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Items tagged with: Virology
Reviewed pre-print at @eLIFE now online which describes our screen for host mechanisms that limit the ability to activate HIV from latency and identifies a target that could be druggable: "Integrator complex subunit 12 knockout overcomes a transcriptional block to HIV latency reversal" https://doi.org/10.7554/eLife.103064.1 Revisions for the paper should not be too difficult. Also good timing for the first author, Carley Gray, whose defense is tomorrow afternoon.
Giant virus creates subcellular environment to overcome codon-tRNA mismatch
https://www.biorxiv.org/content/10.1101/2024.10.07.616867v1
Giant virus creates subcellular environment to overcome codon-tRNA mismatch
Codon usage consonant with the cellular tRNA pool is important for efficient translation. However, many eukaryotic viruses, including amoeba-infecting mimiviruses, have codon usage that is largely deviated from that of their host, despite using the h…bioRxiv
#Virology #ColdSpringHarbor
Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts
https://www.nature.com/articles/s42003-024-05931-1
#viruses #virology #extremophiles
Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts - Communications Biology
Analysis of the virus community associated with red algal mats in Yellowstone National Park shows it to be dominated by Megaviricetes, with resident virus lineages being of ancient origin and encoding genomic footprints of adaptation to thermophily.Nature
Our latest commentary about a cool recent paper on virophage-mediated defense against giant #viruses!
March of the proviruses
Nice paper examining virophage-mediated antiviral defense in protists!
Endogenous virophages are active and mitigate giant virus infection in the marine protist Cafeteria burkhardae
Large language models improve annotation of prokaryotic viral proteins
https://www.nature.com/articles/s41564-023-01584-8
#virology #viruses #bioinformatics #genomics
Large language models improve annotation of prokaryotic viral proteins - Nature Microbiology
Ocean viral proteome annotations are expanded by a machine learning approach that is not reliant on sequence homology and can annotate sequences not homologous to those seen in training.Nature
Another interesting study suggesting that giant viruses can control phototaxis in their hosts during infection
"Hijacking of internal calcium dynamics by intracellularly residing viral rhodopsins"
"... we show here that light irradiation reversibly modified tail movements of OLPVR1-expressing frog tadpoles."
https://www.nature.com/articles/s41467-023-44548-6
#viruses #GiantViruses #virology
Hijacking of internal calcium dynamics by intracellularly residing viral rhodopsins - Nature Communications
Rhodopsins are ubiquitous light-driven membrane proteins that have diverse functions in nature, and value as optogenetics tools.Nature
Daily turnover of active giant virus infection during algal blooms revealed by single-cell transcriptomics
"A consistent percent of infected coccolithophores displayed the early phase of viral replication for several consecutive days, indicating a daily turnover and continuous virocell-associated metabolite production, potentially affecting the surrounding microbiome"
#Viruses of #Plankton: On the Edge of the Viral Frontier
https://www.mdpi.com/2076-2607/12/1/31
Viruses of Plankton: On the Edge of the Viral Frontier
The field of aquatic viral ecology has continued to evolve rapidly over the last three decades [...]MDPI
Gene duplication as a major force driving the genome expansion in some giant viruses
Contrasting drivers of abundant phage and prokaryotic communities revealed in diverse coastal ecosystems
https://www.nature.com/articles/s43705-023-00333-6
#marine #viruses #phages #ocean #microbiology #virology
Contrasting drivers of abundant phage and prokaryotic communities revealed in diverse coastal ecosystems - ISME Communications
ISME Communications - Contrasting drivers of abundant phage and prokaryotic communities revealed in diverse coastal ecosystemsNature
New #ISEPpapers! The #protist #Aurantiochytrium has universal subtelomeric rDNAs and is a host for #mirusviruses: Jackie Collier et al. https://www.cell.com/current-biology/fulltext/S0960-9822(23)01368-4
#protists #microbes #protistology #microbiology #viruses #virology #genomics
Latest taxonomic update for giant viruses, including a new name for the famous mimivirus (now Mimivirus bradfordmassiliense)
Taxonomy for the titans of the virosphere!
https://link.springer.com/article/10.1007/s00705-023-05906-3
#GiantViruses #viruses #virology
Taxonomic update for giant viruses in the order Imitervirales (phylum Nucleocytoviricota) - Archives of Virology
Large DNA viruses in the phylum Nucleocytoviricota, sometimes referred to as “giant viruses” owing to their large genomes and virions, have been the subject of burgeoning interest over the last decade.SpringerLink
Phylogenetic diversity and functional potential of large and cell-associated #viruses in the Bay of Bengal
Nice work from @scubalaina @giant_virus et al!
#GiantViruses encode many strange genes in their genomes - partial TCA cycles, actins and myosins, nutrient transporters, etc
What are they doing with all of these crazy genes?
We discuss this in a recent article - big thanks to all of the collaborators who were willing to help write an extensive review!
Virologs, viral mimicry, and #virocell metabolism: the expanding scale of cellular functions encoded in the complex genomes of giant #viruses
https://academic.oup.com/femsre/article/47/5/fuad053/7280998?login=false
A new episode of the EMBO podcast is out. I spoke with Hsiao-Han Chang, Gytis Dudas, and Hedvig Tamman about viruses, hosts, spillovers, public health... And also starting a new lab, the challenges of mobility, mentorship, and Die Hard Dracula.
#EMBOPodcast #scicomm #SciencePodcast #Virology #Evolution #Microbiology
It’s viruses all the way down: a conversation with Hsiao-Han Chang, Gytis Dudas, and Hedvig Tamman –
As COVID-19 and flu season descends, we talk with three new research group leaders who work on host-virus interactions.Thiago Carvalho (EMBO)
Lessons from Chloroviruses: the Complex and Diverse Roles of Viruses in Food Webs
Virophages are viruses that infect giant viruses, typically resulting in a lower burst size for the giant virus. In our latest preprint we report virophage-like sequences associated with insect poxviruses.
Their genomes of these elements are really interesting. This also opens up the possibility that hyperparasitic viruses are associated with a much broader range of DNA viruses than is commonly thought.
https://doi.org/10.1101/2023.10.16.562556
#viruses #virology #poxviruses #GiantViruses
Polinton-like Viruses Associated with Entomopoxviruses Provide Insight into Replicon Evolution
Polinton-like viruses (PLVs) are a diverse group of small integrative dsDNA viruses that infect diverse eukaryotic hosts. Many PLVs are hypothesized to parasitize viruses in the phylum Nucleocytoviricota for their own propagation and spread.bioRxiv
Nice study on polar giant viruses!
Genomic adaptation of giant viruses in polar oceans
https://www.nature.com/articles/s41467-023-41910-6
#viruses #GiantViruses #virology #oceanography #marine #ocean #polar
Genomic adaptation of giant viruses in polar oceans - Nature Communications
This study examines the biogeography and functional gene repertoires of marine eukaryote-infecting large and giant DNA viruses.Nature
"We are in the midst of the "Platinum Age of Virus Discovery", an era characterized by the exponential growth in the discovery of virus biodiversity. "
A Parasite Odyssey: An RNA virus concealed in Toxoplasma gondii
https://www.biorxiv.org/content/10.1101/2023.09.17.558162v1?rss=1
We are looking for a new colleague to lead the microbiology & immunology section of @PLOSBiology!!
Do you have micro/immuno expertise (including virology of course) & a passion for science away from the bench? This could be for you
Get in touch w/ any Qs!
Associate or Senior level
Applications will be assessed upon receipt
Boosts greatly appreciated!
#editing #careersinscience #microbiology #virology #immmunology
https://us232.dayforcehcm.com/CandidatePortal/en-US/plos/Posting/View/288
#USFCMS #microbiology #micro #virology #phage #virus
https://youtu.be/GOWEANUgzpw
Matters Microbial #2: Shock and awe microbiology and a chat with Mya Breitbart
Mark discusses some “shock and awe” concepts about the microbial world that he introduces to his microbiology students, and asks three important questions ab...YouTube
'She also points out that some viruses such as Ebola and Zika don’t have a known latent phase, yet “we know people where, six months after recovery, you get transmission of #Zika, or #Ebola, or reactivation of problems . . . That means that full length RNA is there and can resume production.”
#Virology
https://www.bmj.com/content/382/bmj.p1156
Where do viruses hide in the human body?
The question of how SARS-CoV-2 persists in the body has refocused scientists on the question of where viruses persist in humans more generally.The BMJ
New BMJ Feature:
"Where do viruses hide in the human body?"
https://doi.org/10.1136/bmj.p1156
#RNA #virus #virology @virology #ViralPersistence
Where do viruses hide in the human body?
The question of how SARS-CoV-2 persists in the body has refocused scientists on the question of where viruses persist in humans more generally.The BMJ
Hello everyone!
I’m an associate prof at Virginia Tech studying viral diversity. Lately my group has been focusing on giant viruses, but we are also interested in other protist viruses, and the role of viral endogenization in host genome evolution.
#GiantViruses #ViralDiversity #TreeOfLife #Protists #Microbiology #Bioinformatics #Evolution #Virology #Genomics
Recently we have been examining the strange and complex genes encoded in giant virus genomes!
https://doi.org/10.1093/femsre/fuad053
'To address this critical knowledge gap, we conducted a comprehensive cross-species analysis of transcriptomic data from over 6000 blood samples from macaques and humans infected with one of 31 viruses, including #Lassa, #Ebola, #Marburg, #Zika, and #dengue.'
#Immunology #Virology #preprint
https://www.biorxiv.org/content/10.1101/2023.06.22.546003v1?med=mas
Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans
Viral pandemics and epidemics pose a significant global threat, with emerging and re-emerging viruses responsible for four pandemics in the 21st century alone.bioRxiv
It's been a big mystery why giant viruses encode so many proteins involved in vesicular transport and cytoskeletal dynamics. This interesting paper examined a dynamin homolog and found evidence that it's involved in mitochondrial membrane remodelling during infection.
A Novel Group of Dynamin-Related Proteins Shared by Eukaryotes and Giant Viruses Is Able to Remodel Mitochondria From Within the Matrix
https://academic.oup.com/mbe/article/40/6/msad134/7190697?login=false
#viruses #GiantViruses #virology
A Novel Group of Dynamin-Related Proteins Shared by Eukaryotes and Giant Viruses Is Able to Remodel Mitochondria From Within the Matrix
Abstract. The diverse GTPases of the dynamin superfamily play various roles in the cell, as exemplified by the dynamin-related proteins (DRPs) Mgm1 and Opa1, whSheikh, Shaghayegh (Oxford University Press)
It was wonderful to speak with Vincent Racaniello during the Aquatic Virus Workshop in Quebec last week! Fun conversation.
#viruses #ecology #evolution #virology
TWiV 1011: Aquatic viruses
Vincent travels to Québec City, Canada and the 11th Aquatic Virus Workshop, where he speaks with Frank Aylward and Jed Furman about the research of their lab...YouTube
1/13
How RNA viruses can use their dsRNA intermediate state as a de facto latent state, facilitating viral persistence.
Positive single-stranded #RNA viruses have a replication cycle that includes a double-stranded RNA (dsRNA) intermediate state.
#virology @virology #virus #virome #ViralPersistence #InfectiousDisease
Holy Crap.
If confirmed, we'll have to figure out how to categorize 180,000 newly discovered viruses.
@RNA has called this the "Platinum Age of Virus Discovery"!
"Identification of #RNA viruses is currently limited to those with sequence similarity to a known #virus, such that... the 'dark matter' of the virosphere remains challenging to detect.
We developed a deep learning algorithm [which] integrates both sequence and structural information..."
https://www.biorxiv.org/content/10.1101/2023.04.18.537342v1
#virology @virology
Artificial intelligence redefines RNA virus discovery
RNA viruses are diverse components of global ecosystems. The metagenomic identification of RNA viruses is currently limited to those with sequence similarity to known viruses, such that highly divergent viruses that comprise the “dark matter” of the …bioRxiv
Mirusviruses link herpesviruses to giant viruses
https://www.nature.com/articles/s41586-023-05962-4
I was honored to be asked to review this paper! Wonderful work.
#virology #viruses #herpesviruses #giantViruses
Mirusviruses link herpesviruses to giant viruses - Nature
A phylogeny-guided genome-resolved metagenomic analysis of DNA viruses in the ocean reveals atypical plankton-infecting relatives of herpesviruses that form a putative new phylum dubbed Mirusviricota.Nature
"The viral inner membrane-integrated anchor protein colocalizes with the endoplasmic reticulum (ER), supporting the hypothesis that the biogenesis of the inner membrane is associated with the ER"
Nice confirmation about where the viral inner membrane comes from.
https://www.nature.com/articles/s41467-023-37681-9
#viruses #giantViruses #virology
Near-atomic architecture of Singapore grouper iridovirus and implications for giant virus assembly - Nature Communications
High morbidity and mortality in aquatic have been caused by iridovirids worldwide. Here the authors present a near-atomic SGIV capsid structure. Functional assays further reveal the relationships between identified capsid proteins and viral assembly.Nature
Hmm...
A recent paper looked at evolution of #SARSCoV2 *within* different tissues, which might raise a few questions.
Specifically, the authors found evidence that the #virus might evolve independently in different tissues, especially in immune-privileged sites.
But that's not all...
"High-depth sequencing characterization of viral dynamics across tissues in fatal COVID-19 reveals compartmentalized infection"
https://www.nature.com/articles/s41467-022-34256-y
#virology #epidemiology #InfectiousDisease
High-depth sequencing characterization of viral dynamics across tissues in fatal COVID-19 reveals compartmentalized infection - Nature Communications
Here, by high-resolution SARS-CoV-2 sequencing, genomic and transcriptomic analyses from tissue samples, Normandin et al.Nature
🦠 A Few More #Mpox ( #MonkeyPox) Pandemic Updates 🦠
"Assuming APOBEC-editing is characteristic of [mpox] infection in human hosts, we propose an APOBEC clock that – at a rate of ~6 APOBEC3 mutations per year – estimates [mpox] has been circulating in humans since 2016."
https://www.biorxiv.org/content/10.1101/2023.01.23.525187v1
#virus #virology @virology #epidemiology #InfectiousDisease
Putative APOBEC3 deaminase editing in MPXV as evidence for sustained human transmission since at least 2016
Mpox is often described as being endemic in West and Central Africa as a zoonotic disease that transmits through contact with the reservoir rodent host, likely a species of African squirrel.bioRxiv
Interesting report on #Mpox #virus:
(AKA #MonkeyPox or #MPXV)
"We monitored SARS-CoV-2 & MPXV genomes in the air... in Madrid nightclubs... in 2022.
...
MPXV in the air had increased considerably on Aug 8, with 57% of positive samples containing more than 100 genomes per [cubic meter]; this date coincided with the peak incidence of mpox in Spain."
The authors suggest that air sampling might be a useful surveillance method.
#virology #epidemiology #InfectiousDisease
https://doi.org/10.1016/S2666-5247(23)00104-0
@annasimsbiol discusses her new paper on superinfection exclusion in influenza virus https://plos.io/3HXscie and working in a #virology lab during a pandemic
#PLOSBiology #academiclife #AcademicChatter
https://biologue.plos.org/2023/03/22/human-collaboration-to-study-virus-interactions/
Behind the paper: human collaboration to study virus interactions - PLOS Biologue
In this ‘behind the paper’ post, Anna Sims discusses her experience working in a virology lab during the height of the COVID-19 pandemic while not working in SARS-COV-2, and the importance of collaboration and discussion with peers in science.PLOS Biology (PLOS Biologue)