Tiago Gräf
@tiagograf.bsky.social
📤 63
📥 140
📝 8
Virologist at Fiocruz Brazil | Phylogenetics, Molecular Evolution & Genomic Epidemiology
Since the topic of the moment is the new betacoronavirus with FCS found in Brazil, I would like to draw attention to this preprint. It describes two new betacoronaviruses found in the same genus of bats as Takada et al, and propose a new subgenus, the ambecoviruses.
www.biorxiv.org/content/10.1...
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Ambecovirus, a novel Betacoronavirus subgenus circulating in neotropical bats sheds new light on bat-borne coronaviruses evolution
Understanding the viral diversity harboured by wildlife is essential for effective prediction and prevention of future zoonotic outbreaks. Bats, in particular, are recognized as natural reservoirs for...
https://www.biorxiv.org/content/10.1101/2025.07.20.665586v2
15 days ago
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Kristian G. Andersen
17 days ago
“Furin cleavage site”, that is. Just casually, and naturally, sitting there in one of the most evolutionarily active parts of the genome. Mystery solved.
add a skeleton here at some point
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Kosuke Takada
21 days ago
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...
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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...
https://www.biorxiv.org/content/10.1101/2025.10.24.684489v1
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www.bbc.com/portuguese/a...
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Inteligência artificial: a brasileira em lista dos 100 mais influentes de IA que oferece solução gratuita ao SUS — 'Nunca quisemos ser milionários' - BBC News Brasil
Ana Helena Ulbrich aparece em lista da revista Time ao lado de líderes como Elon Musk e Sam Altman.
https://www.bbc.com/portuguese/articles/cddmrprjpllo?at_ptr_name=twitter&at_format=image&at_link_type=web_link&at_link_id=FF3D56BC-A07C-11F0-BD03-C320E7583283&at_campaign=Social_Flow&at_medium=social&at_campaign_type=owned&at_link_origin=bbcbrasil&at_bbc_team=editorial
about 1 month ago
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Ulad Litvin
about 2 months ago
Viro3D paper is out! We predicted 85,000 protein structures from human & animal viruses. 1/5 🧵 📑 Paper
doi.org/10.1038/s443...
🔭 Explore virosphere
viro3d.cvr.gla.ac.uk
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Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology
imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for >4,400 viruses, allowing mapping of form and function across the human and animal virosphere. Viro3D i...
https://doi.org/10.1038/s44320-025-00147-9
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Chantal Vogels
about 2 months ago
📢New preprint on the impact of dengue virus genetic diversity on inhibition by Wolbachia 🦟🦠🧬 Project led by Afeez Sodeinde,
@emiliefinch.bsky.social
, and
@keli5734.bsky.social
! ✨ Key findings in thread below 👇
www.biorxiv.org/content/10.1...
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Heterogeneity in inhibition of genetically diverse dengue virus strains by Wolbachia
The release of Aedes aegypti mosquitoes transinfected with the virus-inhibiting Wolbachia bacterium has the potential to reduce the burden caused by dengue virus (DENV). However, the robustness of thi...
https://www.biorxiv.org/content/10.1101/2025.09.18.677129v1
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Wayne Maddison
2 months ago
Confused writing is usually a symptom of confused thinking. As we struggle to clarify writing, we clarify our thoughts. AI writing aids rob us of that struggle, leaving clean-looking text and thoughts still confused for lack of inspection. Writing is not just a product; it is a diagnostic tool.
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Kai Kupferschmidt
2 months ago
Sequence data from the new Ebola outbreak in DRC suggests it is indeed a new spillover. And just incredible to see the virus sequenced and the data publicly shared less than 24 hours after confirmation of the outbreak.
#IDsky
🧪
virological.org/t/the-16th-e...
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The 16th Ebola Virus Disease Outbreak in Bulape Health Zone, Kasai, Democratic Republic of the Congo: A new spillover event from an unknown reservoir host
Background The Democratic Republic of the Congo (DRC) is currently facing concurrent outbreaks including mpox, cholera and malaria (1-4). The Ministry of Public Health, DRC has declared the 16th Ebola...
https://virological.org/t/the-16th-ebola-virus-disease-outbreak-in-bulape-health-zone-kasai-democratic-republic-of-the-congo-a-new-spillover-event-from-an-unknown-reservoir-host/1003
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Holly Nichols
4 months ago
I’m thrilled to share my first review about microbial ecology + mosquito-borne disease control! Bacteria block pathogen development in the mosquito gut, but which bacteria will produce long-lasting results in the field? Let’s think about colonization and persistence in the mosquito gut! (1/4)
add a skeleton here at some point
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Andrew Rambaut
5 months ago
Handy to keep up with the ICTV's changes to virus taxonomy and species names:
taxonomy.onecodex.com/taxon/694009...
vs:
taxonomy.onecodex.com/taxon/694009...
or
taxonomy.onecodex.com/taxon/11676/...
vs
taxonomy.onecodex.com/taxon/11676/...
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Provavelmente os casos brasileiros de HPAI em 2025 devem ser devido a esta nova linhagem recombinante. Muito importante sequenciar e analisar o genoma do vírus circulando atualmente no país.
add a skeleton here at some point
6 months ago
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Tulio de Oliveira
6 months ago
A not very happy Friday. CERI had 6 NIH grants canceled, which will impact operations, surveillance and response to epidemics. We are working to try to minimize disturbance but not easy with 6 grants terminated at the same moment. A crisis is unfolding in SA
www.news24.com/southafrica/...
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SA universities face funding crisis as US federal agencies freeze research grants | News24
An investigation into the impact of the US aid freeze on research funding to South African universities has found that 44 programmes worth R2.5 billion were affected.
https://www.news24.com/southafrica/education/sa-universities-face-funding-crisis-as-us-federal-agencies-freeze-research-grants-20250522-1276
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Mario dos Reis
7 months ago
Frustrated that MCMCtree does not have complex substitution models? The IQ-tree team has now developed IQ2MC, an interface for seamless integration of IQ-tree's substitution models with MCMCtree's fast Bayesian pipeline for clock dating. Read the preprint here:
ecoevorxiv.org/repository/v...
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IQ2MC: A New Framework to Infer Phylogenetic Time Trees Using IQ-TREE 3 and MCMCTree with Mixture Models
https://ecoevorxiv.org/repository/view/9125/
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Colin Carlson
7 months ago
🦟🦠 NEW! We looked at every experiment going back to the 1960s, and found that mosquitoes are almost certainly not primary or secondary vectors of Oropouche virus - a common claim in both the scientific literature and public health communication.
#EpiSky
#IDSky
😷🧪
journals.plos.org/plosntds/art...
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Vector competence for Oropouche virus: A systematic review of pre-2024 experiments
Oropouche virus has recently become an urgent threat to public health in Central and South America. OROV is mainly transmitted by biting midges; however, some public health agencies and scientific sou...
https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0013014
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Vasilakis Lab
7 months ago
We celebrated the 100th anniversary of HR Carter's seminal lecture on YF's potential threat to Asia-Pacific area with a perspective to draw attention to the potential reasons why YF epidemics have not occurred in urban centers in the region.
@sbvirologia.bsky.social
@mauriciolnogueira.bsky.social
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Alex Sundermann, DrPH
7 months ago
“Funding by the CDC for two monthly peer-reviewed journals, Emerging Infectious Diseases and Preventing Chronic Disease, will be cut.” EID has published novel, important work that brings
#IDSky
issues to light. Its loss will hurt.
add a skeleton here at some point
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José Henrique Oliveira
10 months ago
Our latest preprint demonstrates that two strains of DENV4 have distinct impacts on Aedes aegypti vector competence and life-history traits.
www.biorxiv.org/content/10.1...
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A Laboratory-Adapted and a Clinical Isolate of Dengue Virus Serotype 4 Differently Impact Aedes aegypti Life-History Traits Relevant to Vectorial Capacity
Dengue virus cases are on the rise globally, and strategies to reduce new infections by controlling its primary vector, the mosquito Aedes aegypti , represent a promising biotechnological approach. Ho...
https://www.biorxiv.org/content/10.1101/2024.06.07.597920v3.abstract
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Leo Bastos
8 months ago
On the verge: outbreak risk after two years of record-breaking dengue epidemics in Brazil - The Lancet Regional Health – Americas
www.thelancet.com/journals/lan...
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On the verge: outbreak risk after two years of record-breaking dengue epidemics in Brazil
Over the last seasons of dengue, the disease has reached record-breaking numbers of confirmed cases both globally and in the Americas.1 That is speculated to be a consequence of two-fold climate drive...
https://www.thelancet.com/journals/lanam/article/PIIS2667-193X%2825%2900078-X/fulltext
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Infectious Diseases
8 months ago
Hantavirus: Global emerging disease with 2 major syndromes Hantavirus Pulmonary Syndrome (HPS) – Americas: 130 cases/year, 30-60% mortality, depending on type Hemorrhagic Fever with Renal Syndrome (HFRS) – Asia/Europe: 100K cases/year, 5-10% fatality rate Spread by rodents primarily 🧵
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This is my first post here and I would like to share this important work that I collaborated on. We analyzed some of the factors impacting the spread of dengue in the Brazilian southern most state, where outbreaks are getting larger each year.
www.medrxiv.org/content/10.1...
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Increasing dengue outbreaks in temperate Brazil is linked to Aedes aegypti invasion and infestation level driving widespread virus transmission
Dengue fever, caused by the dengue virus (DENV), is the most important mosquito-borne disease impacting human health globally, it is particularly prevalent in tropical regions where Aedes vectors thri...
https://www.medrxiv.org/content/10.1101/2025.02.24.25322773v1
9 months ago
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Tiago Gräf
PLOS Biology
9 months ago
PLOS has issued a statement on recent US Executive Orders and scientific integrity. We are determined to stand firmly behind our mission, our values and our principles, and against any attempt at censorship or undermining of the core principles of scientific inquiry.
plos.io/3D4O8cH
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PLOS statement on recent US Executive Orders and scientific integrity - The Official PLOS Blog
Since its founding over twenty five years ago PLOS has been dedicated to advancing open science, ensuring that knowledge is accessible to…
https://plos.io/3D4O8cH
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Angie Rasmussen
9 months ago
I have insomnia a lot lately so may as well share what’s literally keeping me up at night. It’s a long list but tonight it’s flu. Yes, H5N1, but also seasonal flu. Firing federal scientists brings a flu-filled future. Have you ever wondered how flu vaccine strains are chosen?
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Alt CDC (they/them)
10 months ago
The entire archive of CDC datasets can be found here. HUGE shoutout to data archivists- this work is important 👏🙌🏻
archive.org/details/2025...
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The Global Vector Hub
10 months ago
🦟🪰"
#Panama
🇵🇦: Dozens of
#Oropouche
cases detected in Darien province" via
@outbreaknewstoday.substack.com.web.brid.gy
outbreaknewstoday.substack.com/p/panama-doz...
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Panama: Dozens of Oropouche cases detected in Darien province
The Panama Ministry of Health (Minsa) through the Epidemiology Department of the General Directorate of Public Health, informs the population of the detection of an outbreak of the Oropouche virus in ...
https://outbreaknewstoday.substack.com/p/panama-dozens-of-oropouche-cases
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Tiago Gräf
Angie Rasmussen
10 months ago
This is bad news. It suggests reassortment of circulating H5N1 viruses with viruses containing N9 NA. Although this indicates reassortment with avian viruses, it's still bad. Reassortment makes pandemics. The last 3/4 flu pandemics (and likely 1918 too) were reassortant viruses.
add a skeleton here at some point
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IAS - the International AIDS Society
10 months ago
The immediate halting of funding to
#PEPFAR
places millions of lives in jeopardy. The IAS urgently calls on policy makers and stakeholders to restore the funding lifeline to this pivotal programme. Lives depend on it, right now. Read our full statement:
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IAS statement: PEPFAR freeze threatens millions of lives
25 January 2025 (
https://www.iasociety.org/ias-statement/pepfar-freeze-threatens-millions-lives
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BK. Titanji
10 months ago
Bolivia has confirmed a death from a case of Chapare virus identified in December 2024. Thankfully all contacts have tested negative so far. Chapare virus is an arena virus transmitted by rodents. It was discovered in 2003.
www.telegraph.co.uk/global-healt...
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Bolivia confirms death from Ebola-like virus so rare only 15 cases have ever been reported
It is still unclear how the farmer contracted Chapare Hemorrhagic Fever, but it is primarily caught through contact with infected rodents
https://www.telegraph.co.uk/global-health/science-and-disease/bolivia-confirms-death-from-chapare-hemorrhagic-fever/
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MichaelW
10 months ago
Somewhat paradoxically,
#tinnitus
(hearding sounds that are not there) is common in people suffering hearing loss. and affects the same sets of frequencies. Treatments are coming, from the understanding of loud-noise-fibre damage
www.newscientist.com/article/mg26...
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A new understanding of tinnitus and deafness could help reverse both
Investigations of the paradoxical link between tinnitus and hearing loss have revealed a hidden form of deafness, paving the way to possible new treatments
https://www.newscientist.com/article/mg26234870-800-a-new-understanding-of-tinnitus-and-deafness-could-help-reverse-both/
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Tiago Gräf
Science Magazine
11 months ago
Five years after
#SARSCoV2
surfaced, scientists reflect and look ahead to the next threat.
scim.ag/4j4CZsn
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COVID 5 years later: Learning from a pandemic many are forgetting
Five years after SARS-CoV-2 surfaced, scientists reflect and look ahead to the next threat
https://scim.ag/4j4CZsn
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Thelonevirologist
11 months ago
Zoonotic transmission of novel Influenza A variant viruses detected in Brazil during 2020 to 2023
www.nature.com/articles/s41...
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Zoonotic transmission of novel Influenza A variant viruses detected in Brazil during 2020 to 2023 - Nature Communications
Human infections with swine-origin influenza A viruses occur sporadically. Here, the authors describe the genomic and epidemiological characteristics of eight cases detected in southern Brazil between...
https://www.nature.com/articles/s41467-024-53815-z
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Tiago Gräf
MRC-LMB Cell Biology Division
11 months ago
40 years ago all of Genbank was published in print form by NAR. The same format today would require over 4 light seconds of shelf space. To a year of progress in 2025.
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Theo Sanderson
11 months ago
Some small quality of life improvements to Gensplore (
gensplore.genomium.org
): - right-click brings up a menu for copying (ctrl-C still works, as ever) - clicking on a feature now selects it 🧪
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Kai Kupferschmidt
11 months ago
CDC just confirmed the first severe case of
#H5N1
in the US in a patient in Louisiana. This virus seems to be the same genotype D1.1 that is spreading in birds at the moment (so not the cattle genotype B3.13) that severely sickened the teenager in Canada.
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Martin Enserink
11 months ago
Goodbye SARS-CoV-2, hello 'Betacoronavirus pandemicum'?
@cofford.bsky.social
reports on the controversial renaming of thousands of viruses.
www.science.org/content/arti...
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‘Silly and pompous’: Official new names for viruses rile up researchers
An overhaul of viruses’ scientific naming system has incensed some virologists, but others are more accepting
https://www.science.org/content/article/silly-and-pompous-official-new-names-viruses-rile-researchers
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Andrew Rambaut
11 months ago
There is a new alternative to the MCC summary tree in BEAST X - the 'highest independent posterior sub-tree reconstruction' or HIPSTR tree. First implemented over 5 years ago (something distracted us from writing it up) we now have a preprint describing it:
www.biorxiv.org/content/10.1...
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HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X
In Bayesian phylogenetic and phylodynamic studies it is common to summarise the posterior distribution of trees with a time-calibrated consensus phylogeny. While the maximum clade credibility (MCC) tr...
https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biorxiv.org%2Fcontent%2F10.1101%2F2024.12.08.627395v1&data=05%7C02%7C%7C6f88d8c9f56c43ccb14608dd19d40541%7C2e9f06b016694589878910a06934dc61%7C0%7C0%7C638695120632859615%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=CJ%2Bo04GWQzKZXaMX8KkHUqeujF59qinrOJh0i2U%2Fgfg%3D&reserved=0
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Isabella Eckerle
11 months ago
I cannot understand that the US can’t just stop selling of raw milk with all that’s going on with H5N1 + implement strict biosafety on the farms. Do you know the level of protection required when working with the virus in the laboratory? The current situation US is a global health security risk
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Pathoplexus
11 months ago
Today Pathoplexus announces the inclusion of a new viral pathogen: mpox (previously known as monkeypox). Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response. 1/7
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Mellanie Fontes-Dutra
12 months ago
Estamos a UMA MUTAÇÃO de distância para a gripe aviária H5N1 se transmitir mais efetivamente ENTRE HUMANOS? Estudos mostram que versões atuais se replicam melhor no tecido respiratório humano, com maior capacidade de serem expelidas no ar ao infectar mamíferos. Atualizações, incluindo VACINAS 🧵🔻
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Kai Kupferschmidt
12 months ago
If an
#H5N1
pandemic starts tomorrow or in three months, there will be little mystery as to how it happened. The conditions are all there. They have been for a while. So in some ways the more interesting question to me at the moment is: Why aren’t we in a pandemic yet? Story here, 🧵 to come: 🧪#IDSky
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Why hasn’t the bird flu pandemic started?
Some scientists examining mutations found in H5N1 viruses fear major outbreak is imminent but others says pathogen remains unpredictable
https://www.science.org/content/article/why-hasn-t-bird-flu-pandemic-started
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Simon Dellicour
12 months ago
How fast are viruses spreading in the wild? Check out our latest study now published in
@plosbiology.bsky.social
:
doi.org/10.1371/jour...
. A study performed with Paul Bastide, Pauline Rocu, Denis Fargette, Olivier Hardy,
@msuchard.bsky.social
,
@stephaneguindon.bsky.social
, and Philippe Lemey (1/7)
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DefinitelyNotAlice
12 months ago
This is a very big problem, that we need to discuss... As a non-native English speaker I find AI tools help a lot in making my writing sound much more like proper English.
journals.plos.org/plosbiology/...
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The manifold costs of being a non-native English speaker in science
This study reveals that non-native English speakers, especially early in their careers, spend more effort than native English speakers in conducting scientific activities, from reading and writing pap...
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002184
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