Mastodawn

John Dennehy May 18, 2023

I wrote this piece about my experiences as a deaf individual in science during the pandemic when our world irrevocably changed. It was a tough transition, but ultimately I am in a better place now.

https://elifesciences.org/articles/89322

Equity, Diversity and Inclusion: When communication all changed

Between early challenges and lasting opportunities, a deaf virologist reflects on how the pandemic transformed his access to academic spaces.

eLife

John Dennehy Feb 21, 2023

Vivek Mutalik Feb 21, 2023

Polyamines and linear DNA mediate bacterial threat assessment of #bacteriophage infection | PNAS

https://www.pnas.org/action/oidcCallback?idpCode=connect&error=login_required&error_description=Login+required&state=aBGxy0GISKTeY6cM9J5Xj1mYAxgGN0Ka7ABI41zNFrw

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.

PNAS

John Dennehy Feb 8, 2023

High-throughput droplet-based analysis of influenza A virus genetic reassortment by single-virus RNA sequencing

"Results were highly reproducible, confirmed that genetic reassortment is far from random, and allowed accurate quantification of reassortants including rare events."

https://www.pnas.org/doi/10.1073/pnas.2211098120

John Dennehy Feb 7, 2023

Frank Aylward Jan 27, 2023

Isolation and infection cycle of a polinton-like virus virophage in an abundant marine alga

This is an important study that shows how #virophage have evolved multiple times independently in distinct viral groups. Turns out that #viruses infecting other viruses are quite common!

Also gotta love the opening sentence: "Eukaryotic genomes are a hub where viruses and selfish genetic elements convene" - so true.

Amazing work by the @BejaLab lab!

https://www.nature.com/articles/s41564-022-01305-7

Isolation and infection cycle of a polinton-like virus virophage in an abundant marine alga - Nature Microbiology

Isolation and characterization of a selfish genetic element with a virophage lifestyle that co-infects a bloom-forming polar algae along with a partner virus.

Nature

John Dennehy Feb 3, 2023

Correlated substitutions reveal SARS-like coronaviruses recombine frequently with a diverse set of structured gene pools

"We apply this approach to infer recombination parameters for a range of positive-sense RNA viruses. We then analyze a set of 191 SL-CoV sequences (including SARS-CoV-2) and find that ORF1ab and S genes frequently undergo recombination."

https://www.pnas.org/doi/10.1073/pnas.2206945119

John Dennehy Jan 13, 2023

Bloom Lab Jan 13, 2023

Lots of questions about if future SARS-CoV-2 variants might be more or less severe.

I don’t have a crystal ball.

But in this thread, I’ll describe what happened w other rapidly evolving respiratory viruses after initial pandemic, & describe some relevant SARS-CoV-2 data.

Plot below shows mortality due to influenza virus in USA during and after 1918 H1N1 & 1968 H3N2 influenza pandemics.

Interactive version of plot is at https://jbloomlab.github.io/flu_mortality/ and data are taken from https://academic.oup.com/jid/article/178/1/53/919896

John Dennehy Jan 8, 2023

Eric Pyrrhus Jan 6, 2023

1/6
😲 Two recent studies from China look at the truly wide diversity of RNA viruses found in ticks.

"Extensive diversity of RNA viruses in ticks revealed by meta #genomics in northeastern China"
https://doi.org/10.1371/journal.pntd.0011017

"Metavirome of 31 tick species provides a compendium of 1,801 RNA virus genomes"
https://www.nature.com/articles/s41564-022-01275-w

A lot of insights in these two studies, so I'll just point out a few things that I personally found interesting.

#virology @virology #RNA #virus #virome #InfectiousDisease

Extensive diversity of RNA viruses in ticks revealed by metagenomics in northeastern China

Author summary Ticks are important vectors to transmit many infectious agents. In recent years, many novel tick-borne viruses associated with human illness, including Alongshan virus, Songling virus, and Beiji nairovirus, have been identified in northeastern China. It is necessary to conduct routine surveillance of tick-borne viruses in ticks, however, little is known about the tick virome in northeastern China. In this study, we used metatranscriptomics to investigate the virome diversity in four tick species collected from northeastern China. In total, we identified 22 RNA viruses belonging to eight virus families (exclude an unclassified virus). Of these, five members were established human pathogens, eight viruses were of novel species, and six viruses had close relationship with pathogenic tick-borne viruses with potential public health threats. Moreover, we found that the viromes were significantly affected by the tick species and geographical location in the study. These findings revealed an extensive diversity of RNA viruses in ticks in northeastern China, which will lay the foundation for the prevention and control of emerging tick-borne diseases.

John Dennehy Jan 8, 2023

Akos T Kovacs Jan 8, 2023

Within-host evolution of the gut microbiome

-in Current Opinion in Microbiology by @DapaTanja et al from @benjaminhgood, KC Huang, and @KarinaXavierLab

https://www.sciencedirect.com/science/article/abs/pii/S1369527422001424

John Dennehy Jan 3, 2023

Alex Crits-Christoph Jan 3, 2023

Mutualism-enhancing mutations dominate early adaptation in a two-species microbial community

https://www.nature.com/articles/s41559-022-01923-8#Abs1

Mutualism-enhancing mutations dominate early adaptation in a two-species microbial community - Nature Ecology & Evolution

Barcode lineage tracking of a competitive mutualism between Saccharomyces cerevisiae and Chlamydomonas reinhardtii shows that selection favours yeast mutants that increase the yields of both species and strengthen the mutualism.

Nature

John Dennehy Jan 3, 2023

Bloom Lab Jan 2, 2023

I wanted to summarize what is known about the new XBB.1.5 variant of SARS-CoV-2, which is starting to generate a lot of interest.

(There are no new scientific results in this thread, it simply aggregates previously reported results for those not following topic closely.)

Lab	https://dennehylab.org/
Google Scholar	https://scholar.google.com/citations?hl=en&user=xHV6zmQAAAAJ&view_op=list_works&sortby=pubdate