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Functional variation at an expressed MHC class IIβ locus associates with Ranavirus infection intensity in larval anuran populations


Infectious diseases are causing catastrophic losses to global biodiversity. Iridoviruses in the genus Ranavirus are among the leading causes of amphibian disease-related mortality. Polymorphisms in major histocompatibility complex (MHC) genes are significantly associated with variation in amphibian pathogen susceptibility. MHC genes encode two classes of polymorphic cell-surface molecules that can recognize and bind to diverse pathogen peptides. While MHC class I genes are the classic mediators of viral-acquired immunity, larval amphibians do not express them. Consequently, MHC class II gene diversity may be an important predictor of Ranavirus susceptibility in larval amphibians, the life stage most susceptible to Ranavirus. We surveyed natural populations of larval wood frogs (Rana sylvatica), which are highly susceptible to Ranavirus, across 17 ponds and 2 years in Maryland, USA. We sequenced the peptide-binding region of an expressed MHC class IIβ locus and assessed allelic and genetic diversity. We converted alleles to functional supertypes and determined if supertypes or alleles influenced host responses to Ranavirus. Among 381 sampled individuals, 26% were infected with Ranavirus. We recovered 20 unique MHC class IIβ alleles that fell into two deeply diverged clades and seven supertypes. MHC genotypes were associated with Ranavirus infection intensity, but not prevalence. Specifically, MHC heterozygotes and supertype ST1/ST7 had significantly lower Ranavirus infection intensity compared to homozygotes and other supertypes. We conclude that MHC class IIβ functional genetic variation is an important component of Ranavirus susceptibility. Identifying immunogenetic signatures linked to variation in disease susceptibility can inform mitigation strategies for combatting global amphibian declines.

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Thank you to Nancy McInerney for assistance with lab work, Brian Gratwicke for conceptual feedback, NEARMI field crews for field work, and members of the Savage lab for helpful comments and edits on this manuscript. We thank Jesse Brunner for providing Ranavirus qPCR standards and Jonathon Volante for help with the hurdle model. We thank the US Food and Drug Administration and Marc Allard for providing a GS FLX+ to CCG. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U. S. Government. This is contribution number 683 of the U.S. Geological Survey Amphibian Research and Monitoring Initiative (ARMI).


This study was funded by an Association of Zoos and Aquariums Conservation Grant Fund award (12-1111) to AES and the USGS Amphibian Research and Monitoring Initiative (ARMI). KPM was supported by a doctoral student grant (PD/BD/52604/2014) from the Portuguese “Fundaçao para a Ciencia e a Tecnologia.”

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AES and KPM conceived the study design. EHCG and RCF provided samples. AES, EHCG, and RCF provided funds and laboratory space. KPM and CRMW performed all the lab works. AES, KPM, CRMW, and EHGC analyzed the data. AES wrote the manuscript with input from all other authors.

Correspondence to Anna E. Savage.

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Savage, A.E., Muletz-Wolz, C.R., Campbell Grant, E.H. et al. Functional variation at an expressed MHC class IIβ locus associates with Ranavirus infection intensity in larval anuran populations. Immunogenetics 71, 335–346 (2019).

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  • Major histocompatibility complex
  • Ranidae
  • Amplicon primers
  • Roche
  • 454
  • Rana sylvatica
  • Lithobates sylvaticus