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Volume 32, Number 4—April 2026

Research

Geographically Distinct Circulation of Genotype II and III St. Louis Encephalitis Virus, Texas, USA, 2009–2024

Alexander R. Kneubehl, Daniel P. Rehm, Michael W. Curtis, Bianca M. Wimmer, Bethany Bolling, Angie Broussard, Jeremy Vela, Jennifer Rocha, Lindsey Templeton, Maximea Vigilant, Courtney Standlee, Steven M. Presley, Job E. Lopez, and Shannon E. RoncaComments to Author 
Author affiliation: Baylor College of Medicine, Houston, Texas, USA (A.R. Kneubehl, D.P. Rehm, M.W. Curtis, J.E. Lopez, S.E. Ronca); Texas Children’s Hospital William T. Schearer Center for Human Immunobiology, Houston (A.R. Kneubehl, D.P. Rehm, S.E. Ronca); Texas Tech University Institute of Environmental and Human Health, Lubbock, Texas, USA (B.M. Wimmer, S.M. Presley); Texas Department of State Health Services, Austin, Texas, USA (B. Bolling); Harris County Public Health Division of Mosquito and Vector Control, Houston (A. Broussard, J. Vela, J. Rocha, L. Templeton, M. Vigilant, C. Standlee)

Main Article

Figure 6

Bayesian phylogenetic analysis of SLEV genotype III from Texas and other states from study of circulation of genotype II and III St. Louis encephalitis virus, Texas, USA. Maximum clade credibility time tree of 216 whole genomes inferred by using BEAST (34). Tip colors reflect sample’s place of origin. Texas samples are further subdivided by county. Clade annotations are indicated to right of tips. Posterior probability for each node is indicated at node with a colored diamond. The y-axis scales in years are based on date of sample collection. Arrow labels indicate time to most recent common ancestor and 95% highest posterior density for each clade.

Figure 6. Bayesian phylogenetic analysis of SLEV genotype III from Texas and other states from study of circulation of genotype II and III St. Louis encephalitis virus, Texas, USA. Maximum clade credibility time tree of 216 whole genomes inferred by using BEAST (34). Tip colors reflect sample’s place of origin. Texas samples are further subdivided by county. Clade annotations are indicated to right of tips. Posterior probability for each node is indicated at node with a colored diamond. The y-axis scales in years are based on date of sample collection. Arrow labels indicate time to most recent common ancestor and 95% highest posterior density for each clade.

Main Article

References
  1. Diaz  A, Coffey  LL, Burkett-Cadena  N, Day  JF. Reemergence of St. Louis Encephalitis Virus in the Americas. Emerg Infect Dis. 2018;24:2150–7. DOIPubMedGoogle Scholar
  2. Reisen  WK, Fang  Y, Martinez  VM. Avian host and mosquito (Diptera: Culicidae) vector competence determine the efficiency of West Nile and St. Louis encephalitis virus transmission. J Med Entomol. 2005;42:367–75. DOIPubMedGoogle Scholar
  3. Reisen  WK, Chiles  RE, Martinez  VM, Fang  Y, Green  EN. Experimental infection of California birds with western equine encephalomyelitis and St. Louis encephalitis viruses. J Med Entomol. 2003;40:968–82. DOIPubMedGoogle Scholar
  4. Gruwell  JA, Fogarty  CL, Bennett  SG, Challet  GL, Vanderpool  KS, Jozan  M, et al. Role of peridomestic birds in the transmission of St. Louis encephalitis virus in southern California. J Wildl Dis. 2000;36:13–34. DOIPubMedGoogle Scholar
  5. McLean  RG, Mullenix  J, Kerschner  J, Hamm  J. The house sparrow (Passer domesticus) as a sentinel for St. Louis encephalitis virus. Am J Trop Med Hyg. 1983;32:1120–9. DOIPubMedGoogle Scholar
  6. Leake  J, Musson  E, Chope  H. Epidemiology of epidemic encephalitis, St. Louis type. JAMA. 1934;103:728–31. DOIGoogle Scholar
  7. Curren  EJ, Lindsey  NP, Fischer  M, Hills  SLSS. Louis encephalitis virus disease in the United States, 2003–2017. Am J Trop Med Hyg. 2018;99:1074–9. DOIPubMedGoogle Scholar
  8. Danforth  ME, Snyder  RE, Feiszli  T, Bullick  T, Messenger  S, Hanson  C, et al. Epidemiologic and environmental characterization of the re-emergence of St. Louis encephalitis virus in California, 2015–2020. PLoS Negl Trop Dis. 2022;16:e0010664. DOIPubMedGoogle Scholar
  9. Venkat  H, Krow-Lucal  E, Kretschmer  M, Sylvester  T, Levy  C, Adams  L, et al. Comparison of characteristics of patients with West Nile Virus or St. Louis encephalitis virus neuroinvasive disease during concurrent outbreaks, Maricopa County, Arizona, 2015. Vector Borne Zoonotic Dis. 2020;20:624–9. DOIPubMedGoogle Scholar
  10. Centers for Disease Control and Prevention (CDC). Outbreak of West Nile-like viral encephalitis—New York, 1999. MMWR Morb Mortal Wkly Rep. 1999;48:845–9.PubMedGoogle Scholar
  11. Reisen  WK, Lothrop  HD, Wheeler  SS, Kennsington  M, Gutierrez  A, Fang  Y, et al. Persistent West Nile virus transmission and the apparent displacement St. Louis encephalitis virus in southeastern California, 2003-2006. J Med Entomol. 2008;45:494–508.PubMedGoogle Scholar
  12. Reimann  CA, Hayes  EB, DiGuiseppi  C, Hoffman  R, Lehman  JA, Lindsey  NP, et al. Epidemiology of neuroinvasive arboviral disease in the United States, 1999-2007. Am J Trop Med Hyg. 2008;79:974–9. DOIPubMedGoogle Scholar
  13. Mackenzie  JS, Barrett  AD, Deubel  V. The Japanese encephalitis serological group of flaviviruses: a brief introduction to the group. Curr Top Microbiol Immunol. 2002;267:1–10. DOIPubMedGoogle Scholar
  14. Fang  Y, Reisen  WK. Previous infection with West Nile or St. Louis encephalitis viruses provides cross protection during reinfection in house finches. Am J Trop Med Hyg. 2006;75:480–5. DOIPubMedGoogle Scholar
  15. Bosco-Lauth  AM, Kooi  K, Hawks  SA, Duggal  NK. Cross-protection between West Nile virus and emerging flaviviruses in wild birds. Am J Trop Med Hyg. 2024;112:657–62. DOIPubMedGoogle Scholar
  16. Kramer  LD, Chandler  LJ. Phylogenetic analysis of the envelope gene of St. Louis encephalitis virus. Arch Virol. 2001;146:2341–55. DOIPubMedGoogle Scholar
  17. Rodrigues  SG, Nunes  MR, Casseb  SM, Prazeres  AS, Rodrigues  DS, Silva  MO, et al. Molecular epidemiology of Saint Louis encephalitis virus in the Brazilian Amazon: genetic divergence and dispersal. J Gen Virol. 2010;91:2420–7. DOIPubMedGoogle Scholar
  18. Diaz  LA, Ré  V, Almirón  WR, Farías  A, Vázquez  A, Sanchez-Seco  MP, et al. Genotype III Saint Louis encephalitis virus outbreak, Argentina, 2005. Emerg Infect Dis. 2006;12:1752–4. DOIPubMedGoogle Scholar
  19. Venkat  H, Krow-Lucal  E, Hennessey  M, Jones  J, Adams  L, Fischer  M, et al. Concurrent outbreaks of St. Louis encephalitis virus and West Nile Virus disease—Arizona, 2015. MMWR Morb Mortal Wkly Rep. 2015;64:1349–50.PubMedGoogle Scholar
  20. White  GS, Symmes  K, Sun  P, Fang  Y, Garcia  S, Steiner  C, et al. Reemergence of St. Louis encephalitis Virus, California, 2015. Emerg Infect Dis. 2016;22:2185–8. DOIPubMedGoogle Scholar
  21. Ridenour  CL, Cocking  J, Poidmore  S, Erickson  D, Brock  B, Valentine  M, et al. St. Louis encephalitis virus in the southwestern United States: a phylogeographic case for a multi-variant introduction event. Front Genet. 2021;12:667895. DOIPubMedGoogle Scholar
  22. Swetnam  DM, Stuart  JB, Young  K, Maharaj  PD, Fang  Y, Garcia  S, et al. Movement of St. Louis encephalitis virus in the Western United States, 2014- 2018. PLoS Negl Trop Dis. 2020;14:e0008343. DOIPubMedGoogle Scholar
  23. Chandler  LJ, Parsons  R, Randle  Y. Multiple genotypes of St. Louis encephalitis virus (Flaviviridae: Flavivirus) circulate in Harris County, Texas. Am J Trop Med Hyg. 2001;64:12–9. DOIPubMedGoogle Scholar
  24. Lillibridge  KM, Parsons  R, Randle  Y, Travassos da Rosa  AP, Guzman  H, Siirin  M, et al. The 2002 introduction of West Nile virus into Harris County, Texas, an area historically endemic for St. Louis encephalitis. Am J Trop Med Hyg. 2004;70:676–81. DOIPubMedGoogle Scholar
  25. Williams  KH, Hollinger  FB, Metzger  WR, Hopkins  CC, Chamberlain  RW. The epidemiology of St. Louis encephalitis in Corpus Christi, Texas, 1966. Am J Epidemiol. 1975;102:16–24. DOIPubMedGoogle Scholar
  26. Luby  JP, Miller  G, Gardner  P, Pigford  CA, Henderson  BE, Eddins  D. The epidemiology of St. Louis encephalitis in Houston, Texas, 1964. Am J Epidemiol. 1967;86:584–97. DOIPubMedGoogle Scholar
  27. Kneubehl  AR. Texas-SLEV-genome-surveillance. 2025 [cited 2025 Jan 1]. https://github.com/kneubehl/Texas-SLEV-Genome-Surveillance
  28. Lanciotti  RS, Kerst  AJ. Nucleic acid sequence-based amplification assays for rapid detection of West Nile and St. Louis encephalitis viruses. J Clin Microbiol. 2001;39:4506–13. DOIPubMedGoogle Scholar
  29. Wang  MX, Lou  EG, Sapoval  N, Kim  E, Kalvapalle  P, Kille  B, et al. Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens. Nat Commun. 2024;15:6306. DOIPubMedGoogle Scholar
  30. Katoh  K, Standley  DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80. DOIPubMedGoogle Scholar
  31. Hoang  DT, Chernomor  O, von Haeseler  A, Minh  BQ, Vinh  LS. UFBoot2: Improving the ultrafast bootstrap approximation. Mol Biol Evol. 2018;35:518–22. DOIPubMedGoogle Scholar
  32. Minh  BQ, Schmidt  HA, Chernomor  O, Schrempf  D, Woodhams  MD, von Haeseler  A, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37:1530–4. DOIPubMedGoogle Scholar
  33. Rambaut  A, Lam  TT, Max Carvalho  L, Pybus  OG. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2016;2:vew007. DOIPubMedGoogle Scholar
  34. Drummond  AJ, Rambaut  A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007;7:214. DOIPubMedGoogle Scholar
  35. May  FJ, Li  L, Zhang  S, Guzman  H, Beasley  DWC, Tesh  RB, et al. Genetic variation of St. Louis encephalitis virus. J Gen Virol. 2008;89:1901–10. DOIPubMedGoogle Scholar
  36. Auguste  AJ, Pybus  OG, Carrington  CV. Evolution and dispersal of St. Louis encephalitis virus in the Americas. Infect Genet Evol. 2009;9:709–15. DOIPubMedGoogle Scholar
  37. Lincoln  FC. The waterfowl flyways of North America. Washington: US Department of Agriculture; 1935. p. 7–8.
  38. Tasi  TF, Smith  GC, Ndukwu  M, Jakob  WL, Happ  CM, Kirk  LJ, et al. Entomologic studies after a St. Louis encephalitis epidemic in Grand Junction, Colorado. Am J Epidemiol. 1988;128:285–97. DOIPubMedGoogle Scholar
  39. Hayes  RO, LaMotte  LC, Holden  P. Ecology of arboviruses in Hale County, Texas, during 1965. Am J Trop Med Hyg. 1967;16:675–87.PubMedGoogle Scholar
  40. Gorris  ME, Bartlow  AW, Temple  SD, Romero-Alvarez  D, Shutt  DP, Fair  JM, et al. Updated distribution maps of predominant Culex mosquitoes across the Americas. Parasit Vectors. 2021;14:547. DOIPubMedGoogle Scholar
  41. Luby  JP, Haley  RW. Recurrent St. Louis encephalitis infection in residents of a flood plain of the Trinity River, Roosevelt Heights (Dallas, Texas). Am J Epidemiol. 1972;96:107–13. DOIPubMedGoogle Scholar
  42. Wiseman  J, Grimes  J, Eads  RS. Louis encephalitis outbreak in Cameron County, Texas. Mosq News. 1959;19. DOIGoogle Scholar
  43. Erickson  TA, Ronca  SE, Gunter  SM, Brown  EL, Hasbun  R, Murray  KO. Zoonotic disease testing practices in pediatric patients with meningitis and encephalitis in a subtropical region. Pathogens. 2022;11:501. DOIPubMedGoogle Scholar
  44. Vanichanan  J, Salazar  L, Wootton  SH, Aguilera  E, Garcia  MN, Murray  KO, et al. Use of testing for West Nile virus and other arboviruses. Emerg Infect Dis. 2016;22:1587–93. DOIPubMedGoogle Scholar

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Page created: March 04, 2026
Page updated: March 31, 2026
Page reviewed: March 31, 2026
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