Reovirus genomic diversity confers plasticity for protease utility during adaptation to intracellular uncoating
Bibliographic record
Abstract
ABSTRACT Mammalian orthoreoviruses (reoviruses) infect many mammals and provide a safe model to study enteric viruses. Knowledge of reoviruses is derived from prototypic lab strains, notably T1L and T3D. Based on these prototypic strains, reoviruses can efficiently utilize gut or lysosomal proteases for uncoating and penetration into host cytoplasm. To discover natural reovirus characteristics, we isolated four genetically diverse wastewater reovirus samples and compared their genetic and phenotypic characteristics to those of T1L/T3D. On L929 cells, the most commonly used model for reovirus studies, naturally derived reoviruses displayed lower fitness than T1L/T3D, evident from smaller plaques and higher relative particle-to-PFU ratios. In contrast to T1L/T3D, which are uncoated efficiently by lysosomal-mediated proteolysis, naturally derived reoviruses displayed poor uncoating kinetics. Exposure of naturally derived reoviruses to gut proteases led to rapid extracellular uncoating and significantly improved infectivity relative to T1L/T3D, indicating that wild reoviruses depended more on extracellular gut proteases. To discover if reovirus can adapt to new host proteases, naturally derived samples were passaged on L929 cells, and large and small plaque-forming isolates were evaluated. Larger plaque sizes correlate with faster intracellular uncoating. Whole-genome sequencing identified the outer capsid σ3 protein as the determinant of uncoating proficiency between wild reoviruses. Interestingly, mutations that permitted intracellular uncoating were found in 0.01% of the parental quasispecies, suggesting that variants with altered protease sensitivity were rapidly selected for during cell culture propagation. Altogether, these findings indicate that naturally circulating reoviruses are more reliant on gut proteases, but the genetic diversity of reovirus quasispecies bestows tremendous plasticity toward protease utility. IMPORTANCE Reoviruses infect many mammals and are widely studied as a model system for enteric viruses. However, most of our reovirus knowledge comes from laboratory strains maintained on immortalized L929 cells. Herein, we asked whether naturally circulating reoviruses possess the same genetic and phenotypic characteristics as laboratory strains. Naturally circulating reoviruses obtained from sewage were extremely diverse genetically. Moreover, sewage reoviruses exhibited poor fitness on L929 cells and relied heavily on gut proteases for viral uncoating and productive infection compared to laboratory strains. We then examined how naturally circulating reoviruses might adapt to cell culture conditions. Within three passages, virus isolates from the parental sewage population were selected, displaying improved fitness and intracellular uncoating in L929 cells. Remarkably, selected progeny clones were present at 0.01% of the parental population. Altogether, using reovirus as a model, our study demonstrates how the high genetic diversity of naturally circulating viruses results in rapid adaptation to new environments.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".