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Items tagged with: Virus
Benchmarking #bioinformatic #virus identification tools using real-world #metagenomic data across biomes
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03236-4
Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes - Genome Biology
Background As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial.BioMed Central
๐ New preprint from the (MDM) lab:
๐ https://www.biorxiv.org/content/10.1101/2023.11.22.567924v1
โ How accurately can we predict diverse #bacteriophage bacteria-interactions from their #genomes only ?
๐ฆ We created a matrix of >38k #phage-#bacteria interactions to find out (=> AUROC 86%) & used our predictions to recommend tailored phage cocktails.
Predicting which phages infect which specific strains would allow to better fight bacterial infections and understand #microbial ecology.
1/n
#microbiology #virus #phagotherapy
Predicting phage-bacteria interactions at the strain level from genomes
Predicting how phages can selectively infect specific bacterial strains holds promise for developing novel approaches to combat bacterial infections and better understanding microbial ecology.bioRxiv
#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 โshock and aweโ concepts about the microbial world that he introduces to his microbiology students, and asks three important questions ab...YouTube
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
A third of US deer have had COVIDโand they infected humans at least 3 times
New study builds on data suggesting white-tailed deer could be a virus reservoir.Ars Technica
From Jing Wang et al. at Sun Yat-sen University, this is a new Nature Communications publication describing the virome of 149 bats collected in Yunan Provinde from 2015-2019. A metagenomic assembly produced contigs from 55 different mammal-associated viral species, including 5 similar to known human or livestock pathogens, including 2 Sarbecoviruses, with evidence of recombination.
https://www.nature.com/articles/s41467-023-39835-1
#virus #virome #bats #coronavirus #virology #metagenomics
Individual bat virome analysis reveals co-infection and spillover among bats and virus zoonotic potential - Nature Communications
Viral diversity and abundance in bats are incompletely understood. Here, analyzing individual bat viromes, the authors observe a high frequency of co-infection and spillover among the animals and identify viruses with the potential to infect humans oโฆNature
Plant virus movement proteins originated from jelly-roll capsid proteins
Movement proteins, a signature of plant RNA and DNA viruses, enable cell-to-cell movement of the virus via plasmodesmata channels.plos.io
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 โdark matterโ of the โฆbioRxiv
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
๐ฆ A Few More #Mpox ( #MonkeyPox) Pandemic Updates ๐ฆ
"Assuming APOBEC-editing is characteristic of [mpox] infection in human hosts, we propose an APOBEC clock that โ at a rate of ~6 APOBEC3 mutations per year โ 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
"Of Murines and Humans: Modeling Persistent Powassan Disease in C57BL/6 Mice"
https://doi.org/10.1128/mbio.03606-22
๐ฒ 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 โ and be fatal:
https://pubmed.ncbi.nlm.nih.gov/6879001/
#virology #ViralPersistence
Persistent measles infection of the central nervous system: subacute sclerosing panencephalitis - PubMed
Measles can persist in the central nervous system and cause subacute sclerosing panencephalitis (SSPE), a progressive disease that is almost always fatal.PubMed
Need a #virus or #phage bioinformatics tool?
Have a #virus or #phage bioinformatics tool?
Check out this google sheet and add your new tools
https://docs.google.com/spreadsheets/d/1ClNgip08olKK-oBMMlPHBwIcilqSxsan8MEaYphUei4/edit#gid=0
Viral Bioinformatics Tools
Sheet1 Name,Category,Phage, Virus, or Both,Methods,Citation,URL,Last update (YYYMMDD),Notes,Install from conda,Install from pip,Install from source,Database size if required for download,Dependencies,Runs on a laptop,Runs on a cluster MaGplotR,CRISPโฆGoogle Docs
Have a #virus or #phage bioinformatics tool?
Check out this google sheet and add your new tools
https://docs.google.com/spreadsheets/d/1ClNgip08olKK-oBMMlPHBwIcilqSxsan8MEaYphUei4/edit?usp=sharing
Viral Bioinformatics Tools
Sheet1 Tool name,Category,Phage, Virus, or Both,Methods,Citation,URL,Last update,Notes,Install from conda,Install from pip,Install from source,Database size if required for download,Dependencies,Runs on a laptop,Runs on a cluster Pharokka,AnnotationโฆGoogle Docs
"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"
https://www.biorxiv.org/content/10.1101/2023.02.06.527325v1
#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
One recurring problem with #epidemiology of #flavivirus #InfectiousDisease is that antibody tests for one flavivirus happen to be highly crossreactive with other flaviviruses.
That is a problem addressed in:
"Co-Circulation of West Nile, Usutu, and Tick-Borne Encephalitis Viruses in the Same Area: A Great Challenge for Diagnostic and Blood and Organ Safety"
https://www.mdpi.com/1999-4915/15/2/366
@virology
Co-Circulation of West Nile, Usutu, and Tick-Borne Encephalitis Viruses in the Same Area: A Great Challenge for Diagnostic and Blood and Organ Safety
Viral infections caused by viruses from the family Flaviviridae such as Zika (ZIKV), Dengue (DENV), yellow fever (YFV), tick-borne encephalitis (TBEV), West Nile (WNV), and Usutu (USUV) are some of the most challenging diseases for recognition in cliโฆMDPI
This exciting new research explores the influence of #virus #infection in changing the balance of organic matter degradation between #bacteria and #eukaryotes in #marine #carboncycling during #phytoplankton blooms.
Based on #mesocosm studies, this research demonstrates how #viruses infecting different #microorganisms change community dynamics and the release and potential fate of marine carbon from primary production.
Learn more in this new research in Nature Communications on:
https://www.nature.com/articles/s41467-023-36049-3
#microbiology #ecology #MicrobialEcology
Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms - Nature Communications
Algal blooms are hotspots of marine primary production that play central roles in microbial ecology and global elemental cycling.Nature
๐ 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
https://doi.org/10.3389/fmars.2022.945289
Targeted surveillance detected novel beaked whale circovirus in ten new host cetacean species across the Pacific basin
The first cetacean circovirus, beaked whale circovirus (BWCV), was recently reported in a Longmanโs beaked whale (Indopacetus pacificus) stranded in Hawaiโi and represents an emergent disease with unknown population impacts.Frontiers
"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:
https://c.im/@andrew_a_lover/109673550181706348
This may be what a very very very slow pandemic looks like.
๐ฆ
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"
https://doi.org/10.1126/science.ade6360
#virology @virology
Andrew Lover (@andrew_a_lover@c.im)
Attached: 1 image New #mpox in CDC EID (title only); seems... important. ๐ Anecdata ----> Case reports ----> (๐๐๐ฉ'๐จ ๐๐ช๐จ๐ฉ ๐จ๐ฉ๐ค๐ฅ ๐ง๐๐๐๐ฉ ๐๐๐ง๐, ๐จ๐๐๐ก๐ก ๐ฌ๐? ๐๐ค ๐ฃ๐๐๐ ๐ฉ๐ค ๐๐ค๐ฃ๐ฉ๐๐ฃ๐ช๐.) Case series ----> Epi studies ----> New Knowledge. https://wwwnc.cdc.C.IM
Daniel Rลฏลพek'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.
https://doi.org/10.1016/j.antiviral.2022.105511
#virus #virology @virology
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"
https://doi.org/10.1186/s40168-022-01446-1
(shamelessly scooping @eddieholmes here ๐คญ)
#virus #virology @virology
Nationwide genomic surveillance reveals the prevalence and evolution of honeybee viruses in China - Microbiome
Background The economic and environmental value of honeybees has been severely challenged in recent years by the collapse of their colonies worldwide, often caused by outbreaks of infectious diseases.BioMed Central
๐ฒ 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"
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 nortโฆdoi.org