Alex
@miidalex.bsky.social
Researcher in training with focus on viral immunology & molecular pathogenesis. Interested in emerging/zoonotic infectious disease, immune imprinting, SARS-CoV-2, and (mainly) food.
Reposted by Alex
This is finally out.
Very short take home. All the variation in spike that produced the immune escape characteristics of Omicron can occur in one single persistently infected individual over the period of a year.
This is why persistent infections matter
www.cell.com/cell-reports...
Very short take home. All the variation in spike that produced the immune escape characteristics of Omicron can occur in one single persistently infected individual over the period of a year.
This is why persistent infections matter
www.cell.com/cell-reports...
Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections
Snell et al. develop sequencing methodology to identify full-length spike haplotypes
and show that persistent SARS-CoV-2 infections drive divergent haplotype emergence,
accelerating viral evolution an...
www.cell.com
February 2, 2026 at 4:09 PM
This is finally out.
Very short take home. All the variation in spike that produced the immune escape characteristics of Omicron can occur in one single persistently infected individual over the period of a year.
This is why persistent infections matter
www.cell.com/cell-reports...
Very short take home. All the variation in spike that produced the immune escape characteristics of Omicron can occur in one single persistently infected individual over the period of a year.
This is why persistent infections matter
www.cell.com/cell-reports...
Reposted by Alex
🚨New Pre-Print🚨
Although H3N2 subclade K has multiple mutations in HA, neutralisation assays with pre-epidemic human sera show only moderate antigenic drift, and vaccines used in the 2024/2025 flu season induced cross-neutralising immunity
www.medrxiv.org/content/10.6...
Although H3N2 subclade K has multiple mutations in HA, neutralisation assays with pre-epidemic human sera show only moderate antigenic drift, and vaccines used in the 2024/2025 flu season induced cross-neutralising immunity
www.medrxiv.org/content/10.6...
January 30, 2026 at 12:01 PM
🚨New Pre-Print🚨
Although H3N2 subclade K has multiple mutations in HA, neutralisation assays with pre-epidemic human sera show only moderate antigenic drift, and vaccines used in the 2024/2025 flu season induced cross-neutralising immunity
www.medrxiv.org/content/10.6...
Although H3N2 subclade K has multiple mutations in HA, neutralisation assays with pre-epidemic human sera show only moderate antigenic drift, and vaccines used in the 2024/2025 flu season induced cross-neutralising immunity
www.medrxiv.org/content/10.6...
Reposted by Alex
Amazing work by Erik Karlsson and co - a huge diversity of viruses in animal markets, detected through both sampling of birds, but also environmental surveillance approaches.
👉https://www.nature.com/articles/s41467-025-68245-8
👉https://www.nature.com/articles/s41467-025-68245-8
January 15, 2026 at 2:23 AM
Amazing work by Erik Karlsson and co - a huge diversity of viruses in animal markets, detected through both sampling of birds, but also environmental surveillance approaches.
👉https://www.nature.com/articles/s41467-025-68245-8
👉https://www.nature.com/articles/s41467-025-68245-8
Reposted by Alex
We find that subclade K viruses are antigenically advanced; however, this year's flu vaccine surprisingly elicited antibodies in many individuals that efficiently recognized these viruses. The implications are clear: go get this year’s vaccine if you haven’t already!
www.medrxiv.org/content/10.6...
www.medrxiv.org/content/10.6...
Antibodies elicited by the 2025-2026 influenza vaccine in humans
A new H3N2 variant (named subclade K) possesses several key hemagglutinin substitutions and is circulating widely during the 2025-2026 influenza season. In this report, we completed experiments to det...
www.medrxiv.org
January 7, 2026 at 1:34 PM
We find that subclade K viruses are antigenically advanced; however, this year's flu vaccine surprisingly elicited antibodies in many individuals that efficiently recognized these viruses. The implications are clear: go get this year’s vaccine if you haven’t already!
www.medrxiv.org/content/10.6...
www.medrxiv.org/content/10.6...
Reposted by Alex
I am excited to share that our work, in which we have dissected the signals driven by the nucleoside-modified mRNA and LNP components of mRNA vaccines that regulate germinal center (GC) responses, is now published in Cell! www.cell.com/cell/fulltex...
Distinct components of mRNA vaccines cooperate to instruct efficient germinal center responses
This study dissects the individual contributions of the different components of mRNA
vaccines to immune responses. Nucleoside-modified mRNA promotes the production of
type I interferons that act on de...
www.cell.com
December 16, 2025 at 5:40 PM
I am excited to share that our work, in which we have dissected the signals driven by the nucleoside-modified mRNA and LNP components of mRNA vaccines that regulate germinal center (GC) responses, is now published in Cell! www.cell.com/cell/fulltex...
Reposted by Alex
Massive and incredible study here from CVR Glasgow led team to consider the *contingency* of #H5N1 #influenza adaptation to bovine host.
Stars often need to align for unique emergence events.
www.nature.com/articles/s41...
Stars often need to align for unique emergence events.
www.nature.com/articles/s41...
The potential of H5N1 viruses to adapt to bovine cells varies throughout evolution - Nature Communications
H5N1 avian influenza viruses caused an outbreak in dairy cattle. We show that the potential for avian viruses to replicate in cow cells varies across H5N1 evolution, suggesting that the risk of spillo...
www.nature.com
December 15, 2025 at 3:46 PM
Massive and incredible study here from CVR Glasgow led team to consider the *contingency* of #H5N1 #influenza adaptation to bovine host.
Stars often need to align for unique emergence events.
www.nature.com/articles/s41...
Stars often need to align for unique emergence events.
www.nature.com/articles/s41...
Reposted by Alex
Current H5N1 avian influenza viruses replicate better in human respiratory tissues than a historic one, warranting "the urgency to prevent cross-species transmission to humans by controlling spillover events to mammals and limiting viral spread in farmed mammals." www.thelancet.com/journals/lan...
December 16, 2025 at 5:54 AM
Current H5N1 avian influenza viruses replicate better in human respiratory tissues than a historic one, warranting "the urgency to prevent cross-species transmission to humans by controlling spillover events to mammals and limiting viral spread in farmed mammals." www.thelancet.com/journals/lan...
Reposted by Alex
1/2 🚨New paper
In a collab b/w my group + @nathangrubaugh.bsky.social, led by a fabulous doctoral student, we synthesize the data on epistasis across several viral pathogen systems (e.g., influenza, HIV, SARS-CoV-2, tobacco etch virus, etc).
academic.oup.com/ve/article/1...
In a collab b/w my group + @nathangrubaugh.bsky.social, led by a fabulous doctoral student, we synthesize the data on epistasis across several viral pathogen systems (e.g., influenza, HIV, SARS-CoV-2, tobacco etch virus, etc).
academic.oup.com/ve/article/1...
December 11, 2025 at 5:36 PM
1/2 🚨New paper
In a collab b/w my group + @nathangrubaugh.bsky.social, led by a fabulous doctoral student, we synthesize the data on epistasis across several viral pathogen systems (e.g., influenza, HIV, SARS-CoV-2, tobacco etch virus, etc).
academic.oup.com/ve/article/1...
In a collab b/w my group + @nathangrubaugh.bsky.social, led by a fabulous doctoral student, we synthesize the data on epistasis across several viral pathogen systems (e.g., influenza, HIV, SARS-CoV-2, tobacco etch virus, etc).
academic.oup.com/ve/article/1...
Reposted by Alex
Theory @cp-immunity.bsky.social
Quantifying the waning of humoral immunity
www.cell.com/immunity/ful...
Quantifying the waning of humoral immunity
www.cell.com/immunity/ful...
November 29, 2025 at 2:29 AM
Theory @cp-immunity.bsky.social
Quantifying the waning of humoral immunity
www.cell.com/immunity/ful...
Quantifying the waning of humoral immunity
www.cell.com/immunity/ful...
Reposted by Alex
How does fever work?
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Avian-origin influenza A viruses tolerate elevated pyrexic temperatures in mammals
Host body temperature can define a virus’s replicative profile—influenza A viruses (IAVs) adapted to 40° to 42°C in birds are less temperature sensitive in vitro compared with human isolates adapted t...
www.science.org
November 27, 2025 at 7:55 PM
How does fever work?
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Reposted by Alex
Mutational spectra reveal influenza virus transmission routes and adaptation https://www.biorxiv.org/content/10.1101/2025.11.26.690773v1
November 26, 2025 at 8:16 PM
Mutational spectra reveal influenza virus transmission routes and adaptation https://www.biorxiv.org/content/10.1101/2025.11.26.690773v1
Reposted by Alex
Unraveling the mechanism behind the probable extinction of the B/Yamagata lineage of influenza B viruses
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Unraveling the mechanism behind the probable extinction of the B/Yamagata lineage of influenza B viruses - Nature Communications
Influenza B/Yamagata lineage has rarely been detected since COVID-19 non-pharmaceutical interventions were introduced, while transmission of other influenza lineages resumed. Here, the authors investi...
www.nature.com
November 25, 2025 at 2:09 PM
Unraveling the mechanism behind the probable extinction of the B/Yamagata lineage of influenza B viruses
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Alex
This preprint just came out. @wchnicholas.bsky.social and team reconstructed and tested the NJ Spike and found that it has the tightest ACE2 binding of any SC2 Spike ever measured.
2/
www.medrxiv.org/content/10.1...
2/
www.medrxiv.org/content/10.1...
www.medrxiv.org
November 21, 2025 at 3:19 PM
This preprint just came out. @wchnicholas.bsky.social and team reconstructed and tested the NJ Spike and found that it has the tightest ACE2 binding of any SC2 Spike ever measured.
2/
www.medrxiv.org/content/10.1...
2/
www.medrxiv.org/content/10.1...
Reposted by Alex
This is an interesting case of a patient from Chad infected with a novel arenavirus species/variant/strain, presenting with meningoencephalitis.
IMO, could be classified as a highly divergent Lassa virus strain in a new country (similar to what Togo has observed).
www.nejm.org/doi/10.1056/...
IMO, could be classified as a highly divergent Lassa virus strain in a new country (similar to what Togo has observed).
www.nejm.org/doi/10.1056/...
A Mammarenavirus Close to Lassa Virus in a Patient with Meningoencephalitis | NEJM
A 37-year-old man in Chad presented with a fever and a headache. An extensive evaluation
identified a mammarenavirus, close to Lassa virus, in samples of cerebrospinal fluid.
www.nejm.org
November 17, 2025 at 4:47 PM
This is an interesting case of a patient from Chad infected with a novel arenavirus species/variant/strain, presenting with meningoencephalitis.
IMO, could be classified as a highly divergent Lassa virus strain in a new country (similar to what Togo has observed).
www.nejm.org/doi/10.1056/...
IMO, could be classified as a highly divergent Lassa virus strain in a new country (similar to what Togo has observed).
www.nejm.org/doi/10.1056/...
Reposted by Alex
Ongoing surveillance of viruses & microbes (bacteria, fungi, and parasites) in farmed mammals is crucial for revealing #publichealth threats
@cellpress.bsky.social
www.sciencedirect.com/science/arti...
@cellpress.bsky.social
www.sciencedirect.com/science/arti...
Extensive cross-species transmission of pathogens and antibiotic resistance genes in mammals neglected by public health surveillance
Non-traditional farmed and wild mammals are often neglected in pathogen surveillance. Through metagenomic and metatranscriptomic sequencing of fecal a…
www.sciencedirect.com
November 15, 2025 at 5:55 AM
Ongoing surveillance of viruses & microbes (bacteria, fungi, and parasites) in farmed mammals is crucial for revealing #publichealth threats
@cellpress.bsky.social
www.sciencedirect.com/science/arti...
@cellpress.bsky.social
www.sciencedirect.com/science/arti...
Reposted by Alex
The deadly fever in Ethiopia has been identified as Marburg disease.
It’s the first time a Marburg outbreak has been identified in Ethiopia.
#IDsky 🧪
www.afro.who.int/countries/et...
It’s the first time a Marburg outbreak has been identified in Ethiopia.
#IDsky 🧪
www.afro.who.int/countries/et...
Ethiopia confirms first outbreak of Marburg virus disease
Ethiopia’s Ministry of Health has confirmed an outbreak of Marburg virus disease in the South Ethiopia Region, the first of its kind in the country, following laboratory testing of samples from a clus...
www.afro.who.int
November 14, 2025 at 8:07 PM
The deadly fever in Ethiopia has been identified as Marburg disease.
It’s the first time a Marburg outbreak has been identified in Ethiopia.
#IDsky 🧪
www.afro.who.int/countries/et...
It’s the first time a Marburg outbreak has been identified in Ethiopia.
#IDsky 🧪
www.afro.who.int/countries/et...
Reposted by Alex
Our lab's paper describing the North American H5N1 epizootic is out now in Nature! So thrilled to have this out, and congratulations to @lambod50.bsky.social for all the fantastic work on this: www.nature.com/articles/s41...
Ecology and spread of the North American H5N1 epizootic - Nature
The panzootic of highly pathogenic H5N1 since 2021 was driven by around nine introductions into the Atlantic and Pacific flyways, followed by rapid dissemination through wild migratory birds, primaril...
www.nature.com
November 12, 2025 at 7:33 PM
Our lab's paper describing the North American H5N1 epizootic is out now in Nature! So thrilled to have this out, and congratulations to @lambod50.bsky.social for all the fantastic work on this: www.nature.com/articles/s41...
Reposted by Alex
"SARS-CoV-2 is too well-adapted to humans [hence, insert your favorite conspiracy theory]".
That was never right because, for one, SARS-CoV-2 is a pandemic virus so it necessarily had to be "well-adapted".
Now, a new study shows the same is true for BANAL-236 - a related virus isolated from bats.
That was never right because, for one, SARS-CoV-2 is a pandemic virus so it necessarily had to be "well-adapted".
Now, a new study shows the same is true for BANAL-236 - a related virus isolated from bats.
November 10, 2025 at 8:09 PM
"SARS-CoV-2 is too well-adapted to humans [hence, insert your favorite conspiracy theory]".
That was never right because, for one, SARS-CoV-2 is a pandemic virus so it necessarily had to be "well-adapted".
Now, a new study shows the same is true for BANAL-236 - a related virus isolated from bats.
That was never right because, for one, SARS-CoV-2 is a pandemic virus so it necessarily had to be "well-adapted".
Now, a new study shows the same is true for BANAL-236 - a related virus isolated from bats.
Reposted by Alex
Check out our latest preprint on the effects of antibody-mediated feedback on ongoing germinal center reactions, led by Alex Barbulescu and @janabilanovic.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Antibody-mediated feedback modulates interclonal competition in the germinal center
Serum antibodies from prior immune responses regulate B cell activation and germinal center (GC) access upon recall immunization. However, how antibodies produced by an ongoing immune response influen...
www.biorxiv.org
November 8, 2025 at 3:04 PM
Check out our latest preprint on the effects of antibody-mediated feedback on ongoing germinal center reactions, led by Alex Barbulescu and @janabilanovic.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Alex
JAMA Netw Open: Asymptomatic Influenza A(H5N1) Infections and Sustained Surveillance—Sustaining Surveillance Beyond the Crisis
by Rick Bright and Nicole Lurie
#h5n1
bit.ly/4qzttRL
by Rick Bright and Nicole Lurie
#h5n1
bit.ly/4qzttRL
October 30, 2025 at 1:31 PM
JAMA Netw Open: Asymptomatic Influenza A(H5N1) Infections and Sustained Surveillance—Sustaining Surveillance Beyond the Crisis
by Rick Bright and Nicole Lurie
#h5n1
bit.ly/4qzttRL
by Rick Bright and Nicole Lurie
#h5n1
bit.ly/4qzttRL
Reposted by Alex
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 6, 2025 at 9:46 PM
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
Reposted by Alex
A cattle-derived human H5N1 isolate suppresses innate immunity despite efficient replication in human respiratory organoids https://www.biorxiv.org/content/10.1101/2025.11.02.684669v1
November 3, 2025 at 2:17 AM
A cattle-derived human H5N1 isolate suppresses innate immunity despite efficient replication in human respiratory organoids https://www.biorxiv.org/content/10.1101/2025.11.02.684669v1
Reposted by Alex
Viral epidemic potential is not uniformly distributed across the bat phylogeny
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Viral epidemic potential is not uniformly distributed across the bat phylogeny - Communications Biology
Phylogenetic and machine learning analyses reveal that bats (order: Chiroptera) are not a group with uniform viral epidemic potential: virulence, transmissibility, and death burden cluster within dist...
www.nature.com
October 30, 2025 at 12:53 PM
Viral epidemic potential is not uniformly distributed across the bat phylogeny
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Reposted by Alex
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...
Another fascinating reminder of how diverse coronavirus evolution is in wildlife reservoirs.
#Virology #VirusEvolution #Bats #Coronavirus
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
October 27, 2025 at 9:32 PM
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...
Another fascinating reminder of how diverse coronavirus evolution is in wildlife reservoirs.
#Virology #VirusEvolution #Bats #Coronavirus
www.biorxiv.org/content/10.1...
Reposted by Alex
I beg to differ! If it's not a sequencing mistake—and it looks clean—one of these BA.3.2 has something completely novel in SARS-CoV-2 evolution: an FCS-adjacent deletion!
One of the two QT repeats appears to have been deleted. I've never seen anything like this before. BA.3.2 is a different beast.
One of the two QT repeats appears to have been deleted. I've never seen anything like this before. BA.3.2 is a different beast.
October 22, 2025 at 11:46 AM
I beg to differ! If it's not a sequencing mistake—and it looks clean—one of these BA.3.2 has something completely novel in SARS-CoV-2 evolution: an FCS-adjacent deletion!
One of the two QT repeats appears to have been deleted. I've never seen anything like this before. BA.3.2 is a different beast.
One of the two QT repeats appears to have been deleted. I've never seen anything like this before. BA.3.2 is a different beast.