Mahan Ghafari
@mghafari.bsky.social
Molecular evolution of pathogens | Wellcome Trust Fellow @biology.ox.ac.uk | Independent Investigator Data Analytics & Epi Group @psioxford.bsky.social | MedSci Fellow @lincoln.ox.ac.uk | Oxford DTP & Zoology alum | https://users.ox.ac.uk/~univ4613/
Pinned
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
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
Reposted by Mahan Ghafari
I'm excited to introduce our new workflow for detecting endogenous viral elements - HI-FEVER. 🖥️🧬
academic.oup.com/bioinformati...
🧵
Big thanks to @ariskatzourakis.bsky.social, @humanceae.bsky.social, José Gabriel and Cormac for bringing this from conception to fruition!
academic.oup.com/bioinformati...
🧵
Big thanks to @ariskatzourakis.bsky.social, @humanceae.bsky.social, José Gabriel and Cormac for bringing this from conception to fruition!
HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements
AbstractSummary. Endogenous viral elements (EVEs) offer valuable insights into virus and host evolution, but their detection remains computationally and bi
academic.oup.com
November 13, 2025 at 11:14 AM
I'm excited to introduce our new workflow for detecting endogenous viral elements - HI-FEVER. 🖥️🧬
academic.oup.com/bioinformati...
🧵
Big thanks to @ariskatzourakis.bsky.social, @humanceae.bsky.social, José Gabriel and Cormac for bringing this from conception to fruition!
academic.oup.com/bioinformati...
🧵
Big thanks to @ariskatzourakis.bsky.social, @humanceae.bsky.social, José Gabriel and Cormac for bringing this from conception to fruition!
Reposted by Mahan Ghafari
Congratulations to @mghafari.bsky.social who has been selected as one of the New Voices in Virology!
Mahan's research focuses on the evolution of pathogens, particularly those with epidemic or pandemic potential and with implications for human, animal, and plant health 🦠
Mahan's research focuses on the evolution of pathogens, particularly those with epidemic or pandemic potential and with implications for human, animal, and plant health 🦠
🎉 #JVirology is pleased to announce the selectees for our inaugural New Voices in Virology collection! Chosen from 275+ applicants, these early-career scientists stood out for their creative proposals & strong career trajectories. ➡️ Meet the New Voices: asm.social/2HY
December 9, 2025 at 10:07 AM
Congratulations to @mghafari.bsky.social who has been selected as one of the New Voices in Virology!
Mahan's research focuses on the evolution of pathogens, particularly those with epidemic or pandemic potential and with implications for human, animal, and plant health 🦠
Mahan's research focuses on the evolution of pathogens, particularly those with epidemic or pandemic potential and with implications for human, animal, and plant health 🦠
Reposted by Mahan Ghafari
Feeling festive?
Why not deck the halls with @cvrinfo.bsky.social's papercraft #VirusSnowflakes and celebrate the science of viruses and the fight against viral diseases.
Download for free: cvr-engagement.co.uk/virus-snowfl...
#scicomm #sciart #decorations
Why not deck the halls with @cvrinfo.bsky.social's papercraft #VirusSnowflakes and celebrate the science of viruses and the fight against viral diseases.
Download for free: cvr-engagement.co.uk/virus-snowfl...
#scicomm #sciart #decorations
December 1, 2025 at 9:51 AM
Feeling festive?
Why not deck the halls with @cvrinfo.bsky.social's papercraft #VirusSnowflakes and celebrate the science of viruses and the fight against viral diseases.
Download for free: cvr-engagement.co.uk/virus-snowfl...
#scicomm #sciart #decorations
Why not deck the halls with @cvrinfo.bsky.social's papercraft #VirusSnowflakes and celebrate the science of viruses and the fight against viral diseases.
Download for free: cvr-engagement.co.uk/virus-snowfl...
#scicomm #sciart #decorations
Reposted by Mahan Ghafari
H3N2 preprint: there are concerns of a severe incoming influenza season due to the drifted H3N2 K clade. We at @psioxford.bsky.social analysed epi data and ran scenario models to see what we could discern about K clade transmission dynamics: zenodo.org/records/1770....
(1/18)
(1/18)
Evaluation of the epidemiological outlook of the influenza A/H3N2 clade K in England during the 2025-26 season
Key findings England is currently experiencing a high growth rate of infections caused by the influenza A/H3N2 K clade. Antigenic change from the previously dominant clade, a rapid selective sweep evi...
zenodo.org
November 25, 2025 at 1:51 PM
H3N2 preprint: there are concerns of a severe incoming influenza season due to the drifted H3N2 K clade. We at @psioxford.bsky.social analysed epi data and ran scenario models to see what we could discern about K clade transmission dynamics: zenodo.org/records/1770....
(1/18)
(1/18)
Reposted by Mahan Ghafari
Guess the news is officially out! Extremely excited to announce that I will be starting my own laboratory at Institut Pasteur @pasteur.fr this coming spring!
Slight change to my office window view from Tokyo Tower🗼 to the Tour Eiffel. 🇫🇷
Slight change to my office window view from Tokyo Tower🗼 to the Tour Eiffel. 🇫🇷
November 15, 2025 at 6:42 AM
Guess the news is officially out! Extremely excited to announce that I will be starting my own laboratory at Institut Pasteur @pasteur.fr this coming spring!
Slight change to my office window view from Tokyo Tower🗼 to the Tour Eiffel. 🇫🇷
Slight change to my office window view from Tokyo Tower🗼 to the Tour Eiffel. 🇫🇷
Reposted by Mahan Ghafari
I gave a talk last year at TEDxNewEngland aimed at introducing the idea of viral sociality to a general audience, including implications for evolution & virology. Video now available online below.
#socialviruses #evosky #virosky 🧪
#socialviruses #evosky #virosky 🧪
The social lives of viruses | Asher Leeks | TEDxNewEngland
YouTube video by TEDx Talks
www.youtube.com
October 7, 2025 at 10:38 PM
I gave a talk last year at TEDxNewEngland aimed at introducing the idea of viral sociality to a general audience, including implications for evolution & virology. Video now available online below.
#socialviruses #evosky #virosky 🧪
#socialviruses #evosky #virosky 🧪
Had an absolutely wonderful few days at #JSV72 in Hamamatsu & IMSUT in Tokyo.
Huge thanks to @shusukekawakubo.bsky.social, @shigeru0701.bsky.social, @spyroslytras.bsky.social & everyone in the @systemsvirology.bsky.social lab for being such brilliant hosts. Japan has been an amazing experience 🇯🇵✨
Huge thanks to @shusukekawakubo.bsky.social, @shigeru0701.bsky.social, @spyroslytras.bsky.social & everyone in the @systemsvirology.bsky.social lab for being such brilliant hosts. Japan has been an amazing experience 🇯🇵✨
October 31, 2025 at 2:40 PM
Had an absolutely wonderful few days at #JSV72 in Hamamatsu & IMSUT in Tokyo.
Huge thanks to @shusukekawakubo.bsky.social, @shigeru0701.bsky.social, @spyroslytras.bsky.social & everyone in the @systemsvirology.bsky.social lab for being such brilliant hosts. Japan has been an amazing experience 🇯🇵✨
Huge thanks to @shusukekawakubo.bsky.social, @shigeru0701.bsky.social, @spyroslytras.bsky.social & everyone in the @systemsvirology.bsky.social lab for being such brilliant hosts. Japan has been an amazing experience 🇯🇵✨
🚨 DPhil opportunity at Pandemic Sciences Institute🚨
Excited to be co-supervising a new DPhil theme with Christophe Fraser and Yvonne Jones on Developing methods for accurate reconstruction of viral histories to guide pandemic preparedness & targeted interventions.
Read more here: lnkd.in/eJXSXkia
Excited to be co-supervising a new DPhil theme with Christophe Fraser and Yvonne Jones on Developing methods for accurate reconstruction of viral histories to guide pandemic preparedness & targeted interventions.
Read more here: lnkd.in/eJXSXkia
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
October 25, 2025 at 6:42 AM
🚨 DPhil opportunity at Pandemic Sciences Institute🚨
Excited to be co-supervising a new DPhil theme with Christophe Fraser and Yvonne Jones on Developing methods for accurate reconstruction of viral histories to guide pandemic preparedness & targeted interventions.
Read more here: lnkd.in/eJXSXkia
Excited to be co-supervising a new DPhil theme with Christophe Fraser and Yvonne Jones on Developing methods for accurate reconstruction of viral histories to guide pandemic preparedness & targeted interventions.
Read more here: lnkd.in/eJXSXkia
Reposted by Mahan Ghafari
We are thrilled to welcome the members of our new Early Career Researcher Advisory Panel! Discover more about the researchers who are helping shape the future of scientific communication: buff.ly/5abtNWQ #ECR 🧪
October 14, 2025 at 12:30 PM
We are thrilled to welcome the members of our new Early Career Researcher Advisory Panel! Discover more about the researchers who are helping shape the future of scientific communication: buff.ly/5abtNWQ #ECR 🧪
Reposted by Mahan Ghafari
“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...
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
September 11, 2025 at 1:20 PM
“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...
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...
🚨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...
👉 www.sciencedirect.com/science/arti...
July 30, 2025 at 11:47 AM
🚨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...
👉 www.sciencedirect.com/science/arti...
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!
July 24, 2025 at 6:55 PM
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!
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
#GlobalHealth #VirusEvolution #PandemicPreparedness
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
@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
July 22, 2025 at 10:35 AM
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
#GlobalHealth #VirusEvolution #PandemicPreparedness
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.
June 15, 2025 at 9:01 PM
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.
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…
BREAKING: Trump signs travel ban for citizens from 12 countries, including Iran, Haiti, Somalia, and Sudan - CBS
June 7, 2025 at 9:58 AM
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…
Reposted by Mahan Ghafari
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:
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
May 30, 2025 at 7:26 AM
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:
May 20, 2025 at 11:27 AM
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...
May 13, 2025 at 6:28 AM
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...
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👇
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
May 10, 2025 at 5:09 PM
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👇
🚨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
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
May 9, 2025 at 2:39 PM
🚨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
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
Reposted by Mahan Ghafari
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
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
May 1, 2025 at 11:58 AM
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
Hosted by the Pandemic Genomics program and moderated by @jessmetcalf.bsky.social
Reposted by Mahan Ghafari
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
May 7, 2025 at 3:00 PM
Now online! The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2
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/...
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
February 22, 2025 at 1:19 PM
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/...
royalsocietypublishing.org/doi/10.1098/...
Reposted by Mahan Ghafari
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
January 16, 2025 at 2:10 PM
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.