An Atlas of Adaptive Evolution in Endemic Human Viruses
Kistler, K.; Bedford, T.
Show abstract
Through antigenic evolution, viruses like seasonal influenza evade recognition by neutralizing antibodies elicited by previous infection or vaccination. This means that a person with antibodies well-tuned to an initial infection will not be protected against the same virus years later and that vaccine-mediated protection will decay. It is not fully understood which of the many endemic human viruses evolve in this fashion. To expand that knowledge, we assess adaptive evolution across the viral genome in 28 endemic viruses, spanning a wide range of viral families and transmission modes. We find that surface proteins consistently show the highest rates of adaptation, and estimate that ten viruses in this panel undergo antigenic evolution to selectively fix mutations that enable the virus to escape recognition by prior immunity. We compare overall rates of amino acid substitution between these antigenically-evolving viruses and SARS-CoV-2, showing that SARS-CoV-2 viruses are accumulating protein-coding changes at substantially faster rates than these endemic viruses.
Matching journals
The top 5 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Genome data artifacts and functional studies of deletion repair in the BA.1 SARS-CoV-2 spike protein 95%
- Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat 95%
- Immune Pressure is Key to Understanding Observed Patterns of Respiratory Virus Evolution in Prolonged Infections 95%
Similar papers in this journal
- Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229E 96%
- Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution 96%
- Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin 95%
Similar papers in this journal
- Weak selection and stochastic processes limit the emergence of antigenic variants during household transmission of influenza A viruses 96%
- A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection 96%
- Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck 95%
Similar papers in this journal
- Identifying and prioritizing potential human-infecting viruses from their genome sequences 96%
- Viral expansion after transfer is a primary driver of influenza A virus transmission bottlenecks 95%
- Reconstructed influenza A/H3N2 infection histories reveal variation in incidence and antibody dynamics over the life course 95%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.