 2013 Sep; 7 Suppl 2:52-3. View in: PubMed

  55. Cobey S, Lipsitch M. Pathogen diversity and hidden regimes of apparent competition. Am Nat. 2013 Jan; 181(1):12-24. View in: PubMed

  56. Cobey S, Lipsitch M. Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes. Science. 2012 Mar 16; 335(6074):1376-80. View in: PubMed

  57. Flanagan ML, Parrish CR, Cobey S, Glass GE, Bush RM, Leighton TJ. Anticipating the species jump: surveillance for emerging viral threats. Zoonoses Public Health. 2012 May; 59(3):155-63. View in: PubMed

  58. Improving influenza vaccine virus selection: report of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14-16 June 2010. Influenza Other Respir Viruses. 2012 Mar; 6(2):142-52, e1-5. View in: PubMed

  59. Bedford T, Cobey S, Pascual M. Strength and tempo of selection revealed in viral gene genealogies. BMC Evol Biol. 2011 Jul 25; 11:220. View in: PubMed

  60. Goldstein E, Cobey S, Takahashi S, Miller JC, Lipsitch M. Predicting the epidemic sizes of influenza A/H1N1, A/H3N2, and B: a statistical method. PLoS Med. 2011 Jul; 8(7):e1001051. View in: PubMed

  61. Cobey S, Pascual M. Consequences of host heterogeneity, epitope immunodominance, and immune breadth for strain competition. J Theor Biol. 2011 Feb 07; 270(1):80-7. View in: PubMed

  62. Bedford T, Cobey S, Beerli P, Pascual M. Global migration dynamics underlie evolution and persistence of human influenza A (H3N2). PLoS Pathog. 2010 May 27; 6(5):e1000918. View in: PubMed

  63. Cobey S, Pascual M, Dieckmann U. Ecological factors driving the long-term evolution of influenza's host range. Proc Biol Sci. 2010 Sep 22; 277(1695):2803-10. View in: PubMed

  64. Cobey S, Koelle K. Capturing escape in infectious disease dynamics. Trends Ecol Evol. 2008 Oct; 23(10):572-7. View in: PubMed

  65. Koelle K, Cobey S, Grenfell B, Pascual M. Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science. 2006 Dec 22; 314(5807):1898-903. View in: PubMed
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