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Reposted by Mahan Ghafari

Contagion® @contagionlive.bsky.social · 27d

“Fast change, little spread”

The University of Oxford’s Prof Katrina Lythgoe and Dr. Mahan Ghafari unpack ONS-CIS data on 576 persistent infections, rapid within-host evolution, and rare transmission after 1 month. #IDsky #MEDsky

Read our Q&A: www.contagionlive.com/view/persist...

Persistent SARS-CoV-2 Infections in the Community Show Fast Within-Host Change but Little Late Transmission

Oxford’s Prof Katrina Lythgoe and Mahan Ghafari, DPhil, report ONS-CIS data on 576 persistent UK infections with rapid within-host evolution and rare transmission after one month.

www.contagionlive.com

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Mahan Ghafari @mghafari.bsky.social · Aug 28

how is the syn vs nonsyn MOV context score/likelihood calculated in these cases?

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Mahan Ghafari @mghafari.bsky.social · Jul 30

Grateful to @ryanhisner.bsky.social for his thoughtful comments on the work. Huge thanks also to the incredible ONS-CIS team—especially Sarah Walker—for making this study possible, and to Katrina Lythgoe for her leadership throughout.

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Mahan Ghafari @mghafari.bsky.social · Jul 30

We analysed 576 persistent infections and found:
– More common in men & those >60yrs
– Most variation driven by nonsynonymous mutations, esp. in spike NTD & RBD
– Longer infection → higher viral clock rates
– Onward transmission is rare
– Only ~2% showed viral rates on par with highly divergent VOCs

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Mahan Ghafari @mghafari.bsky.social · Jul 30

🚨Our study on characterising the within-host SARS-CoV-2 evolution during persistent infections is now out in @lancetmicrobe.bsky.social!
👉 www.sciencedirect.com/science/arti...

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Mahan Ghafari @mghafari.bsky.social · Jul 24

Looking forward to welcoming you tomorrow, @spyroslytras.bsky.social! Spyros will be giving a seminar in Biology (Mansfield Road) at 11am on ‘AI-enabled structural comparisons uncover the deep evolutionary histories of viral glycoproteins’ — come along if you’re around!

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Mahan Ghafari @mghafari.bsky.social · Jul 22

Very grateful to the @biology.ox.ac.uk for the kind spotlight — and for the opportunity to do meaningful work alongside such brilliant and thoughtful colleagues across Biology, Pandemic Sciences Institute, and Lincoln College.

#GlobalHealth #VirusEvolution #PandemicPreparedness

Oxford Biology @biology.ox.ac.uk · Jul 22

Outbreaks and inequities 🦠

@mghafari.bsky.social is tracing viruses back through time — not just to illuminate potential threats, but also to build more equitable and effective responses to epidemics and pandemics.

Read our new spotlight on Mahan! 👇
bit.ly/4m8sSDO

Text reads: Spotlight: Dr Mahan Ghafari, Outbreaks and inequities. Image of Mahan speaking at an event.

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Mahan Ghafari @mghafari.bsky.social · Jun 15

I don’t have the words to describe what it feels like to watch my home city of Tehran and the neighbourhoods I haven’t seen in almost a decade, now burning on the news. Then getting messages from family and friends asking where it’s safest to flee, with empty pockets and no fuel to escape.

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Mahan Ghafari @mghafari.bsky.social · Jun 7

But I also think that leaving when I did was the right move. And to fellow academics affected by this — you’re not alone. And to colleagues in the US: please speak up, advocate for inclusion, and keep those bridges open however you can. Science doesn’t thrive in isolation. And neither do we.

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Mahan Ghafari @mghafari.bsky.social · Jun 7

I’ve been very fortunate in my academic journey and the support I’ve found elsewhere. But it’s disheartening to think how many doors remain closed for reasons far beyond our control. I still carry a deep appreciation for my time in the US — mentors, friends, opportunities.

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Mahan Ghafari @mghafari.bsky.social · Jun 7

Well, it didn’t, did it? And now, years later, we’re watching history repeat itself — not just in policy, but in the way it quietly redirects the paths of young researchers who simply want to engage, collaborate, and contribute to global science. A lot has changed in my life since then.

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Mahan Ghafari @mghafari.bsky.social · Jun 7

When I abruptly left my PhD in the US in 2017 and moved to the UK — ‘mastered out,’ as they say — many told me I shouldn’t have. That it was all just temporary. That it would pass soon enough…

BNO News @bnonews.com · Jun 4

BREAKING: Trump signs travel ban for citizens from 12 countries, including Iran, Haiti, Somalia, and Sudan - CBS

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Reposted by Mahan Ghafari

Sebastian Duchene @sebduchene.bsky.social · May 30

I'm super proud to share this piece of work, led by @nrascovan.bsky.social, @avanzich.bsky.social and @marialopopolo.bsky.social. See details in Maria's post here:

Maria Lopopolo @marialopopolo.bsky.social · May 29

Did leprosy exist in the Americas before European invasion? Our lab #aDNA study at @institutpasteur.bsky.social supervised by @nrascovan.bsky.social in collab with @avanzich.bsky.social (CSU) finds M.lepromatosis in pre-colonial Ancestors from North and South America www.science.org/doi/10.1126/...

Pre-European contact leprosy in the Americas and its current persistence

Leprosy, primarily caused by Mycobacterium leprae, is considered a disease introduced into the Americas during European colonization. However, the recent discovery of a second pathogen causing leprosy...

www.science.org

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Mahan Ghafari @mghafari.bsky.social · May 20

Only 10 days left to apply! 👇

my.corehr.com/pls/uoxrecru...

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Mahan Ghafari @mghafari.bsky.social · May 13

Apologies, the link above was incorrect — this one should work: stanford.zoom.us/meeting/regi...

Welcome! You are invited to join a meeting: My Meeting. After registering, you will receive a confirmation email about joining the meeting.

stanford.zoom.us

Mahan Ghafari @mghafari.bsky.social · May 13

Sorry, my fault—sent the wrong link! This one should work: stanford.zoom.us/meeting/regi...

Society for Modeling and Theory in Population Biology - Mini-Symposium: Theory in understanding viral dynamics and evolution

smtpb.org

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Mahan Ghafari @mghafari.bsky.social · May 13

Looking forward to tomorrow’s @smtpb.bsky.social event (5:30–7:00pm UK time)! If you’re interested, you can register here: stanford.zoom.us/meeting/regi...

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Mahan Ghafari @mghafari.bsky.social · May 10

Great thread by Spyros on this long-in-the-making paper which I also contributed to — a deep dive into the timing and origins of both SARS-CoVs👇

Spyros Lytras @spyroslytras.bsky.social · May 10

Sooo happy to finally have this one published!! (3 years in the making… 👀) A comprehensive investigation into the recency and geographical origins of both SARS-CoVs that spilled to humans in the past few decades, now in @cp-cell.bsky.social www.cell.com/cell/fulltex...

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

Recombination-aware evolutionary analyses of the entire genomes of SARS-CoV-1-like and SARS-CoV-2-like viruses indicate that SARS-CoV-1 and SARS-CoV-2 descend from bat coronaviruses that circulated as...

www.cell.com

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Mahan Ghafari @mghafari.bsky.social · May 9

Looks like there was an issue with the earlier link!
This one should work:
my.corehr.com/pls/uoxrecru...

Job Details

my.corehr.com

Mahan Ghafari @mghafari.bsky.social · May 9

🚨We’re hiring a Postdoc to join our group at Oxford!

We’re developing methods to understand how pathogens evolve—across hosts, over time, & through molecular & structural change.

Keen or know someone who is? Please share!

🕒 3-year post
📅 Deadline: 30 May
🔗 Apply: www.jobs.ox.ac.uk/vacancy/179640

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Reposted by Mahan Ghafari

Moritz Kraemer @mugkraemer.bsky.social · May 1

Really looking forward to this event @oxmartinschool.bsky.social on what turns spillovers into epidemics/pandemics in human populations: www.oxfordmartin.ox.ac.uk/events/what-... with exciting speakers.

Hosted by the Pandemic Genomics program and moderated by @jessmetcalf.bsky.social

Panel Discussion: 'What turns spillovers into epidemics?'

This talk brings together experts in pathogen genomics, virology, ecology, climate science, and data science to explore how AI, genomic surveillance, and…

www.oxfordmartin.ox.ac.uk

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Reposted by Mahan Ghafari

Cell - a Cell Press journal @cp-cell.bsky.social · May 7

Now online! The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

Recombination-aware evolutionary analyses of the entire genomes of SARS-CoV-1-like and SARS-CoV-2-like viruses indicate that SARS-CoV-1 and SARS-CoV-2 descend from bat coronaviruses that circulated as recently as one to six years before their respective dates of human emergence. These inferred virus ancestors likely needed to travel faster than closely related bat viruses in order to reach their respective sites of emergence.

dlvr.it

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Mahan Ghafari @mghafari.bsky.social · Feb 22

Actually, the entire Special Issue features a range of interesting papers.
royalsocietypublishing.org/toc/rstb/202...

Philosophical Transactions of the Royal Society B: Biological Sciences: Vol 380, No 1919

royalsocietypublishing.org

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Mahan Ghafari @mghafari.bsky.social · Feb 22

A really nice analysis by Katia Koelle and David Rasmussen on the impact of purifying selection on evolutionary rate estimates, tree topology, and phylodynamic parameters.
royalsocietypublishing.org/doi/10.1098/...

Phylodynamics beyond neutrality: the impact of incomplete purifying selection on viral phylogenies and inference | Philosophical Transactions of the Royal Society B: Biological Sciences

Viral phylodynamics focuses on using sequence data to make inferences about the population dynamics of viral diseases. These inferences commonly include estimation of growth rates, reproduction numbers and times of most recent common ancestor. With few ...

royalsocietypublishing.org

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Reposted by Mahan Ghafari

ilesla.bsky.social @ilesla.bsky.social · Jan 16

Two weeks to go until the application deadline for ILESLA. If you or anyone you know would benefit from full funding to carry out a PhD in Life and/or Environmental Science please visit/refer to our website page iles.web.ox.ac.uk/how-apply where you can see open day videos and get full guidance.

How to Apply and Funding

iles.web.ox.ac.uk

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