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Fernando Gonzalez-Candelas

@fgonzalef.bsky.social
702 followers 719 following 12 posts

Evolutionary biology, genomic epidemiology, pathogens, phylogenies, phylogenomics, bioinformatics, population genetics and genomics, forensics, and anything to which evolutionary analyses of genes and genomes can be applied to. Squash player (still).

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Reposted by Fernando Gonzalez-Candelas
Delegación del CSIC Castilla y León @csiccyl.bsky.social · 16/09/2026
Con: 🦠 Noemí Sevilla (CISA-INIA-CSIC) - enfermedades emergentes. 💉 Margarita del Val (CBMSO-CSIC) - inmunología y vacunas. 🧬 Fernando González-Candelas (I2SysBio-FISABIO) @fgonzalef.bsky.social - epidemiología molecular y resistencia a los antimicrobianos. ¡La Ciencia nuestra mejor herramienta!
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Reposted by Fernando Gonzalez-Candelas
PathoGenOmics Lab @pathogenomics.bsky.social · 15/09/2026
Want to analyse bacterial genomes yourself? ONE-BAG 2026 at @i2sysbio.es takes you from raw reads to interpretable phylogenies, with hands-on training in QC, SNPs, assembly, annotation, pangenomes, outbreaks, AMR and typing. Learn more: onebag.uv.es
onebag.uv.es
ONE-BAG 2026 | Bacterial Genomics for One Health
From raw reads to a tree you can defend. Four days in Valencia, free for EOHA full members and 300 euro for everyone else. Applications close 1 October 2026.
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Fernando Gonzalez-Candelas @fgonzalef.bsky.social · 22/04/2026
We are hiring a PhD candidate! Only for non-EU graduates. To work on the molecular and genomic epidemiology of Treponema pallidum, based on our recent publication (doi:10.1128/mbio.00358-26). Interested? Send your CV and an expression of interest to fernando.gonzalez@uv.es before May 20th, 2026.
uv.es
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Reposted by Fernando Gonzalez-Candelas
Jose A Escudero @jaescudero.bsky.social · 08/05/2025
🧪 Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉 Short 🧵 www.science.org/doi/10.1126/...
science.org
Mobile integrons encode phage defense systems
Integrons are bacterial genetic elements that capture, stockpile, and modulate the expression of genes encoded in integron cassettes. Mobile integrons (MIs) are borne on plasmids, acting as a vehicle ...
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Reposted by Fernando Gonzalez-Candelas
Earth BioGenome Project 🌍 @ebpgenome.bsky.social · 28/05/2025
(1/2) 🌍 Don't miss this groundbreaking study by Guo et al., 2025 and the 10,000 Plant Genomes Project. Profiling over one million nuclei across 20 tissues, the authors have further unraveled the genome of one of the most well studied plant genera: Arabidopsis. #plantgenomics #agriculture
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Reposted by Fernando Gonzalez-Candelas
Daniel Tamarit @danieltamarit.bsky.social · 14/05/2025
New vacancy in my team! PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture. Please repost and share with talented MSc students in #evobio, bioinformatics or related :) www.uu.nl/en/organisat... #MEvoSky #MicroSky
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Fernando Gonzalez-Candelas @fgonzalef.bsky.social · 07/05/2025
Good papers, like good wine, need maturing. I'm proud and thrilled to share our work on genomic epidemiology of K.pneumoniae in Valencia and differential transmission patterns of resistances, part of Neris Garcia's PhD thesis and the NLSAR consortium. go.uv.es/td8iL4c #publichealth #EpiSky 🧬🖥️
go.uv.es
Genomic surveillance reveals different transmission patterns between third-generation cephalosporin and carbapenem resistance in Klebsiella pneumoniae in the Comunidad Valenciana (Spain), 2018–2020 - ...
Background The emergence and spread of third-generation cephalosporins (3GC) and carbapenem-resistant Klebsiella pneumoniae pose a global critical challenge. Understanding the transmission dynamics wi...
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Fernando Gonzalez-Candelas @fgonzalef.bsky.social · 24/02/2025
Febrero de 2020: el mes en el que España convivió con el coronavirus sin saberlo #publichealth #publichealthsky elpais.com/sociedad/202...
elpais.com
Febrero de 2020: el mes en el que España convivió con el coronavirus sin saberlo
El patógeno llegó y se propagó masivamente sin ser detectado durante esos días hasta hacer inevitables los confinamientos. Miles de casos de covid fueron confundidos con otras infecciones respiratoria...
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Reposted by Fernando Gonzalez-Candelas
PopGen Vienna @popgenviennaphd.bsky.social · 13/02/2025
The PopGen Vienna Seminar series schedule is ready for the next term (Mar-Jun). It's jam-packed with fantastic speakers in #evolution, #genetics, #genomics, #popgen, and more! Details and streaming link signup can be found on our website www.popgen-vienna.at/news/seminars/
PopGen Seminar Series
Summer Term 2025

04.03.25 – Lutz Becks (Univ. of Konstanz, DE)
The evolutionary dynamics of novel endosymbiosis.
11.03.25 – Ilkka Kronholm (Univ. of Jyväskylä, FI)
How chromatin structure influences genetic and epigenetic variation.
18.03.25 – Katja Hoedjes (Vrije Univ. Amsterdam, NL)
Understanding functional impact of genetic variation on complex traits at a single nucleotide resolution.
25.03.25 – Sophie Armitage (Freie Univ. of Berlin, DE)
Evolutionary ecology of host-pathogen interactions.
01.04.25 – Matthew Rockman (New York Univ., US)
Developmental evolution is a population-genetics problem.
08.04.25 – Wen-Juan Ma (Vrije Univ. Brussels, BE)
The evolution of sex chromosomes and sex determination in frogs.
15.04.25 – Almorò Scarpa (Vetmeduni, AT)
Two centuries of transposable element invasions in Drosophila melanogaster
22.04.25 – Julia Kreiner (Univ. of Chicago, US)
The mode and tempo of genomic adaptation to contemporary agriculture.
29.04.25 – Martin Kaltenpoth (Max Planck Inst. for Chemical Ecology, DE)
Microbial symbionts as sources of evolutionary innovations in beetles.
06.05.25 – Luisa Pallares (Friedrich Miescher Laboratory, DE)
Phenotypic robustness across the genotype-phenotype map, from genes to environment and back.
13.05.25 – Diana Rennison (Univ. of Calif., San Diego, US)
Understanding the predictability of evolutionary trajectories using threespine stickleback.

20.05.25 – Filipa Sousa (Univ. of Vienna, AT)
Bioenergetics Evolution: The link between Earth’s and Life’s history.
27.05.25 – Yun Song (Univ. of California, Berkeley, US)
Learning and applying complex probability distributions over biological sequences.
03.06.25 – April Wei (Cornell Univ., US)
Enabling efficient analysis of biobank-scale data with genotype representation graphs.

ALT TEXT OUT OF SPACE, GO TO https://www.popgen-vienna.at/news/seminars/
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Reposted by Fernando Gonzalez-Candelas
Rhys White @rhystwhite.bsky.social · 13/02/2025
📌The need for speed: ultra-rapid high-resolution outbreak analysis in a front-line hospital microbiology laboratory |@medrxivpreprint See how hospital labs can analyse outbreaks fast - no on-site #Bioinformatics needed, cutting delays doi.org/10.1101/2025... 🖥️🧬💻 #AcademicSky #MicroSky 🧪🧫🦠
doi.org
The need for speed: ultra-rapid high-resolution outbreak analysis in a front-line hospital microbiology laboratory
Many hospital laboratories have technical capacity to perform whole-genome sequencing but lack bioinformatic expertise to analyse sequence data. Sending isolates to reference laboratories creates dela...
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Fernando Gonzalez-Candelas @fgonzalef.bsky.social · 24/01/2025
bsky.app/profile/flod...
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Reposted by Fernando Gonzalez-Candelas
Wolfgang Huber @wkhuber.bsky.social · 24/01/2025
CompBio method developers: software that only runs on your computer and is not available via a repository like CRAN, PyPI, Bioconductor, is not a proper research output — just like a set of scribbled notes on your desktop is not the same as a preprint or a paper. Finish the job.
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Reposted by Fernando Gonzalez-Candelas
Matt Jago @mattjago.bsky.social · 18/01/2025
Very excited that my 1st first-author paper has just been published!! We present a novel mutant screening technique that can rapidly identify 100s of antibiotic resistance mutations, while evaluating how likely they are in different genetic backgrounds. www.nature.com/articles/s41...
nature.com
High-throughput method characterizes hundreds of previously unknown antibiotic resistance mutations - Nature Communications
Resistance mutations are challenging to characterize because their effects are highly context dependent. Here, authors present a quantitative mutant screening technique that deconstructs how factors l...
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Reposted by Fernando Gonzalez-Candelas
Ilan Schwartz @germhuntermd.bsky.social · 17/01/2025
#IDSky #MedSky required reading: Multidrug-resistant Gram-negative bacterial infections Nenad Macesic, Anne-Catrin Uhlemann, Anton Peleg Review in @thelancet.bsky.social doi.org/10.1016/S014...
Figure 1 Mechanisms of action of key antibiotics for the treatment of multidrug-resistant Gram-negative bacterial infections

Several classes of antibiotics are available for the treatment of multidrug-resistant Gram-negative bacterial infections. Their mechanisms of action focus on key aspects of bacterial cell function, such as inhibiting cell wall synthesis (ie, β-lactams and fosfomycin) and function (ie, polymyxins), protein synthesis (ie, aminoglycosides and tetracyclines), folic acid synthesis (ie, trimethoprim and sulphonamides), and DNA replication (ie, fluoroquinolones). Because of increasing antimicrobial resistance, novel antibiotics have been developed to overcome some of these mechanisms; for example, by inhibiting antibiotic modification (ie, β-lactamase inhibitors) or by altering entry pathways (ie, cefiderocol, which enters via iron transporters). DHF=dihydrofolic acid. PABA=para-aminobenzoic acid. THF=tetrahydrofolate.Figure 2 Diagnostic testing of multidrug-resistant Gram-negative bacteria

Diagnosis of multidrug-resistant Gram-negative bacterial infections involves both species identification and antibiotic susceptibility testing. Although clinical microbiology laboratories have undergone automation of these processes and have seen the introduction of proteomic methods, such as MALDI-TOF, delays in turnaround time remain and might affect patient outcomes. New biochemical, molecular (eg, PCR), automated microscopy, and hybridisation-based rapid diagnostics now allow faster detection of antimicrobial resistance, including by testing clinical samples directly. Emerging technologies are seeking to improve both the speed of testing and provide more detailed information regarding the underlying mechanisms of antimicrobial resistance. MALDI-TOF=matrix-assisted laser desorption/ionisation time-of-flight.Figure 3 Summary of new antibiotic agents for the treatment of multidrug-resistant Gram-negative bacterial infections

Green=antibiotic is reliably active in vitro and guideline recommended. Yellow=variable activity; antibiotic might be effective if in vitro susceptibility is shown, clinical data might be lacking to support routine use. Red=not recommended, likely absence of in vitro susceptibility. IV=intravenously. *Administered simultaneously via Y-site administration. †Administration was studied in combination with imipenem–cilastatin.Figure 4 Summary of IDSA and ESCMID guidelines for the treatment of multidrug-resistant Gram-negative bacterial infections

3GCephR-E=third-generation cephalosporin-resistant Enterobacterales. AmpC-E=β-lactamase producing Enterobacterales. CRAB=carbapenem-resistant Acinetobacter baumannii. CRE=carbapenem-resistant Enterobacterales. DTR-P aeruginosa=difficult-to-treat resistant-Pseudomonas aeruginosa. ESBL-E=extended-spectrum β-lactamase-producing Enterobacterales. ESCMID=European Society for Clinical Microbiology and Infectious Diseases. IDSA=Infectious Diseases Society of America. MBL=metallo-β-lactamase. UTI=urinary tract infection.
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Reposted by Fernando Gonzalez-Candelas
Flo Débarre @flodebarre.eurosky.social · 12/01/2025
Five years ago (Sunday 12 Jan 2020), five sequences of the new coronavirus were officially shared via GISAID, on a dedicated page revealed by a link on the GISAID homepage. ▫️1/ (🖼️: virological.org/t/novel-2019... by @arambaut.bsky.social)
screenshot of the new webpage: 

[Title] Newly discovered betacoronavirus, Wuhan 2019-2020

A previously unknown betacoronavirus was detected in patients during an outbreak of respiratory illnesses, including atypical pneumonia, that started mid-December 2019 in the city of Wuhan, the capital of Central China's Hubei Province.
The newly discovered coronavirus is similar to some of the betacoronaviruses detected in bats, but it is distinct from SARS-CoV and MERS-CoV.
The genome of the newly discovered CoV consists of a single, positive-stranded RNA that is approximately 30k nucleotides long. The overall genome organization of the newly discovered CoV is similar to that of other coronaviruses. The newly sequenced virus genome encodes the open reading frames (ORFs) common to all betacoronaviruses, including ORF1 ab that encodes many enzymatic proteins, the spike-surface glycoprotein (S), the small envelope protein (E), the matrix protein (M), and the nucleocapsid protein (N), as well as several nonstructural proteins.

[Table]
Virus name
Accession ID

Passage det Collection date
Host
Originating lab
BetaCoV/Wuhan/IVDC-HB-01/2019 EPIISL_402119 Virus Isolate


2019-12-30
Human
National Institute for Viral Disease Control and Prevention, China CDC
BetaCoV/Wuhan/IVDC-HB-04/2020
EPIISL_402120 Original

2020-01-01
Human
National Institute for Viral Disease Control and Prevention, China CDC
BetaCoV/Wuhan/IVDC-HB-05/2019
EPI_ISL_402121
Original
2019-12-30

Human National Institute for Viral Disease Control and Prevention, China CDC
BetaCoV/Wuhan/IPBCAMS-WH-01/2019 EPI_ISL_402123

Original
2019-12-24

Human Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Pel
BetaCoV/Wuhan/WIV04/2019
EPLISL_402124 Original

2019-12-30

Human Wuhan Jinyintan Hospital
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Reposted by Fernando Gonzalez-Candelas
Infectious Disease Tracker @hmpxvt.bsky.social · 12/01/2025
H5 bird flu was found in wastewater in Los Angeles, San Francisco, Palo Alto, Paso Robles, Redwood City, Sacramento, San Jose, Santa Rosa, Sunnyvale and Turlock, according to WastewaterSCAN.
A chart showing wastewater sample stations in California and if H5 bird flu was found there.
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Reposted by Fernando Gonzalez-Candelas
Flo Débarre @flodebarre.eurosky.social · 11/01/2025
Five years ago (Saturday 11 Jan 2020), first public announcement and availability of a sequence of the new coronavirus. It was posted by @eddieholmes.bsky.social at 01:05 UTC on Virological, and announced on Twitter at 01:08 UTC. ▫️1/ web.archive.org/web/20200118... archive.is/z880d
screenshot of Eddie Holmes' tweet:
@edwardcholmes
All, an initial genome sequence of the coronavirus associated with the Wuhan outbreak is now available at Virological.org here: [link to virological]
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Reposted by Fernando Gonzalez-Candelas
Alexandre Almeida @alexmsalmeida.bsky.social · 10/01/2025
Delighted to share the first peer-reviewed paper from our team @camvetschool.bsky.social where we investigate the ecological dynamics of Enterobacteriaceae in the human gut #microbiome: www.nature.com/articles/s41... @naturemicrobiol.bsky.social
nature.com
Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations - Nature Microbiology
Assessing more than 12,000 metagenomic samples from across the world using computational approaches, the authors determined interactions between species that co-colonize or co-exclude Enterobacteriace...
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Reposted by Fernando Gonzalez-Candelas
Adam Kucharski @adamjkucharski.bsky.social · 07/01/2025
Suppose a new flu pandemic were to emerge. How quickly could we get going with key epidemiological analysis and modelling? To find out, I went back through the dozens of reports I was involved in for SPI-M for COVID and estimated where we currently stand: epiverse-trace.github.io/posts/covid-...
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Reposted by Fernando Gonzalez-Candelas
TARGetAMR @target-amr.bsky.social · 08/01/2025
🔥 Webinar Series Launch! 🔥 ‘#Genomics and Beyond: A Holistic Approach to Tackling #AMR in East Africa’ 🌍 Don't miss Prof. Matthew Holden #StAndMedicine sharing his expertise. Register Now www.targetamr.org.uk/hdrevents/ja...
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Reposted by Fernando Gonzalez-Candelas
The Public Domain Review @publicdomainrev.bsky.social · 08/01/2025
🥁 Announcing the Public Domain Image Archive! 🥁 We are v excited to share our new sister-project, the Public Domain Image Archive (PDIA), a curated collection of 10k+ out-of-copyright historical images, all free to explore and reuse: pdimagearchive.org @pdimagearchive
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 09/01/2025
*** Notification: New class in Evolutionary Cell Biology open to the public during Spring 2025 semester The class is taught by Dr. Michael Lynch every Tuesday and Thursday, 9:00-10:15 am (MST), starting on 16 January 2025 Join the class on asu.zoom.us/j/86824596554 Details victor.chai@asu.edu
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Reposted by Fernando Gonzalez-Candelas
Anna Dewar @annadewar.bsky.social · 08/01/2025
Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2 We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets. These methods must be considered an essential part of the comparative genomics toolkit. @lauriebelch.bsky.social @stuwest.bsky.social
rdcu.be
A phylogenetic approach to comparative genomics
Nature Reviews Genetics - Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The...
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Fernando Gonzalez-Candelas @fgonzalef.bsky.social · 09/01/2025
Very excited to share our recent publication with Verena Schuenemann and other excellent collaborators, including my former student Marta Pla-Diaz. We have improved the analysis of Treponema pallidum genomes with a Multiple_Reference_Based mapping. Useful for many other bacteria Enjoy rdcu.be/d5GGx
urldefense.com
Insights into Treponema pallidum genomics from modern and ancient genomes using a novel mapping strategy
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Tom Peacock @peacockflu.bsky.social · 07/01/2025
Really proud to share our preprint describing early adaptation of H5N1 to US dairy cattle, and showing how these mutations enhance the ability of the virus to infect other mammals, such as pigs and humans. With @influenzal.bsky.social @vidhid.bsky.social @drclairesmith.bsky.social and many more!
biorxiv.org
Polymerase mutations underlie adaptation of H5N1 influenza virus to dairy cattle and other mammals.
In early 2024, an unprecedented outbreak of H5N1 high pathogenicity avian influenza was detected in dairy cattle in the USA. The epidemic remains uncontrolled, with spillbacks into poultry, wild birds...
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Reposted by Fernando Gonzalez-Candelas
Ryan Wick @rrwick.bsky.social · 31/12/2024
New year, new assemblies! I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes! It's the successor to Trycycler, designed to be faster and less reliant on user intervention. Check it out: github.com/rrwick/Autoc... (1/5)
github.com
Home
A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler
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Brandy Schillace @bschillace.brandyschillace.com · 03/01/2025
History doesn’t lie. Polio—and other disease epidemics—killed, paralyzed, ravaged lives. It’s still here, waiting. 🧪♿️🗃️ #vaccines #polio brandy-schillace.medium.com/american-ing...
brandy-schillace.medium.com
American Ingenuity Beat the Polio Outbreak
So Why Risk Letting It Return?
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Reposted by Fernando Gonzalez-Candelas
Noémie Lefrancq @noemielefrancq.bsky.social · 02/01/2025
Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉 buff.ly/4gyYCzx We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies. 🧵 A thread... 1/n #IDSky #IDModelling
buff.ly
Learning the fitness dynamics of pathogens from phylogenies - Nature
Phylowave, an innovative phylogenetic approach, can identify the main circulating pathogen lineages with increased fitness and the associated genetic changes, enabling the timely identification of…
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Infectious Disease Tracker @hmpxvt.bsky.social · 23/12/2024
⚠️ BREAKING: H5N1 bird flu virus levels in San Francisco wastewater surged to a record high of 228.8, according to WastewaterSCAN. This wastewater treatment plant handles 80% of the city's wastewater.
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Reposted by Fernando Gonzalez-Candelas
Joe Grove @grovearmada.bsky.social · 20/12/2024
🎁 Early Xmas present from your friends at the MRC-University of Glasgow Centre for Virus Research @cvrinfo.bsky.social We're thrilled to unwrap Viro3D - a comprehensive database of virus protein structures: >85,000 predicted structures from 4,400 human & animal viruses! 🦠 viro3d.cvr.gla.ac.uk
viro3d.cvr.gla.ac.uk
Viro3D
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Dr Edward Hill @edmhill.bsky.social · 20/12/2024
1/ Highly pathogenic avian influenza (HPAI) in Great Britain & Europe - DEFRA outbreak assessment for 18 Dec 2024. #IDsky 🧪 🗓️ Report period: 06 Nov – 18 Dec 2024 🔗 to report: assets.publishing.service.gov.uk/media/6765a0...
Department for Environment, Food and Rural Affairs
Updated Outbreak Assessment #6
High pathogenicity avian influenza (HPAI) in Great Britain and Europe
18 December 2024

Disease report.

Since our previous outbreak assessment on 6 November 2024, there have been ten reports of high pathogenicity avian influenza (HPAI) H5 clade 2.3.4.4b in domestic poultry. All reports have been confirmed as HPAI H5N1, the first confirmation of the subtype in commercial poultry since February 2024.

There has also been a further 18 HPAI H5 clade 2.3.4.4b events involving 30 “found-dead” wild birds in Great Britain. Of these, 15 have been confirmed as HPAI H5N1,13 as HPAI H5N5 and 2 as HPAI H5Nx. The wild bird risk level across Great Britain has been raised to very high.

The risk level for HPAI H5 incursion in poultry:
• With stringent biosecurity is increased to medium with medium uncertainty; and
• With non-stringent or suboptimal biosecurity is increased to high with medium uncertainty.

HPAI H5 reports continue across Europe, with continued incidences of poultry outbreaks of H5N1 in Germany and France and the first HPAI outbreak in commercial poultry in the Netherlands. Wild bird reports have also increased, with 240 reports between 06 November and 18 December.

There have been no further reports of HPAI H5 in mammals in Europe.
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Zamin Iqbal @zaminiqbal.bsky.social · 20/12/2024
This is super interesting, have never seen tiled amplicons for bacteria. I can see why it works with (non recombining, v few mobile elements) Mtb, seems like it would be v hard to design primer schemes for other things. V keen to see the pneumococcus results . Will read!
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Jonathan Howard @joho.bsky.social · 20/12/2024
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Claus Wilke @clauswilke.com · 17/12/2024
Bioart, courtesy of the NIH. All images are in the public domain and available for download as high-quality SVGs. bioart.niaid.nih.gov
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Pandemic Center at Brown University’s School of Public Health @pandemiccenter.bsky.social · 20/12/2024
Today, the Ministry of Health of #Rwanda has declared the end of the #Marburg virus disease outbreak, following a 42 day case-free countdown. As of 19 December 2024, 66 cases were confirmed, including 15 deaths (CFR 23%) and 51 recovered cases. More here: www.who.int/emergencies/...
who.int
Marburg virus disease - Rwanda
On 20 December 2024, after two consecutive incubation periods (total of 42 days) since the second negative PCR test was conducted on 7 November for the last confirmed Marburg case, and without a new...
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🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 19/12/2024
Ngl, I think this will be one of the more meaningful tools I've ever engineered. Orthogroups inferred using HMMs have greater precision and recall compared to traditional sequence search approaches bsky.app/profile/jlst...
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Angie Rasmussen @angierasmussen.bsky.social · 19/12/2024
For months now, the CDC has described H5N1 as “mild” compared to prior H5N1 viruses. I disagree—the virus alone doesn’t determine pathogenicity. I hypothesize that the 2 most critical determinants of H5N1 severity are the host (it’s always the host 🥰) & the route of infection.
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Healthcare-Global @healthcare-global.bsky.social · 19/12/2024
news.un.org/en/story/202...
news.un.org
Avian flu reported in 108 countries across five continents, says UN health agency
Avian influenza has caused the deaths of more than 300 million birds worldwide and the virus “is increasingly crossing species barriers”, according to UN health officers.
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Olaya Rendueles @olayarendueles.bsky.social · 19/12/2024
Really glad I could contribute to this work exploring biofilm formation, mucoidy and tip adhesin diversity in #klebsiella. For those in #KLEBS2024, I provided a sneak peak of the potential relation between K3 serotype & HMV This is also my first publication since I joined @cbitoulouse.bsky.social !
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Adam Kucharski @adamjkucharski.bsky.social · 19/12/2024
A widely quoted COVID theory was that once individuals with lots of contacts become immume, outbreaks will end with relatively small % infected. But when we looked at real-life networks, we found popularity isn't stable enough to predict 'superspreaders': royalsocietypublishing.org/doi/10.1098/...
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Healthcare-Global @healthcare-global.bsky.social · 13/12/2024
onlinelibrary.wiley.com/doi/abs/10.1...
onlinelibrary.wiley.com
Multi‐Organ Spread and Intra‐Host Diversity of SARS‐CoV‐2 Support Viral Persistence, Adaptation, and a Mechanism That Increases Evolvability
Intra-host diversity is an intricate phenomenon related to immune evasion, antiviral resistance, and evolutionary leaps along transmission chains. SARS-CoV-2 intra-host variation has been well-eviden...
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Reposted by Fernando Gonzalez-Candelas
Joanna Masel @joannamasel.bsky.social · 12/12/2024
We identified protein domains in LUCA (Last Universal Common Ancestor). Their distinctive amino acid usage reveals the order amino acids were added to the genetic code, based mostly on size. Older proteins hint at earlier alternative codes. 1/15 @seekingluca.bsky.social www.pnas.org/doi/10.1073/...
pnas.org
Order of amino acid recruitment into the genetic code resolved by last universal common ancestor’s protein domains | PNAS
The current “consensus” order in which amino acids were added to the genetic code is based on potentially biased criteria, such as the absence of s...
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Reposted by Fernando Gonzalez-Candelas
Matthew Hahn @3rdreviewer.bsky.social · 13/12/2024
New paper with @snaildit.bsky.social❗ You can use paralogs to reduce long-branch attraction! This will be especially helpful when there are no extant taxa that can be sampled to break up these branches. www.biorxiv.org/content/10.1...
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Reposted by Fernando Gonzalez-Candelas
Bryan White, MS Bio, MPH 🧬 @crvscience.com · 13/12/2024
Gene flow between Homo sapiens and Neanderthals started ~50,000 years ago and lasted around 6000 years (~100 generations) 🧪🧬🖥️ #AnthroSky #EvoSky #PaleoSky www.science.org/doi/10.1126/...
science.org
Neanderthal ancestry through time: Insights from genomes of ancient and present-day humans
Gene flow from Neanderthals has shaped genetic and phenotypic variation in modern humans. We generated a catalog of Neanderthal ancestry segments in more than 300 genomes spanning the past 50,000 year...
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I2SysBio @i2sysbio.es · 10/12/2024
Pathogenomics group leader Mireia Coscolla had a talk at FiSABIO about their M. #tuberculosis research 🔬🦠🧫🖥🧬
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Reposted by Fernando Gonzalez-Candelas
Krutika Kuppalli, MD FIDSA @krutikakuppalli.bsky.social · 10/12/2024
Grateful for @who.int updates on the undiagnosed illness in #DRC. - 10/12 samples (+) for #malaria. - Could be solely malaria or a mix with another disease. - Important to remember malnutrition may increase severity and risk of complications. - Critical to monitor developments closely.
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Reposted by Fernando Gonzalez-Candelas
mmctester.bsky.social @mmctester.bsky.social · 10/12/2024
And if you want to read more about this new research program in English, here you have an article in #PRBBellipse :) 👍 #genomics #evolution ellipse.prbb.org/harnessing-e...
ellipse.prbb.org
Harnessing evolution and genomics to improve health - El·lipse
The Evolutionary Medical Genomics Program, a shared project between CRG, MELIS-UPF and IBE, is a pioneering initiative to harness evolutionary principles to better understand the molecular roots of di...
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Reposted by Fernando Gonzalez-Candelas
BK. Titanji @boghuma.bsky.social · 08/12/2024
"Given the clinical presentation and symptoms reported, and a number of associated deaths, acute pneumonia, influenza, COVID-19, measles and malaria are being considered as potential causal factors with malnutrition as a contributing factor." Update on outbreak unfolding in DRC" #IDSky #MedSky
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Reposted by Fernando Gonzalez-Candelas
Bryan White, MS Bio, MPH 🧬 @crvscience.com · 04/12/2024
Question of how is #H5N1 spreading in North America given in theory its been isolated to poultry/cattle herds that are quarantined. One metric to look at is a weighted diffusion coefficient (WDC). Using this, avian influenzas rank in the upper-echelon of dispersal potential: 🧪🛟 #EpiSky #IDSky 1/🧵
Fig 3. Comparison of dispersal metrics estimated for different genomic data sets of viruses spreading in animal populations.

Specifically, we here report posterior estimates obtained for 2 metrics estimated from trees sampled from the posterior distribution of a Bayesian continuous phylogeographic inference: the WDC and the IBD signal estimated by the Pearson correlation coefficient (rP) between the patristic and log-transformed great-circle geographic distances computed for each pair of virus samples. We report the posterior distribution of both metrics estimated through continuous phylogeographic inference for the following data sets: West Nile virus in North America , Lumpy skin disease virus, Porcine deltacoronavirus in China, Getah virus in China  AIV in the Mekong region  and H3N1 in Belgium, rabies virus (dogs) in Iran, rabies virus (bats) in Peru, rabies virus (dogs) in northern Africa, rabies virus (bats) in Argentina, rabies virus (skunks) in the USA, rabies virus (raccoons) in the USA, Tula virus in central Europe, rabies virus (bats) in eastern Brazil, Powassan virus in the USA , Lassa virus in Africa, Puumala virus in Belgium, and Nova virus in Belgium . (*) Estimates based on the analysis of the wild-type strains; (**) estimates based on the combined analysis of lineages L1 and L3. See also Table A in S1 Text for the related 95% HPD intervals and number of samples associated with each data set. The data underlying this figure can be found in https://doi.org/10.5281/zenodo.13984927. AIV, avian influenza virus; HPD, highest posterior density; IBD, isolation-by-distance; WDC, weighted diffusion coefficient.

https://doi.org/10.1371/journal.pbio.3002914.g003
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Reposted by Fernando Gonzalez-Candelas
Sam Scarpino @scarpino.bsky.social · 26/11/2024
1/ Influenza wastewater activity levels are currently low across the US, aside from conspicuous areas in CA where #H5N1 is spreading in dairy cows. A deeper dive into the Wastewater Scan data paints a very concerning picture and should add to our sense of urgency.
Map shows the location of wastewater sampling locations around the US. Most of the sites indicate low levels and are colored blue. However, there are a number of sites in CA with high levels and few other scattered sites around the US with medium/high levels and are colored in orange/red
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