What’s up. #Evoluncheons runs Fridays this fall

Been slammed in the lab before I travel next week (if you’re at Cornell, would love to hang), so we're late with the applied #evolution paper list. But wow some absolute bangers ⬇️

https://evoluncheons.blogspot.com/2023/09/14-sep-2023.html

14 Sep 2023

How         zit        errbady Been absolutely slammed in the lab before I travel next week, so we're late and not going in depth today. But...

Lots of zoonosis and wildlife epidemiology, theme of this issue. Sorry cancer folks, this one's almost all infection biology.

We have:

1. Engineering is evolution: a perspective on the biological design process. Philosophical musings from other like-minded synthetic biologists turning to evolution. Directed evolution is rational engineering. osf.io/urq9w @chofski.bsky.social
2. Host functional traits as the nexus for multilevel infection patterns. Short perspective of how host biology and ecology across scales shapes disease ecology. https://www.sciencedirect.com/science/article/abs/pii/S0169534723002227
3. Viperin immunity evolved across the tree of life through serial innovations on a conserved scaffold. You share an antiviral defense mechanism with the gunk growing on your teeth, probably. https://doi.org/10.1101/2023.09.13.557418
Tweetorial: https://twitter.com/MDMlab_Paris/status/1702228421240099171
4. A short course of antibiotics selects for persistent resistance in the human gut. We used to think resistance after antibiotics was temporary. Nope! https://doi.org/10.1101/2023.09.04.556257
5. Coinfection with chytrid genotypes drives divergent infection dynamics reflecting regional distribution patterns. Now this is brilliant. Frog-killer fungus is selected for higher virulence in areas where different lineages overlap and compete with each other. https://www.nature.com/articles/s42003-023-05314-y
Coinfection with chytrid genotypes drives divergent infection dynamics reflecting regional distribution patterns - Communications Biology

Integration of experimental and epidemiological data on chytrid infection in frogs reveals the effect of multi-strain coinfection on virulence and transmission of the pathogen.

Nature
6. Reservoir host immunology and life history shape virulence evolution in zoonotic viruses. Models show why are bats full of germs out to kill us. https://doi.org/10.1371/journal.pbio.3002268
Reservoir host immunology and life history shape virulence evolution in zoonotic viruses

Bats are natural reservoir hosts for viruses that cause higher case fatality rates in humans than do zoonoses derived from any other source. This study builds a nested within-host, population-level model to offer a mechanistic explanation for this phenomenon.

7. Crossing host boundaries: the evolutionary drivers and correlates of viral host jumps. Look at boatloads of viral sequencing, find we're sick and making animals more sick than they make us. https://www.biorxiv.org/content/10.1101/2023.09.01.555953v1
Tweetorial: https://twitter.com/cedriccstan/status/1699316840349208849
8. Optimizing the delivery of self-disseminating vaccines in fluctuating wildlife populations. Modeling shows timing is key to success of replicating vaccines when given to changing populations. https://doi.org/10.1371/journal.pntd.0011018
Optimizing the delivery of self-disseminating vaccines in fluctuating wildlife populations

Author summary Pathogens such as Ebola, rabies, and Lassa virus that usually infect wildlife can jump to the human population. In the worst case, this can lead to outbreaks or pandemics such as happened in 2014 with Ebola and 2019 with SARS-CoV-2. One approach to mitigate the threat of pathogens spilling into the human population is to proactively vaccinate wildlife harboring these pathogens before the pathogens infect humans. With traditional vaccines, administering enough vaccines to the wildlife population to limit pathogen spread is challenging. To address this challenge, recent technological advances have allowed the development of vaccines that allow some degree of spread of the vaccine from animal to animal. However, for a vaccination campaign using these self-disseminating vaccines to be implemented successfully, we need to know when vaccines should be administered. We used mathematical models to explore how the reservoir host’s population ecology and properties of the vaccine affect the success of a vaccination campaign. Our results demonstrate that the timing of vaccine delivery relative to seasonal reproduction can make or break the success of vaccination programs. The effectiveness of self-disseminating vaccines is optimized by introducing vaccine after the peak of seasonal reproduction when the number of animals available for vaccination is highest.

9. The first arriving virus shapes within-host viral diversity during natural epidemics. Field experiments! in plants show the importance of priority effects in outbreaks. https://doi.org/10.1098/rspb.2023.1486
10. Broad receptor tropism and immunogenicity of a clade 3 sarbecovirus. Non-covid coronaviruses in bats that we should keep an eye on! https://doi.org/10.1101/2023.09.12.557371
Tweetorial: https://twitter.com/veeslerlab/status/1702111775871881446
11. Importation of Alpha and Delta variants during the SARS-CoV-2 epidemic in Switzerland: Phylogenetic analysis and intervention scenarios. Impressed with the estimates of numbers of independent introductions with models matching data. https://doi.org/10.1371/journal.ppat.1011553
Thread: https://bsky.app/profile/firefoxx66.bsky.social/post/3k6sq2upkpq2f
Importation of Alpha and Delta variants during the SARS-CoV-2 epidemic in Switzerland: Phylogenetic analysis and intervention scenarios

Author summary We were interested in quantifying the number of imports of SARS-CoV-2 variants of concern (VoCs) and assessing the potential impact of travel restrictions and surveillance strategies in Switzerland. We used genomic surveillance data to calculate when and how often two different VoCs, Alpha and Delta, were imported into Switzerland. We used these estimates to simulate the spread of VoCs in a transmission model and investigated counterfactual intervention scenarios. Even though there were hundreds to a thousand imports, implementing border closures following the announcement of VoCs would have had limited impact on delaying their spread. However, improved surveillance of travelers would be a more effective measure to delay the spread of VoCs. In conclusion, our study illustrates that phylogenetic analysis combined with mathematical transmission models can be used to inform the public health response during pandemics.

12. Deep mutational scans of XBB.1.5 and BQ.1.1 reveal ongoing epistatic drift during SARS-CoV-2 evolution. Epistasis continues to kick butt. Notably, a scan of deletions in Spike RBD. https://www.biorxiv.org/content/10.1101/2023.09.11.557279v1
Tweetorial: https://twitter.com/tylernstarr/status/1702137362019750163
That wraps it for now. See you next week, except probably not, week after that. En la buena mai fishes