Guha Arunkumar

This is so embarrassing.

It's astounding. They hold faculty positions, have labs, and publish. That presentation was ridiculous.

High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains Human influenza viruses rapidly acquire mutations in their hemagglutinin (HA) protein that erode neutralization by antibodies from prior exposures. Here, we use a sequencing-based assay to measure neu...

In study led by @ckikawa.bsky.social & Andrea Loes, we use new assay to measure ~10,000 neutralization titers to recent influenza strains & show titers correlate w evolutionary success of viral strains

Similar data could help forecast evolution for vaccine selection

www.biorxiv.org/content/10.1...

If NCBI servers are down and you need to access or deposit sequence data, check out the International Nucleotide Sequence Database Collaboration.

NCBI and the other two participating organizations share data on a daily basis.
www.insdc.org

Your favourite #sequence database is also available on two other continents, together with tools such as #BLAST: www.insdc.org (International Nucleotide Sequence Database Collaboration) 🧪

🚨🚨🚨 For everyone who's using BLAST+ through EBI be aware, the default settings for some tools differ and will give different results and will take a lot longer than you're used unless you change these parameters. 🚨🚨🚨 1/n

These are the WHO-recommended influenza viruses to include in the 2025-26 season's influenza vaccine. Nation and Union experts (e.g. the FDA in the US) then review the data and decide if they go with this recommendation (usual) or adjust it.
Global health goes on.
www.who.int/publications...

JUST IN: Arizona Reports H5N1 Genotype D1.1 In Maricopa County Dairy Herd.

Full seq from first human #H5N1 D1.1 w/ PB2 D701N uploaded to GISAID

A/Nevada/10/2025

Not in BLAST database yet
Has additional changes compared to
A/dairy cow/USA/002645-005/2025

Wyoming’s First Human Bird Flu Case Confirmed - Wyoming Department of Health Wyoming’s first case of H5N1 avian influenza in a human has been confirmed in a Platte County older adult, according to the Wyoming Department of Health (WDH). The woman represents the third confirmed...

A woman in Wyoming has been hospitalized with #H5N1 #birdflu, WY's health dept announced Friday. Likely exposure was to backyard poultry. Wyoming said #CDC confirmed the infection, though CDC did not add it to its H5 page today. Not clear if this is B3.13 or D1.1. health.wyo.gov/wyomings-fir...

Wyoming identifies first human case of bird flu The Wyoming Department of Health said on Friday it has identified its first human case of H5N1 bird flu in the region, making it the third confirmed instance of hospitalization related to the infection in the United States.

The most fitting end to a day in which the regime just curbstomped our outbreak response capacity: an H5N1 patient in a hospital that’s also presumably full of seasonal flu patients.

www.reuters.com/business/hea...

#USDA has confirmed that the discovery of #H5N1 #birdflu in Arizona — found through bulk milk testing — does indeed represent a new spillover from wild birds into cows. This is the third time this has been observed to have happened. www.aphis.usda.gov/news/program...

BREAKING: VIRUS FROM NEVADA DAIRY WORKER WITH BIRD FLU HAS THE SAME GENETIC MUTATION seen in the Nevada cows – a change of PB2 D701N that has previously been assoc with more efficient virus replication in ppl & mammals.

CDC told Fortune that the D1.1 variant in this worker is the same strain of

ÅNGSTRÖM-RESOLUTION IMAGING OF CELL-SURFACE GLYCANS 🧬🎨🍬

The glycocalyx, our cells' sugar coat, holds secrets in immunology, cancer, viral infections, and more. Visualizing its molecular architecture was impossible… until now. #glycotime #microscopy

www.biorxiv.org/content/10.1...

New bird flu infections in Nevada dairy cattle signal the virus may be here to stay | CNN Six dairy herds in Nevada have tested positive for a newer variant of the H5N1 bird flu virus that’s been associated with severe infections in humans, according to the Nevada Department of Agriculture...

The D1.1 strain of H5N1 bird flu has been detected in dairy herds in Nevada, meaning for at least a second time the virus has jumped from birds to cows (and a strain that's shown it can be severe in humans). CIDRAP's @mtosterholm.bsky.social joins CNN now to discuss www.cnn.com/2025/02/05/h...

Interesting note: Nevada has detected a total of 5 #H5N1 #birdflu infected dairy herds — these 4 & one confirmed in early December. The December herd was infected with the version of H5 that has been spreading in cows in multiple states, ie a different virus than the new infections.

The 2nd tweet in this thread says there have been 2 confirmed #Ebola cases in Uganda, per @WHOAFRO.
@AfricaCDC says 4. No details of who the cases are, but there is the nurse (dead) & his wife. Another family member & some HCWs were being tested so....
africacdc.org/download/afr...

Extremely naive Bluesky question - how does one save a post for later referencing? (I've seen people leave a bulletin board pin in the comments but wasn't sure if that's the way)

Sick goose is 1st case of bird flu in Philadelphia amid national outbreak A sick snow goose found in West Philadelphia earlier this month has tested positive for the avian influenza A(H5), making it the first bird in the city to test positive for the highly-pathogenic bird ...

A sick snow goose in West Philly has tested positive for H5N1. This is a very urban/populated area not too far from our lab. It is important for everyone to stay away from sick birds to avoid H5N1 exposures.

www.nbcphiladelphia.com/news/health/...

De novo designed proteins neutralize lethal snake venom toxins - Nature Deep learning methods have been used to design proteins that can neutralize the effects of three-finger toxins found in snake venom, which could lead to the development of safer and more accessible an...

EXTREMELY cool and demonstrates clearly the promise of deep learning + bio.

www.nature.com/articles/s41...

Clade names getting you down? Now, simply drag and drop and you will have the clade information. Based on 3 Nextclade datasets, can assign clades to H5 HA sequences, call mutations relative to reference strains.
Interface: clades.nextstrain.org?dataset-url=...
👉 www.biorxiv.org/content/10.1...

self-amplifying RNA vaccines against Vietnam/2004/ H5N1 and A/Anhui/2013 H7N9. In mice: IM vaccination = humoral + cellular, not mucosal response. IN vaccination = systemic + mucosal immunity. complete protection in ferret challenge
👉 www.biorxiv.org/content/10.1...

A replicating RNA vaccine w HA of bovine H5N1 confers complete protection against homologous lethal challenge in mice, but HA using Vietnam/2004 confers only partial protection.
👉 www.nature.com/articles/s41...

CDC is recommending a shortened timeline for subtyping all influenza A specimens among hospitalized patients and increasing efforts at clinical laboratories to identify non-seasonal influenza particularly human cases of #H5N1. This is a good recommendation.
bit.ly/3DSmr6Q

WHO Disease Outbreak News: Outbreak of suspected Marburg Virus Disease - United Republic of Tanzania Outbreak of suspected Marburg Virus Disease– United Republic of Tanzania 14 January 2025 Description of the situation Introduction On 13 January 2025, WHO informed its Member States and IHR State Parties of an outbreak of suspected Marburg Virus Disease (MVD) in the Kagera region of the United Republic of Tanzania using our secure web-based platform—the Event Information Site (EIS). Under the International Health Regulations, the EIS is used to issue rapid alerts to Member States of acute and rapidly developing public health risks and events with possible international implications.

Marburg in Tanzania: WHO reports the outbreak was first detected on Jan. 10, with 9 suspected cases and 8 deaths so far.

Tanzania doesn’t have the surveillance Rwanda does. But it’s good they’ve identified this.

Check out the newest preprint from the Schultz-Cherry lab on susceptibility of primary cells to H5N1 clade 2.3.4.4b viruses! -->

The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure RNA viruses like SARS-CoV-2 have a high mutation rate, which contributes to their rapid evolution. The rate of mutations depends on the mutation type (e.g., A→C, A→G, etc.) and can vary between sites ...

Building on the UShER tree of millions of SARS-CoV-2 genomes maintained by Angie Hinrichs, Hugh Haddox and Georg Angehrn (and others in @matsen.bsky.social lab and @jbloomlab.bsky.social) have looked into how the neutral mutation rate varies along the genome:

[1/N]

www.biorxiv.org/content/10.1...

Shades of similarity to the Alameda county toddler. Glad to hear of a full recovery but unfortunate that this occurs to start with.

In the last ~24h, #H5N1 picked up in Maryland in poultry, a now total of up to over 900 dairy cattle herds testing positive, a death in Cambodia, suspected case w/unknown source in California. Unclear on genotypes/H5 clades for some of these. But this is by no means a path we should be on globally.