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H5N1 genetic sequences - 2024+

Welcome SeniorLearner! Thank you for posting this substack essay. ​

I also agree with this snip:

"I don’t want to drone on. We have a relatively new zoonotic H5N1 2.3.4.4b D1.3 genotype that has killed over 19 million chickens on 84 farms in a small area in less than 2 1/2 months! It put one poultry worker in the hospital. No one has even bothered to publicly announce the new genotype to my knowledge! CDC has likely sequenced it from the hospitalized human patient yet has failed to deposit the sequence or even inform the public of its findings."

https://substack.com/home/post/p-159188160
​

edited to add links to pertinent threads...

Please see:

Ohio - Avian flu in poultry 2024-2025​

Indiana: 2024 & 2025 Avian Flu in poultry​

Ohio reports state's first human case of bird flu - February 12, 2025​
 
Substack Home - Hogvet51’s Livestock Emerging and Zoonotic Disease Forum​

H5N1 2.3.4.4b D1.3 in Ohio-Indiana Poultry Outbreak with Associated Undisclosed Human Sequence Data

Background phylogenetic work on USDA raw sequence submissions reveals a surprise unpublicized emerging avian genotype (D1.3) as a common source in the large multi-state poultry outbreak

more....
​

Update by the CDC today addresses the above issue (among others):


CDC A(H5N1) Bird Flu Response Update March 19, 2025
​
 
4/1/25

@RajlabN
​Quick analysis of 2 #AvianFlu sequences sampled from #Bears (Collection date: 2025; Location: unknown) to
@gisaid
from #USA | D.1.1 genotype PB2 mutations: K389R, V478I, E627K, M676T Ref: A/Duck/Guangdong/E1/2012​

​
Screenshot 2025-04-01 at 6.53.12 AM.webp
 
4/1/25
@RajlabN

NA mutations: T8I, V16I, V20I, M23V, Y44N, Q45H, P48T, I53V, V67I, F74L, L75I, V80I, T81D, S82P, T84A, N221S, V234I, V241I, K257R, D259E, E268D, P272S, G286S, D287E, I288V, N329S, S336G, M338V, E395A Ref: A/AmericanWigeon/SouthCarolina/22-000345-001/2021​

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Raj Rajnarayanan
@RajlabN
·
8h




#H5N1 #AvianInfluenza Quick analysis of the sequence uploaded to
@gisaid
from Khett Kampong Spoe, #Cambodia (11 yr, male patient) HA mutations: E2K, K3R, S12N, H44Q, T87I, D136N, G179D, R205K, S233P, V285A, E286Q, N325S, I351K, I390V, Q506R Ref: Duck/VietnamNCVD-1584/2012
Quote
Ngt0V722_normal.jpg

Raj Rajnarayanan
@RajlabN
·
22h
[HASHTAG="c2811"]H5N1[/HASHTAG] updates [HASHTAG="c1781"]Cambodia[/HASHTAG] reports 4th fatal human case this year! Will update sequence information as soon as its available x.com/CIDRAP/status/…


1


9


33

1.3K




Raj Rajnarayanan
@RajlabN
·
8h




NA mutations: A46T, L60V, V79I, I129V, I191L, N250D, R293Q, R312T, I376M, N396D Ref: A/Cambodia/NPH230032/2023 2/n


1


4


10

479




Raj Rajnarayanan
@RajlabN




HA mutation 205 is flagged in literature as antigenic drift / escape mutant and virulence
​
https://pubmed.ncbi.nlm.nih.gov/31635227/​
 
from my email: [TABLE="class: yiv2212227425gd_tbl_wrap, align: center, width: 0"]
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[TD="class: yiv2212227425abe-column-block-padding"]DATCPanimals@wisconsin.gov | (608) 224-4872 | datcp.wi.gov [/TD]
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[TD="class: yiv2212227425abe-column-block-padding"]Update on Highly Pathogenic Avian Influenza (HPAI)

Today, the U.S. Department of Agriculture (USDA) announced information on the genetic sequencing of the highly pathogenic avian influenza (HPAI) that was detected in Dodge County, Wisconsin last week. Access USDA's press release here.
On December 17, the National Veterinary Services Laboratories (NVSL) completed whole genome sequencing and confirmed that the virus is H5N1 clade 2.3.4.4b genotype D1.1. Analysis indicates that this detection is a new spillover event from wildlife into dairy cattle, separate from previous events.
Some key points from USDA's news release include:

  • Most detections in U.S. dairy herds have resulted from movements linked to the original spillover event that occurred in the Texas Panhandle in late 2023, involving the B3.13 strain.
  • In early 2025, through the National Milk Testing Strategy, USDA detected two spillover events in Arizona and Nevada dairy herds. Both were identified early, with limited spread to other farms. These events involved the D1.1 strain.
  • The Wisconsin herd, also detected through the National Milk Testing Strategy, represents a new, separate spillover event and involves the D1.1 strain. At this time, no additional dairy herds have been identified as infected in association with this event.
Wisconsin and the National Milk Testing Strategy (NMTS)
With help from industry partners, Wisconsin is sampling milk at the farm level for the mandatory USDA Animal and Plant Health Inspection Service (APHIS) NMTS. When Wisconsin began NMTS testing in May 2025, the goal was to test each farm approximately every month. Wisconsin achieved unaffected Gold Status under the NMTS in September 2025. In October, DATCP reduced its testing frequency to 50%.
Wisconsin will resume NMTS testing at a 100% frequency statewide. DATCP will continue to utilize milk samples that are already collected through existing, routine sampling to streamline the NMTS testing process. The DATCP HPAI in Dairy Cattle webpage will continue to be updated weekly as the testing continues.
Biosecurity and Monitoring
It is important to remain vigilant and utilize enhanced biosecurity measures.

H5N1 Protocol: What to Do if H5N1 is Confirmed on Your Dairy Farm
DATCP created a resource document in case of a detection of H5N1 on a dairy farm. The document is intended to serve as a general reference for industry, but individual needs and response actions may differ for H5N1 detections depending on the operation and specific circumstances. Access the H5N1 Protocol: What to Do if H5N1 is Confirmed on Your Dairy Farm document.
Human Health Precautions
Human cases of H5N1 have been reported following exposure to infected animals. Access the confirmed cases and exposure sources for human infections.
The Wisconsin Department of Health Services (DHS) advises those working with animals to take precautions and wear PPE per CDC guidance. According to the Centers for Disease Control and Prevention (CDC), the public health risk from HPAI detections remains low.
Additional Resources:

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​:datcp@service.govdelivery.com
 
Zoonotic Implications of the Co-Circulation of Clade 2.3.4.4b and 2.3.2.1a H5N1 Avian Influenza Viruses in Nepal in 2023

​ 2025 Nov 6;17(11):1481. doi: 10.3390/v17111481​

Abstract

Samples collected from two avian influenza outbreaks in Bagmati Province in central Nepal between January and March 2023 were positive for H5N1. Full genomes were generated for both viruses, which revealed that one of the viruses was very similar to clade 2.3.4.4b H5N1 identified in Bangladesh in 2021/2022. The second virus was a reassortant H5N1 virus consisting of four genes (HA, NA, NP, and M) originating from a clade 2.3.2.1a H5N1 and the remaining four genes (NS, PB1, PB2, and PA) originating from a 2.3.4.4b H5N1. Notably, this second virus had a high identity with 2.3.2.1a clade viruses identified in humans and cats in India in 2024–2025. These are the first full genome sequences of H5N1 avian influenza viruses from Nepal and given the recent human infections by 2.3.2.1a H5N1 viruses in the region, these data will be of interest to both public health and veterinary authorities.
​
https://pmc.ncbi.nlm.nih.gov/articles/PMC12656878/
 
A Global Review of Highly Pathogenic Avian Influenza (HPAI) and Control Strategies in Nepal

​Submission received: 22 January 2026 / Revised: 1 March 2026 / Accepted: 25 March 2026 /Published: 1 April 2026​

Simple Summary

Highly pathogenic avian influenza (HPAI) remains one of the most significant viral diseases affecting poultry production in Nepal. Since 2009, the country has experienced repeated outbreaks, mainly due to high poultry density, migratory wild birds, and informal cross-border trade. These outbreaks have caused major economic losses and continue to threaten animal and public health. This review summarizes the global outbreak patterns of avian influenza and evaluates current surveillance, diagnostic capacity, and control measures in Nepal. It also identifies key gaps and highlights the need for stronger biosecurity, improved preparedness, and better coordination through a One Health approach to reduce the impact of avian influenza in Nepal.

-snip-
2. Influenza A Viruses

​... Among all avian influenza subtypes, H5 and H7 subtypes are of particular concern due to their ability to mutate into highly pathogenic forms, causing severe losses in poultry production and posing significant zoonotic risks to humans [21]. H9N2 viruses have zoonotic potential and play a critical role as internal gene donors for other reassortant influenza viruses, including H5 and H7 subtypes. Thus, H9N2 represents a persistent endemic and evolutionary reservoir risk rather than an acute high-mortality threat [22].​

... In Nepal, HPAI H5 viruses have been identified from multiple genetic clades, reflecting repeated introductions over time. The principal clades detected include clade 2.2, clade 2.3.2, and clade 2.3.2.1, with subclades 2.3.2.1a and 2.3.2.1c representing the predominant lineages in earlier outbreaks. More recently, viruses belonging to clade 2.3.4.4, particularly subclade 2.3.4.4b, have been reported [23]. Overall, clade 2.3.2.1 has historically dominated HPAI circulation in Nepal, whereas clade 2.3.4.4b represents more recent incursions, occasionally detected alongside reassortant H5N1 viruses [24].​

continued:
https://www.mdpi.com/2813-0227/6/2/11
​
 
J Virol . Isolation and characterization of a clade 2.3.4.4b genotype D1.1 H5N1 virus from dairy cattle in Wisconsin

J Virol


. 2026 Jul 10:e0076126.
doi: 10.1128/jvi.00761-26. Online ahead of print.
Isolation and characterization of a clade 2.3.4.4b genotype D1.1 H5N1 virus from dairy cattle in Wisconsin

Daria Mezhenskaia[SUP] 1 [/SUP], Lavanya Babujee[SUP] 1 [/SUP], Ailam Lim[SUP] 2 [/SUP], Lizheng Guan[SUP] 1 [/SUP], Dani Nguyen[SUP] 1 [/SUP], Chunyang Gu[SUP] 1 [/SUP], Gabriele Neumann[SUP] 1 [/SUP], Keith Poulsen[SUP] 2 [/SUP], Amie J Eisfeld[SUP] 1 [/SUP], Yoshihiro Kawaoka[SUP] 1 3 4 5 [/SUP]


Affiliations
Abstract

Highly pathogenic avian influenza A(H5N1) (HPAI H5N1) viruses of clade 2.3.4.4b have recently been detected in U.S. dairy cattle following multiple spillover events from avian reservoirs. In December 2025, HPAI H5N1 virus was identified in a dairy herd in Wisconsin through the National Milk Testing Strategy. Here, we report the isolation of a clade 2.3.4.4b, genotype D1.1 H5N1 virus, A/dairy cow/Wisconsin/25G05743-001/2025 (WI5743-H5N1), from bulk milk associated with the affected herd, describe its phylogenetic relationships, and assess its pathogenicity in mice. Infectious virus was recovered following blind passage in embryonated chicken eggs. Phylogenetic analysis demonstrated that WI5743-H5N1 is distinct from previously reported D1.1 viruses detected in dairy cattle in Nevada and Arizona, supporting an independent introduction into cattle, and indicating a likely local avian source. Compared with closely related avian viruses, WI5743-H5N1 encoded the mammalian-adapting substitution PB2-E627K and additional amino acid differences in HA, PB1-F2, and NS1. In mice, WI5743-H5N1 replicated efficiently in respiratory tissues and was detectable in the brain but exhibited lower lethality relative to other recent clade 2.3.4.4b, genotype B3.13 viruses. Together, these findings highlight the genetic and phenotypic diversity of HPAI H5N1 viruses infecting dairy cattle and underscore the importance of continued surveillance and functional characterization of emerging strains.IMPORTANCEHighly pathogenic avian influenza A(H5N1) viruses have recently entered U.S. dairy cattle through multiple spillover events from avian reservoirs, creating new opportunities for viral adaptation in mammals. Here, we describe the isolation and characterization of a clade 2.3.4.4b, genotype D1.1 H5N1 virus from bulk milk collected during a spillover event in Wisconsin in December 2025. Phylogenetic analyses demonstrated that this virus represents an independent introduction into dairy cattle distinct from previously reported D1.1 viruses identified in Nevada and Arizona. Although the virus encoded the mammalian-adapting PB2-E627K substitution, it exhibited comparatively low lethality in mice, highlighting the complexity of mammalian adaptation and pathogenicity in H5N1 viruses. These findings expand current understanding of the genetic and phenotypic diversity of H5N1 viruses infecting dairy cattle and emphasize the importance of continued surveillance and functional characterization of emerging strains.

Keywords: H5N1; PB2-E627K; clade 2.3.4.4b; dairy cattle; genotype D1.1; influenza A virus; mammalian adaptation.

​
 
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Translated
[ Date: 2026-11-04 15:06:13 | Source: Internet ]
In Changsha—the "Star City" and birthplace of a great historical figure—the 5th T50 Technical Symposium for the Breeding Poultry Industry, organized by Ringpu Bio, concluded successfully on October 31. Key representatives from 81 breeding poultry enterprises across China—collectively managing a stock of approximately 90 million breeder hens—gathered to focus on the theme: "Joining Forces, Safeguarding Defenses, Stabilizing Production, and Looking Toward the Future." The event brought together senior university professors, veteran veterinary experts, and Ringpu Bio’s core technical team. Together, they addressed critical issues such as disease risks in poultry breeding, biosecurity, immunosuppressive diseases, and emerging pathogens. Through the five dimensions of "production, academia, research, application, and iterative improvement," participants exchanged research findings, academic insights, and actionable disease prevention and control strategies, all aimed at fostering stable production and enhanced efficiency within the poultry industry. ...

...
Professor Jia Weixin from South China Agricultural University delivered a specialized presentation titled "Latest Epidemiological Trends of Avian Influenza in 2026 and Response Strategies." He analyzed the global situation, noting that the 2026 outbreak of highly pathogenic avian influenza (HPAI) is more severe than in the same periods of the previous two years; while concentrated in Europe, the virus has now spread across every continent. Regarding domestic surveillance, he reported that all H5 strains circulating in 2026 belong to Clade 2.3.4.4b, with the b5.5 sub-lineage being the dominant strain. Furthermore, since late 2025, a European-like b5.6 sub-lineage has emerged in regions including Hebei, Shandong, and Henan, with its geographic reach continuing to expand.

Meanwhile, the number of H7N9 isolates has dropped significantly, though the strains continue to diversify, and H9N2 prevalence is characterized by the alternating dominance of the B4.7.2 and B4.7.3 sub-lineages.


Finally, he offered recommendations for disease prevention and control: continuously strengthen proactive surveillance and the tracking of viral mutations,
while proactively stockpiling vaccines matched to circulating strains. Poultry farms should establish a "proactive surveillance + active immunization" mechanism, ensuring comprehensive defense against both highly pathogenic and low-pathogenic avian influenza. ... Liu Yijun, a senior technical expert from the Solutions Department at Ringpu Bio, delivered a presentation titled "Analyzing the Causes of Declining Fertility, Hatchability, and Chick Quality in the Late Laying Period, and Scientific Countermeasures." He clarified the interrelationships among these three key performance indicators and the value of "egg-breakout analysis" (examining unhatched eggs). He systematically outlined the various factors contributing to these declines—including issues with roosters (body weight, uniformity, and health), hens (nutrition and gut health), hatching egg management (collection, disinfection, storage, and transport), and incubation management (temperature, humidity, ventilation, and egg turning). He proposed scientific interventions, emphasizing the need to start at the source—the breeder flock—by managing the body weight and uniformity of both roosters and hens, standardizing the handling of hatching eggs, and precisely optimizing the incubation environment based on the specific embryonic developmental stage at which mortality occurs. Through meticulous management across every stage, the quality of hatched chicks can be improved.
Dr. Wang You, head of the Solutions Department at Ringpu Bio, concluded the session with a report titled "Gaining Insight into Emerging Disease Risks and Strengthening Defenses." Based on an analysis of large-scale epidemiological data, he identified Infectious Bronchitis Virus (IBV), *Mycoplasma synoviae* (MS), and Marek’s Disease Virus (MDV) as the most prevalent diseases currently, while highlighting the need for focused attention on emerging threats such as the H6 subtype of avian influenza, chicken-origin flaviviruses, and chicken-origin *Riemerella anatipestifer* (duck plague/septicemia) infections. Furthermore, an in-depth analysis was conducted on the risks posed by key emerging infectious diseases. In the realm of avian influenza, H5 subtypes—including b5.5, b5.6, and various mutant strains—are now co-circulating, accompanied by a shift in host distribution (with an increased prevalence in chickens and quails). H6 isolates have shown a significant rise in detection rates and exhibit slightly higher pathogenicity than H9, while the 4.2.5C4 lineage remains the dominant strain of H9. Additionally, the chicken-origin flavivirus (Tembusu virus) has crossed the species barrier from waterfowl to chickens; it is capable of vertical transmission and is frequently misdiagnosed. Similarly, *Riemerella anatipestifer* (typically associated with ducks) has breached the host barrier—with a detection rate of 13.9% in chickens—causing oviduct impaction and a triad of inflammatory conditions ("three-itis"). Finally, the Poultry Solutions Department at Ringpu Bio was introduced, highlighting its systematic response framework. Leveraging a specialized service model—comprising "professional diagnostics, monitoring and early warning, scenario-based disease research, and a closed-loop value-added service system"—the department utilizes 10 epidemiological surveillance zones and over 600 professional staff members to cover major poultry-farming regions nationwide. By providing comprehensive solutions—including tailored immunization programs, biosecurity protocols, and precision medication strategies—the company helps poultry enterprises improve performance metrics, mitigate risks, and enhance overall profitability.

continued

zhttp://sqtv.net/news/bencandy.php?&fid=56&id=271746
 

Update: Genetic Sequencing Results for Washington Dairy Herd Detection of Highly Pathogenic Avian Influenza​

Contact: aphispress@usda.gov

WASHINGTON, D.C., November 4, 2026—On October 8, 2026, USDA’s Animal and Plant Health Inspection Service (APHIS) announced the first two detections of highly pathogenic avian influenza (HPAI) in two dairy herds in Washington. On October 8, the National Veterinary Services Laboratories (NVSL) completed whole genome sequencing and confirmed that the virus is H5N1 genotype B3.13. Analysis indicates that this detection is consistent with transmission of virus from Idaho to Washington likely through cattle movement.

Key Points

  • Most cases in U.S. dairy herds have resulted from live animal movements linked to the original spillover event that was detected in the Texas Panhandle in late 2023, involving the B3.13 genotype.
  • The Washington herds, detected after exhibiting clinical signs consistent with H5N1, is due to the B3.13 strain. At this time, surveillance is ongoing around the initial premises and throughout Washington.
Public Health and Food Safety

This detection does not pose a risk to consumer health or affect the safety of the commercial milk supply. Pasteurization effectively inactivates HPAI virus, and milk from affected animals is diverted or destroyed to prevent entry into the food supply. The Centers for Disease Control and Prevention (CDC) continues to consider the risk to the public to be low.

The Importance of Biosecurity

USDA remains committed to working with state partners to monitor, investigate, and mitigate the spread of HPAI in livestock. The detection does not change USDA’s HPAI eradication strategy. Biosecurity is still key to mitigating the risk of disease introduction or spread between premises.

APHIS recommends enhanced biosecurity measures for all dairy farms. Producers should immediately report any livestock with clinical signs, or any unusual sick or dead wildlife, to their state veterinarian.

 
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