Deep Sequencing of MHC-Adapted Viral Lines Reveals Complex Recombinational Exchanges With Endogenous Retroviruses Leading to High-Frequency Variants.

Douglas H Cornwall,Jason L Kubinak,Wayne K Potts,Earl A Middlebrook,Derek L Stark

doi:10.3389/fgene.2021.716623

Abstract

Experimental evolution (serial passage) of Friend virus complex (FVC) in mice demonstrates phenotypic adaptation to specific host major histocompatibility complex (MHC) genotypes. These evolved viral lines show increased fitness and virulence in their host-genotype-of-passage, but display fitness and virulence tradeoffs when infecting unfamiliar host MHC genotypes. Here, we deep sequence these viral lines in an attempt to discover the genetic basis of FVC adaptation. The principal prediction for genotype-specific adaptation is that unique mutations would rise to high frequency in viral lines adapted to each host MHC genotype. This prediction was not supported by our sequencing data as most observed high-frequency variants were present in each of our independently evolved viral lines. However, using a multi-variate approach to measure divergence between viral populations, we show that populations of replicate evolved viral lines from the same MHC congenic mouse strain were more similar to one another than to lines derived from different MHC congenic mouse strains, suggesting that MHC genotype does predictably act on viral evolution in our model. Sequence analysis also revealed rampant recombination with endogenous murine leukemia virus sequences (EnMuLVs) that are encoded within the BALB/c mouse genome. The highest frequency variants in all six lines contained a 12 bp insertion from a recombinant EnMuLV source, suggesting such recombinants were either being favored by selection or were contained in a recombinational hotspot. Interestingly, they did not reach fixation, as if they are low fitness. The amount of background mutations linked to FVC/EnMuLV variable sites indicated that FVC/EnMuLV recombinants had not reached mutation selection equilibrium and thus, that EnMuLV sequences are likely continuously introgressing into the replicating viral population. These discoveries raise the question: is the expression of EnMuLV sequences in mouse splenocytes that permit recombination with exogenous FVC a pathogen or host adaptation?

Highlights

Experimental evolution is a powerful tool for understanding adaptation of organisms to their environments, such as the adaptive response of a pathogen to its host environment
To discover the genetic basis of observed increases in fitness and virulence of Friend virus complex (FVC), we first sequenced FVC provirus from a cell culture stock of virus used to create the serial passage strains used in this study, hereafter referred to as FVC-Boiclone (Kubinak et al, 2012)
MHCdd-derived lines do not show significant patterns of genotype specific adaptation (Figure 3D). These analyses indicate that MHCbb strongly sculpts the variant spectra of FMuLV and Spleen Focus Forming Virus (SFFV) populations, while MHCkk appears to only sculpt SFFV populations, and MHCdd has little predictable effect on variant spectra of either FVC constituent

Summary

Introduction

Experimental evolution is a powerful tool for understanding adaptation of organisms to their environments, such as the adaptive response of a pathogen to its host environment. Experiments have demonstrated that serial passage generally leads to increased pathogen fitness and virulence in hostsof-passage, while fitness and virulence tend to decrease in alternative host genotypes (Ebert, 1998; Kubinak et al, 2012). These decreases are presumably due to host genotype-specific adaptations by the pathogen that are maladaptive in the context of other host genotypes or species, otherwise known as antagonistic pleiotropy or adaptive tradeoffs (Gandon, 2004; White et al, 2020). NFDS has been demonstrated for specific MHC alleles in guppy and stickleback fish (Bolnick and Stutz, 2017; Phillips et al, 2018)

Results

Discussion

Conclusion