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..."

biorxiv.org/content/10.1101/20…
#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

Important study describing a new phylum of herpesvirus relatives that is abundant in the ocean -

Mirusviruses link herpesviruses to giant viruses

nature.com/articles/s41586-023…

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

Near-atomic architecture of Singapore grouper iridovirus and implications for giant virus assembly

"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.

nature.com/articles/s41467-023…

#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

1/2
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"
nature.com/articles/s41467-022…
#virology #epidemiology #InfectiousDisease

1/6
🦠 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."
biorxiv.org/content/10.1101/20…

#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

7/6
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
doi.org/10.1016/S2666-5247(23)…

If you found the above ☝️ study eye-opening, consider that Deer Tick/Powassan Virus (POWV) may persist in the brain, as studied in this new paper:

"Of Murines and Humans: Modeling Persistent Powassan Disease in C57BL/6 Mice"
doi.org/10.1128/mbio.03606-22

😲 Specifically, the authors found that the #virus may persist in the brain without creating infectious particles, just as non-infectious measles can persist in the brain indefinitely — and be fatal:
pubmed.ncbi.nlm.nih.gov/687900…
#virology #ViralPersistence

Excellent commentary urging coupling of field and laboratory research on viruses in just bats but also other animals. Bridging the gaps between ecology, veterinary/wildlife pathology, human health, and lab-based molecular studies are imperative. #OneHealth #veterinarymed #wildlifepathology #virology #ecology

thelancet.com/journals/lanmic/…

Coupling field and laboratory studies of immunity and infection in zoonotic hosts

The COVID-19 pandemic and discovery of SARS-CoV-2-like viruses in Rhinolophus bats has reinforced the need to identify wildlife sources of zoonotic pathogens and to forecast where and when spillover to humans is likely to occur.

^{The Lancet Microbe}

A Phylogenetic Study of Dengue Virus in Urban Vietnam shows Long-term Persistence of Endemic Strains

"We observed 5 viral lineages co-circulating in Nha Trang from three DENV serotypes, with two likely to have remained as uninterrupted transmission chains for a decade. This, suggests clade cryptic persistence in the area, even in during periods of low reported incidence."

academic.oup.com/ve/advance-ar…

#virology #viruses #dengue #flaviviruses

A Phylogenetic Study of Dengue Virus in Urban Vietnam shows Long-term Persistence of Endemic Strains

AbstractBackground. DENV causes repeated outbreaks of disease in endemic areas, with patterns of local transmission strongly influenced by seasonality, importat

^{Ashall, James (Oxford University Press)}

Tripartite interactions between filamentous Pf4 bacteriophage, Pseudomonas aeruginosa, and bacterivorous nematodes

"Collectively, our data support a model where suppression of quorum-regulated virulence factors by Pf4 allows P. aeruginosa to evade detection by innate host immune responses."

journals.plos.org/plospathogen…

#viruses #virology #symbiosis #phage

Tripartite interactions between filamentous Pf4 bacteriophage, Pseudomonas aeruginosa, and bacterivorous nematodes

Author summary Pseudomonas aeruginosa is an opportunistic bacterial pathogen that infects wounds, lungs, and medical hardware. P. aeruginosa strains are often themselves infected by a filamentous virus (phage) called Pf.

^{journals.plos.org}

Viral dew: Phase separation and the formation of viral replication compartments

journals.plos.org/plospathogen…

#virology #viruses

Viral dew: Phase separation and the formation of viral replication compartments

^{journals.plos.org}

The APOBEC3B cytidine deaminase is an adenovirus restriction factor

"we show that adenovirus infection leads to a reduction of the quantity and/or enzymatic activity of the APOBEC3B protein depending on the strains. The A12 strain seems less able to resist APOBEC3B than the B3 or C2 strains, a characteristic which could explain the strong depletion of the APOBEC3-targeted motifs in the A12 genome."

journals.plos.org/plospathogen…

#viruses #virology

The APOBEC3B cytidine deaminase is an adenovirus restriction factor

Author summary The APOBEC3B protein is overexpressed in many human tumors and promotes genetic diversity and resistance to drug and oncolytic viruses.

^{journals.plos.org}

...and now "flavi-like viruses" in plants! 😲

"More recently flavi-like divergent viruses have been identified in marine invertebrate and vertebrate hosts."

"The striking discovery of gentian Kobu-sho-associated virus (GKaV) expanded the host range of #flavivirus to plants, which was complemented by a recently reported flavi-like virus in carrot."

"Two novel flavi-like viruses shed light on the plant-infecting koshuviruses"
biorxiv.org/content/10.1101/20…
#virus #virology

Two novel flavi-like viruses shed light on the plant infecting koshuviruses

The family Flaviviridae is composed of viruses with a positive sense single-stranded RNA genome and includes viruses that are important veterinary and human pathogens.

^bioRxiv

Important to note that this study of whale circovirus only looked at beached whales.

👀 Surprisingly, it found the virus in 50% of animals. 69% of those showed virus in the brain.

Whales are intelligent creatures and probably don't "accidentally" beach themselves on land. If they beach themselves on land, there may be a logical evolutionary explanation.

...Such as fulfilling the need to separate infected individuals from the rest of the group?

#virus #virology
doi.org/10.3389/fmars.2022.945…

Phylodynamics of deer tick virus in North America

academic.oup.com/ve/advance-ar…

#viruses #virology

Phylodynamics of deer tick virus in North America

Abstract. The burden of ticks and the pathogens they carry is increasing worldwide. Powassan virus (POWV, Flaviviridae: Flavivirus), the only known North Americ

^{McMinn, Rebekah J (Oxford University Press)}

Wonderful essay by @vincentflora and Assaf Vardi on viruses in the ocean

Viral infection in the ocean—A journey across scales

"Aquatic virology tackles some of the most challenging questions in microbial ecology and oceanography, trying to understand how microorganisms that are invisible to the naked eye can influence large-scale processes, such as biogeochemical cycles, or affect entire marine food webs."

journals.plos.org/plosbiology/…

#viruses #virology #ocean #marine

Viral infection in the ocean—A journey across scales

Viruses are the most abundant biological entity in the ocean. This Essay journeys across several orders of magnitude of biological organization, time, and space, to investigate interactions between hosts and viruses in the ocean and their relevance f…

^{journals.plos.org}

🦠
"As of 2 December 2022, over 82,000 human #mpox (or #monkeypox) cases have been laboratory confirmed in 110 countries worldwide."

And sporadic reports are still coming in:
c.im/@andrew_a_lover/109673550…

This may be what a very very very slow pandemic looks like.
🦠
As a step towards the development of an #antiviral, (Peng et al., 2022) recently elucidated the structure of the mpox DNA polymerase:

"Structure of monkeypox #virus DNA polymerase holoenzyme"
doi.org/10.1126/science.ade636…
#virology @virology

"An analysis of about 450,000 electronic health records has found a link between infections from influenza and other common viruses and an elevated risk of having a neurodegenerative condition such as Alzheimer’s or Parkinson’s disease later in life."

#Virology #AlzheimersDisease #NeuroDegeneration #Neuroscience #Immunology

nature.com/articles/d41586-023…

Massive health-record review links viral illnesses to brain disease

Study ties common viruses such as flu to Alzheimer’s and other conditions — but the analysis has limitations, researchers warn.

^{Kozlov, Max}

Are you passionate about #bioinformatics / #Virology / #AMR / #Microbiology / #InfectiousDisease? Another amazing faculty opportunity is opening up at the University of Toronto!

apply.interfolio.com/118539

RT 😀

Tick Borne Encephalitis Virus (TBEV) is found in northern latitudes from England to Siberia, with variants across North America.

Daniel Růžek's lab has been doing some great work studying this possibly common, but under-diagnosed, pathogen.

Their latest paper describes how they used a Leishmania expression system to produce TBEV virus-like particles (VLP).

When used as a vaccine, the VLPs provided full protection from lethal TBEV in mice.

doi.org/10.1016/j.antiviral.20…
#virus #virology @virology

🐝 Bees have really had a hard couple of years.

Suggested factors leading to collapse of bee colonies worldwide include pesticides, bacteria, & parasitic mites.

But the picture would not be complete unless we looked into the possible role of viral infections, too.

And so, welcome to the bee #virome :

"Nationwide genomic surveillance reveals the prevalence and evolution of honeybee viruses in China"
doi.org/10.1186/s40168-022-014…

(shamelessly scooping @eddieholmes here 🤭)
#virus #virology @virology

'Gene duplication and diversification allow hosts to mutate otherwise essential genes, whereas changes in transcriptional regulation can selectively activate genes should their constitutive expression be detrimental. To counter mutational tolerance, it has been suggested that viruses target essential genes as host cofactors, because the genes are less prone to variability'

#Virology #HostPathogen #RNASplicing

journals.plos.org/plosbiology/…

Alternative splicing liberates a cryptic cytoplasmic isoform of mitochondrial MECR that antagonizes influenza virus

By studying how influenza virus engages the intercellular environment, this study reveals that host cells use alternative splicing to embed antiviral proteins in essential metabolic enzymes, potentially protecting host defenses from viral countermeas…

^{journals.plos.org}

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 metagenomics in northeastern China"
doi.org/10.1371/journal.pntd.0…

"Metavirome of 31 tick species provides a compendium of 1,801 RNA virus genomes"
nature.com/articles/s41564-022…

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

Nice press release on an study that came out earlier this year-

"Israeli-led study claims to uncover 100,000 previously unknown viruses"

timesofisrael.com/israeli-led-…

and the original study: cell.com/cell/fulltext/S0092-8…

Congrats again @Neri !

#viruses #virology

Israeli-led study claims to uncover 100,000 previously unknown viruses

Researchers hope groundbreaking findings into RNA pathogens could help develop new kinds of antimicrobial drugs and protect against agriculturally harmful fungi and parasites

^{www.timesofisrael.com}