Cristian Koepfli Assistant Professor

Molecular Epidemiology of Infectious Diseases
Cristian Koepfli

Research Interests:

Research in our lab explores how molecular tools can be used to better understand the transmission of malaria and other infectious diseases. Despite recent successes in the reduction of clinical malaria cases, malaria control faces a number of challenges. A large proportion of all infections do not result in febrile illness and thus patients typically do not seek treatment, yet these untreated infections often contribute to onward transmission. Clinical diagnosis in endemic countries often lacks sensitivity, adding to the number of untreated infections. Transmission is often highly focal in space and time, but the drivers of this heterogeneity are poorly understood.

We use a range of methods to diagnose, quantify and genotype parasites and their transmission stages, and in close collaborations with research institutes in endemic countries, we apply them to large population-based surveys. Using sensitive molecular diagnosis we aim to understand the proportion of infections missed by standard clinical diagnosis, and the proportion of infections not associated with fever. Not all infections are equally infective to mosquitos, and infectivity likely changes over the course of an infection. Through the quantification of transmission stages, in combination with experimental mosquito feeding experiments, we can understand what and when individuals are infective. We use genotyping methods to assess transmission networks, and to understand the spread of mutations impairing our ability to detect parasites with common diagnostic tools. Ultimately we aim to contribute to new tools and strategies for the control and eventual elimination of infectious diseases.



  • Assistant Professor, Department of Biological Sciences & Eck Institute for Global Health, University of Notre Dame  2018 - Present
  • Assistant Project Scientist, University of California Irvine, USA  2016-2018
  • Postdoctoral Fellow, Walter and Eliza Hall Institute for Medical Research, Australia  2012-2016
  • PhD, Swiss Tropical and Public Health Institute, Switzerland  2012


Recent Papers:

  • Koepfli C, Yan G. Plasmodium Gametocytes in Field Studies: Do We Measure Commitment to Transmission or Detectability? Trends Parasitol. 2018 May;34(5):378-387. doi: 10.1016/
  • Waltmann A, Koepfli C, Tessier N, Karl S, Fola A, Darcy AW, Wini L, Harrison GLA, Barnadas C, Jennison C, Karunajeewa H, Boyd S, Whittaker M, Kazura J, Bahlo M, Mueller I, Barry AE. Increasingly inbred and fragmented populations of Plasmodium vivax associated with the eastward decline in malaria transmission across the Southwest Pacific. PLoS Negl Trop Dis. 2018 Jan 26;12(1):e0006146. doi: 10.1371/journal.pntd.0006146. eCollection 2018 Jan.
  • Lerch A, Koepfli C, Hofmann NE, Messerli C, Wilcox S, Kattenberg JH, Betuela I, O'Connor L, Mueller I, Felger I. Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections. BMC Genomics. 2017 Nov 13;18(1):864. doi: 10.1186/s12864-017-4260-y.
  • Koepfli C, Ome-Kaius M, Jally S, Malau E, Maripal S, Ginny J, Timinao L, Kattenberg JH, Obadia T, White M, Rarau P, Senn N, Barry AE, Kazura JW, Mueller I, Robinson LJ. Sustained Malaria Control Over an 8-Year Period in Papua New Guinea: The Challenge of Low-Density Asymptomatic Plasmodium Infections. J Infect Dis. 2017 Dec 12;216(11):1434-1443. doi: 10.1093/infdis/jix507.
  • Koepfli C, Rodrigues PT, Antao T, Orjuela-Sánchez P, Van den Eede P, Gamboa D, van Hong N, Bendezu J, Erhart A, Barnadas C, Ratsimbasoa A, Menard D, Severini C, Menegon M, Nour BY, Karunaweera N, Mueller I, Ferreira MU, Felger I. Plasmodium vivax Diversity and Population Structure across Four Continents. PLoS Negl Trop Dis. 2015 Jun 30;9(6):e0003872. doi: 10.1371/journal.pntd.0003872.
  • Koepfli C, Colborn KL, Kiniboro B, Lin E, Speed TP, Siba PM, Felger I, Mueller I. A high force of plasmodium vivax blood-stage infection drives the rapid acquisition of immunity in papua new guinean children. PLoS Negl Trop Dis. 2013 Sep 5;7(9):e2403. doi: 10.1371/journal.pntd.0002403.