Postbac positions available in experimental and computational biology working on #virusevolution, tick-borne viruses and computational drug discovery! Reach out if you’d like to discuss projects in the #QVEU at NIH-NIAID. Please share with any talented undergrads or MS students you know!

Our discovery of novel viruses in invasive camelids in Australia leads us to propose a simple idea: RNA viruses may repeatedly evolve functional modules at the 5′ end of their genomes.

#Virology #RNAvirus #VirusEvolution
#Picornavirus #VirusDiscovery

doi.org/10.64898/202...

SIMPLICITY is an agent-based, multi-scale mathematical model to study SARS-CoV-2 intra- and between-host evolution - Communications Biology SIMPLICITY models multi-scale SARS-CoV-2 evolution by integrating within-host viral dynamics and population-level transmission. Our adaptive fitness landscape model reveals how immune escape prompts evolutionary dynamics akin to the real-world evolution of SARS-CoV-2.

New paper introduces SIMPLICITY, a multi scale agent based model linking within host virus evolution and population spread to dissect SARS-CoV-2 evolutionary dynamics.📊🦠#Epidemiology #Modeling #VirusEvolution
📄 https://doi.org/10.1038/s42003-025-09403-y
👤 EVBC members: Denise Kühnert, Max von Kleist

Transcriptome mining reveals diversity and evolution of circulating and endogenous amphibian retroviruses - Retrovirology Background The evolutionary history of retroviruses and their impact on vertebrate evolution remains poorly understood, particularly in non-mammalian hosts. In this study, we explore retroviruses associated with Amphibia through analysis of 169 RNA sequencing datasets from 102 amphibian species. Using a BLAST-based approach, we identified retroviral transcripts from assembled transcriptomes and phylogenetically characterise both their pol and env regions to elucidate their evolutionary history. Results We identified the transcription of 18 novel and two previously described retroviruses with closest relatives in gammaretrovirus, epsilonretrovirus, betaretrovirus and spumaretrovirinae. Despite their differing pol phylogenies, we found that all amphibian retroviruses belong to the gamma-type envelope group (GTE). This suggests a common selection pressure for amphibian retroviruses to retain GTEs. Within these GTEs we also observed a new clade of alpharetrovirus-like envelopes in amphibians which form a sister clade to avian alpharetrovirus envelopes. Furthermore, we observe correlations between amphibian taxonomical order and retroviral diversity, with Gymnophiona (caecilians) harbouring the widest diversity of retroviruses whilst Anura (frogs and toads) harbour the fewest. Through mapping these transcribed retroviruses to their respective genomes (seven available) supplemented with observing ORF intactness, we determined that 14 of the 20 retroviruses are likely endogenous in origin yet are still transcribed in many amphibian tissues. These amphibian endogenous retroviruses (ERVs) have high genomic copy numbers: most (5/7) ERVs investigated have > 100 copies, and one of which has 9,219 integrations within the Ichthyophis bannanicus caecilian genome. This high retroviral load in amphibian genomes may suggest that these retroviruses have low pathogenicity, or may reflect a lack of transposon control mechanisms in amphibian cells. Conclusions Through the characterisation of metatranscriptomic and genomic data from retroviruses in this study, we provide insights into their evolution in amphibians and exemplify the diversity of Retroviridae in vertebrate genomes. The identification of novel retroviral clades, widespread transcription of endogenous retroviruses in amphibians and abundance of ERV copies suggests that Retroviridae have played a significant role in amphibian evolution.

New study uncovers extensive diversity of circulating and endogenous #amphibian #retroviruses, identifying 20 retrovirus transcripts across 102 species, revealing deep evolutionary patterns in vertebrate hosts.🦎🧬#VirusEvolution
📄 https://doi.org/10.1186/s12977-025-00669-y
👤 EVBC member: Emma Harding

A recurrent adaptive mutation in the transmembrane 2B protein of an insect picorna-like virus in a nonnative host | Journal of Virology The forces driving virus evolution are central to understanding cross-species transmission and virus emergence. It is well established that the adaptive immune system drives virus evolution in mammals...

Study reveals a recurrent adaptive mutation in the transmembrane 2B protein of an insect picorna like virus during cross species passage, highlighting mechanisms of virus #HostAdaptation.🦠🧬 #VirusEvolution #Picornavirales
📄 doi.org/10.1128/jvi....
👤 EVBC members: Niko Beerenwinkel, Ronald P. van Rij

Check the latest preprint from the lab, #Virus, #evolution, #VirusEvolution, armchair #virology

I would have re-posted, but I didn't see it! It looks like you did not include any tags, such as #Virus #Evolution or #VirusEvolution

HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements AbstractSummary. Endogenous viral elements (EVEs) offer valuable insights into virus and host evolution, but their detection remains computationally and bi

HI-FEVER introduces a scalable Nextflow pipeline for rapid, high-throughput discovery and annotation of endogenous virus elements across host genomes. ⚡🧬
#VirusEvolution #Genomics #Bioinformatics
📄 doi.org/10.1093/bioi...
👤 EVBC members: Emma Harding, Cormac Kinsella

Taxonomic expansion and reorganization of Flaviviridae - Nature Microbiology Analysis of RNA polymerase hallmark gene phylogenies supported by protein structure relationships of flaviviruses and ‘flavi-like’ viruses underpins the taxonomic expansion and reorganization of Flaviviridae.

A #taxonomic revision of the human/animal RNA viruses #Flaviviridae identifies 4 divergent RdRP clades and restructures 12 genera across 3 families within Amarillovirales. #VirusEvolution
📄 https://doi.org/10.1038/s41564-025-02134-0
👤 EVBC: P. Simmonds, A. Butković, J. Mifsud, M. Beer, J.H. Kuhn

Study reveals over 3,500 uncharacterized RNA viral RdRp sequences in public protein databases, uncovering many novel endogenous viral elements and misclassified viruses.
#VirusEvolution #RNAvirus #Bioinformatics 🧬🧫
📄 https://doi.org/10.1093/ve/veaf074
👤 EVBC members: Andrew Firth, Katherine Brown

New ViralBottleneck R package integrates six methods to estimate viral transmission bottlenecks from deep-sequencing data, revealing how methodological choices shape bottleneck inference. #VirusEvolution #Rstats 🧬
📄 https://doi.org/10.1093/ve/veaf071
👤 EVBC member: Joseph Hughes

A divergent betacoronavirus with a functional furin cleavage site in South American bats Bats are natural reservoirs for a wide range of RNA viruses. Members of the genus Betacoronavirus, including Severe Acute Respiratory Syndrome virus 2 (SARS-CoV-2) and Middle East Respiratory Syndrome...

We’ve identified a highly divergent betacoronavirus from South American bat that encodes a functional furin cleavage site.
Another fascinating reminder of how diverse coronavirus evolution is in wildlife reservoirs.
#Virology #VirusEvolution #Bats #Coronavirus

www.biorxiv.org/content/10.1...

Experts 👩‍⚕️: Flu virus adapting to post-pandemic world & spreading EASIER! 🌏 "Common scenario" going forward. Resistance to treatments also emerging globally. 🦠💊 #VirusEvolution #HealthAlert

🧬 Fun fact: While he humbly claims to lack fun facts, Dr. Parrish’s long-standing leadership and impact on virology speak for themselves.

#COMPASSCenter #VirusEvolution #JumpThrust #VeterinaryVirology #CornellUniversity #VirusResearch

❄️Tune in to Rebecca Grimwood unveiling the diversity and evolutionary histories of Antarctic fish species from the Ross Sea! 🐟 Critical insights into viral responses to environmental shifts in these vulnerable ecosystems. #MicroSeq2025 #fish #virusevolution #Antarctica

BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference - Nature Methods BEAST X advances Bayesian phylogenetic, phylogeographic and phylodynamic analysis by incorporating a broad range of complex models and leveraging advanced algorithms and techniques to boost statistical inference.

BEAST X accelerates Bayesian phylogenetic and phylodynamic inference with enhanced scalability and geo spread modeling.
#BEASTX #Phylodynamics #VirusEvolution
👤EVBC: Philippe Lemey
🔗

🦠 Modulating human ACE2 protein may be key in blocking coronavirus entry, offering a promising direction amidst ongoing virus evolution and spike protein resistance challenges. Link: https://tinyurl.com/2337brd7 #VirusEvolution #HealthSecurity #BiomedicalResearch

Chikungunya isn’t just painful—it’s a mosquito-borne lesson in how viruses evolve and travel.
To understand more, check out my newest episode:

🎧 Listen or read: infectiousdose.com/post/blood-a...
#VirusEvolution #Chikungunya #SciencePodcast #InfectiousDose

Very grateful to the @biology.ox.ac.uk for the kind spotlight — and for the opportunity to do meaningful work alongside such brilliant and thoughtful colleagues across Biology, Pandemic Sciences Institute, and Lincoln College.

#GlobalHealth #VirusEvolution #PandemicPreparedness

Exciting results from my synthetic virology work

open.substack.com/pub/tahirhb/...

#SyntheticVirology #SARSCoV2 #Bioinformatics #GenomicSurveillance #CoVsurver #VariantTracking #VirusEvolution #GVAtlas

The most reported #SARSCoV2 mutation globally: S:D614G

1,054,433 entries recorded in #GVAtlas

Explore now:

tahirhb.com/GVAtlas

Spike Related:

tahirhb.com/GVAtlas/SARS...

#COVID19 #Genomics #MutationTracking #SpikeProtein #VirusEvolution

8/9 "The overwhelming odds are that what predominates in the next six months will come from something that's circulating now," said FDA's Jerry Weir about virus evolution patterns.
#VirusEvolution #Prediction

4/14 Picture our immune systems as medieval fortresses facing an enemy with supernatural powers. The virus constantly reshapes itself through mutation and genetic reassortment, allowing it to bypass our carefully constructed defences.
#VirusEvolution #ImmuneEvasion

It is not nice to say "I told you so", is it?

Nice preprint on sex-specific evolution of influenza. Host sex as a selective pressure in viral within-host evolution.

#virusevolution #sexualdimorphism #disease www.biorxiv.org/content/10.1...

The virome of the panglobal, wide host-range plant pathogen Phytophthora cinnamomi: phylogeography and evolutionary insights Abstract. Phytophthora cinnamomi stands out as one of the most devastating plant pathogens worldwide, rapidly expanding its range and impacting a wide rang

academic.oup.com/ve/article/1...
Virome as a lens on pathogen evolution and dispersal; Novel viral discoveries and taxonomic expansion; Potential cross-kingdom viral infection and potential modulation of pathogenicity. #Phytophthora, #virusevolution, #forest, #emergingdisease.

Wildlife trade, not bats, likely moved the ancestors of SARS-CoV-2 to humans New genetic analyses reveal that the bat virus ancestors of SARS-CoV-1 and SARS-CoV-2 likely circulated in Western China or Northern Laos just years before human outbreaks. Their rapid appearance thou...

Wildlife trade, not bats, likely moved the ancestors of SARS-CoV-2 to humans 🦇🧬🌏 www.news-medical.net/news/2025050... #COVID19 #Zoonosis #WildlifeTrade #BatViruses #SARSCoV2 #Pandemic #Science #VirusEvolution #Phylogeography @cellpress.bsky.social

5/8 Bird flu's history reveals its unpredictability—in 1997, H5N1 unexpectedly killed six people in Hong Kong, marking the first documented direct bird-to-human transmission without an intermediate host, contradicting previous scientific assumptions.
#VirusEvolution #HealthRisks

2/9 "The overall worsening in antibody affinity to more recent H5N1 isolates indicates current and future H5N1 viral lineages pose an enhanced risk to human health," warns lead author Dr. Colby T. Ford of UNC Charlotte's Centre for Computational Intelligence.
#VirusEvolution #H5N1 #PandemicRisk

4/7 Although H5N1 currently shows low human-to-human transmission with mostly mild cases, Karan warns: "Flu viruses can adapt very quickly. As H5N1 circulates between cows, chickens and humans, it can mutate or mix with seasonal flu strains."
#VirusEvolution #PublicHealth

5/9 The greatest pandemic risk comes from potential reassortment—when H5N1 and human seasonal influenza viruses exchange genes in a co-infected host. Mammals susceptible to both virus types (like pigs or cats) could serve as "mixing vessels."
#PandemicThreat #H5N1 #NextPandemic #VirusEvolution