Guha Arunkumar
@guha.bsky.social
PhD at Mount Sinai (2021) on vaccine & antibody development against Influenza and studied Flu B-like viruses (spiny eel!). Sr. Scientist in industry focusing on viral vaccines.
Opinions/views are my own.
Opinions/views are my own.
Reposted by Guha Arunkumar
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...
Similar data could help forecast evolution for vaccine selection
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
March 12, 2025 at 11:48 PM
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...
Similar data could help forecast evolution for vaccine selection
www.biorxiv.org/content/10.1...
Reposted by Guha Arunkumar
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
NCBI and the other two participating organizations share data on a daily basis.
www.insdc.org
International Nucleotide Sequence Database CollaborationInternational Nucleotide Sequence Database Collaboration
www.insdc.org
March 2, 2025 at 1:57 PM
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
NCBI and the other two participating organizations share data on a daily basis.
www.insdc.org
Reposted by Guha Arunkumar
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) 🧪
International Nucleotide Sequence Database CollaborationInternational Nucleotide Sequence Database Collaboration
www.insdc.org
March 2, 2025 at 11:02 AM
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) 🧪
Reposted by Guha Arunkumar
🚨🚨🚨 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
March 2, 2025 at 2:25 PM
🚨🚨🚨 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
Reposted by Guha Arunkumar
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...
Global health goes on.
www.who.int/publications...
March 2, 2025 at 12:38 AM
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...
Global health goes on.
www.who.int/publications...
Reposted by Guha Arunkumar
JUST IN: Arizona Reports H5N1 Genotype D1.1 In Maricopa County Dairy Herd.
February 14, 2025 at 10:19 PM
JUST IN: Arizona Reports H5N1 Genotype D1.1 In Maricopa County Dairy Herd.
Reposted by Guha Arunkumar
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
A/Nevada/10/2025
Not in BLAST database yet
Has additional changes compared to
A/dairy cow/USA/002645-005/2025
February 14, 2025 at 4:02 PM
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
A/Nevada/10/2025
Not in BLAST database yet
Has additional changes compared to
A/dairy cow/USA/002645-005/2025
Reposted by Guha Arunkumar
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’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...
health.wyo.gov
February 15, 2025 at 4:10 AM
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...
Reposted by Guha Arunkumar
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...
www.reuters.com/business/hea...
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.
www.reuters.com
February 15, 2025 at 4:50 AM
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...
www.reuters.com/business/hea...
Reposted by Guha Arunkumar
#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...
February 15, 2025 at 5:39 AM
#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...
Reposted by Guha Arunkumar
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
CDC told Fortune that the D1.1 variant in this worker is the same strain of
February 11, 2025 at 12:12 AM
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
CDC told Fortune that the D1.1 variant in this worker is the same strain of
Reposted by Guha Arunkumar
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...
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...
February 10, 2025 at 8:21 AM
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...
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...
Reposted by Guha Arunkumar
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...
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...
www.cnn.com
February 6, 2025 at 8:42 PM
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...
Reposted by Guha Arunkumar
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.
4 dairy herds in Nevada recently diagnosed with #H5N1 #birdflu were infected with a different version of the virus than has been spreading in cows elsewhere. Evidence of a second (at a minimum) spillover points to the challenge of stopping spread, experts say. www.statnews.com/2025/02/05/u...
USDA milk testing shows different strain of H5N1 bird flu in Nevada dairy herds
The USDA said four Nevada dairy herds were infected with an H5N1 bird flu strain that has circulated in wild birds, making prospects for containment in cows appear dim.
www.statnews.com
February 6, 2025 at 12:49 AM
Reposted by Guha Arunkumar
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...
@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...
February 6, 2025 at 1:26 AM
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...
@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)
January 23, 2025 at 3:55 PM
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)
Reposted by Guha Arunkumar
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/...
www.nbcphiladelphia.com/news/health/...
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 ...
www.nbcphiladelphia.com
January 22, 2025 at 9:10 PM
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/...
www.nbcphiladelphia.com/news/health/...
Reposted by Guha Arunkumar
EXTREMELY cool and demonstrates clearly the promise of deep learning + bio.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
www.nature.com
January 15, 2025 at 8:25 PM
EXTREMELY cool and demonstrates clearly the promise of deep learning + bio.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Guha Arunkumar
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...
Interface: clades.nextstrain.org?dataset-url=...
👉 www.biorxiv.org/content/10.1...
January 12, 2025 at 9:56 PM
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...
Interface: clades.nextstrain.org?dataset-url=...
👉 www.biorxiv.org/content/10.1...
Reposted by Guha Arunkumar
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...
👉 www.biorxiv.org/content/10.1...
January 16, 2025 at 10:13 PM
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...
👉 www.biorxiv.org/content/10.1...
Reposted by Guha Arunkumar
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...
👉 www.nature.com/articles/s41...
January 16, 2025 at 9:52 PM
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...
👉 www.nature.com/articles/s41...
Reposted by Guha Arunkumar
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
bit.ly/3DSmr6Q
Health Alert Network (HAN) - 00520 | Accelerated Subtyping of Influenza A in Hospitalized PatientsMinusSASstats
bit.ly
January 16, 2025 at 6:01 PM
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
bit.ly/3DSmr6Q
Reposted by Guha Arunkumar
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.
Tanzania doesn’t have the surveillance Rwanda does. But it’s good they’ve identified this.
January 14, 2025 at 10:31 PM
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.
Tanzania doesn’t have the surveillance Rwanda does. But it’s good they’ve identified this.
Reposted by Guha Arunkumar
Check out the newest preprint from the Schultz-Cherry lab on susceptibility of primary cells to H5N1 clade 2.3.4.4b viruses! -->
Susceptibility of bovine respiratory and mammary epithelial cells to avian and mammalian derived clade 2.3.4.4b H5N1 highly pathogenic avian influenza viruses https://www.biorxiv.org/content/10.1101/2025.01.09.632235v1
January 11, 2025 at 5:38 PM
Check out the newest preprint from the Schultz-Cherry lab on susceptibility of primary cells to H5N1 clade 2.3.4.4b viruses! -->