Late yesterday the  https://www.cdc.gov/bird-flu/spotlights/h5n1-response-07192024.html - CDC announced the confirmation  of the (previously known) 5th and an additional 6th human H5 infection from the poultry farm in Weld County, Colorado.  This brings the total number of H5 infections in the United States since March of this year to 10.

This report comes on the heels of the report of a second large poultry farm in Weld County testing positive for H5N1 (see CIDRAP report  https://www.cidrap.umn.edu/avian-influenza-bird-flu/h5n1-strikes-another-large-layer-farm-colorado-dairy-herd-minnesota - H5N1 strikes another large layer farm in Colorado ), and on the eve of the start of the https://www.weldcountyfair.com/Home -  Weld Country Fair (Jul 20th-29th).

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We continue to get more reassurance than details from federal agencies, although it is unclear how much of that is due to difficulties getting information and/or cooperation from local entities.  

Genetic sequences continue to be deposited belatedly, and are often missing critical meta-data (see  https://gisaid.org/resources/gisaid-in-the-news/highly-pathogenic-avian-influenza-outbreak-in-the-united-states/ - GISAID comment  below), making independent analysis difficult. 

This collection includes many virus sequences from dairy cows, but also closely related viruses detected in poultry and wild birds and in mice, cats and other mammals as well as the recent human infections. Although metadata such as sampling date and location are unfortunately missing from recent datasets, the available data allow a close watch on mutations that may arise as a consequence of virus adaptation to new hosts.

Unknown is how the bovine B3.13 genotype has managed to spillover into poultry, and whether it is now spreading via wild birds.  

Other than reporting that PPE use by poultry workers was `not optimal' (blamed on excessive heat and fans inside barns), we've seen little in the way of epidemiological data (not even onset dates) on these cases.  

For now, HPAI H5N1 appears to lack the ability to spark a human pandemic, but that happy state of affairs could literally change overnight. Unfortunately, we continue to treat HPAI as more of an economic or political problem, than a true public health concern. 

A risky strategy that may work in the short term, but has the potential to end very badly. 

Bird flu: How concerned should you be about human infection of H5N1? | Expert Answers | CNA Explains

Both of the layer farms are in Weld County in the northeastern corner of the state, where several outbreaks have been reported in dairy cattle.

In other developments, Minnesota's Board of Animal Health  https://www.bah.state.mn.us/h5n1 - reported  another affected dairy herd, which is located in Stearns County in the central part of the state. 

Wastewater detection in Arkansas

In a new wastewater development,  https://data.wastewaterscan.org/tracker/?charts=CjwKFkg1IERldGVjdGVkLCBBbGwgc2l0ZXMQASABQAFIAFIGMTc2ODhlWgdJbmZBX0g1eD6KAQZiNDUwYmY%3D&selectedChartId=b450bf - WastewaterSCAN  reported a new H5 influenza detection in Arkansas involving the city of Harrison's wastewater treatment plant. No recent outbreaks or detections have been confirmed from the state. 

Wastewater detections aren't able to determine the source of the virus. WastewaterSCAN's H5 tracking has detected the virus in nine other states, all but one of which (California) has reported dairy cattle or poultry outbreaks.

In other  https://www.cdc.gov/bird-flu/h5-monitoring/index.html#cdc_data_surveillance_section_9-monitoring-for-influenza-in-wastewater - wastewater tracking , the Centers for Disease Control and Prevention said that, across the 2 weeks ending July 6, no states were at the high level for influenza A, which can't distinguish H5N1 but can be a surveillance signal for health officials to explore the source.

At the conclusion of today’s session, the participant will be able to accomplish the following:

1. Discuss the epidemiology and clinical features of human cases of HPAI A(H5N1) virus infection.
2. Describe risk of human infection with HPAI A(H5N1) viruses, identify higher risk populations, and what to assess in clinical settings. 
3. Describe testing, using antivirals, and infection prevention and control recommendations for patients with HPAI A(H5N1) virus infection. 

It is a far better source of information than most of what I've seen on trending on social media.  But I digress . . . 

There are also anecdotal reports of symptomatic dairy workers who were never tested for the virus (see  https://afludiary.blogspot.com/2024/06/eid-journal-avian-influenza-ah5n1-virus.html - EID Journal: Avian Influenza A(H5N1) Virus among Dairy Cattle, Texas, USA ), raising the possibility that some cases have gone undetected.

Colorado - with 46 confirmed infected dairy herds - leads the nation in both cattle and human infections with HPAI H5. In the past 10 days  https://afludiary.blogspot.com/2024/07/colorado-doh-reports-their-7th.html - at least 7 poultry workers  have tested positive for the avian virus, and over the past 30 days they've reported  https://www.cidrap.umn.edu/avian-influenza-bird-flu/h5n1-strikes-another-large-layer-farm-colorado-dairy-herd-minnesota - two very large outbreaks in poultry , and 28 new dairy herd infections. 

Until now, most testing (excerpt for interstate transport of cattle) in the United States has been voluntary, and limited to symptomatic dairy cows. As a result, we don't have a very good handle of how many herds are infected.  

Yesterday, the Colorado Department of Agriculture released the  https://drive.google.com/file/d/17KS5LLEG-Dir1s9fpGVL8Mnp62ACCz2a/view - following order  for mandatory weekly bulk-tank testing for HPAI.   I'll have a bit more after the break.

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The industry's hope, that the virus would `burn itself out' in cattle, has not come to fruition.  

Thus, people born before 1968 have tended to escape H5N1’s ravages, because they probably had their first flu infection at a time when the dominant flu virus in circulation matched H5N1. But people born after 1968 eluded the worst of H7N9, because their first encounter with flu was probably with a virus that matched it rather than H5N1. Immunity from a first infection provided 75% protection against severe disease and 80% protection against death with a matching bird-flu virus, the authors found.

If an H5N1 outbreak were to occur, this first-bout effect predicts that older people could once again be largely spared whereas younger people could be more vulnerable, Worobey says. “We should have that somewhere between the back and front of our minds,” he says.

H5N1 is a subtype of Influenza A virus, like all subtypes it is an  https://en.wikipedia.org/wiki/Viral_envelope - enveloped   https://en.wikipedia.org/wiki/Sense_%28molecular_biology%29 - negative-sense   https://en.wikipedia.org/wiki/RNA_virus - RNA virus , with a segmented genome. ^{https://en.wikipedia.org/wiki/Influenza_A_virus_subtype_H5N1#cite_note-:03-36 - [36]}  Subtypes of IAV are defined by the combination of the antigenic  https://en.wikipedia.org/wiki/Hemagglutinin_%28influenza%29 - hemagglutinin  and  https://en.wikipedia.org/wiki/Neuraminidase - neuraminidase  proteins in the  https://en.wikipedia.org/wiki/Viral_envelope - viral envelope . "H5N1" designates an IAV subtype that has a type 5 hemagglutinin (H) protein and a type-1 neuraminidase (N) protein. ^{https://en.wikipedia.org/wiki/Influenza_A_virus_subtype_H5N1#cite_note-:112-37 - [37]}  Further variations exist within the subtypes and can lead to very significant differences in the virus's ability to infect and cause disease, as well as to the severity of symptoms. ^{https://en.wikipedia.org/wiki/Influenza_A_virus_subtype_H5N1#cite_note-:5-38 - [38] https://en.wikipedia.org/wiki/Influenza_A_virus_subtype_H5N1#cite_note-39 - [39]}

Influenza viruses have a relatively high mutation rate that is characteristic of  https://en.wikipedia.org/wiki/RNA_virus - RNA viruses . ^{https://en.wikipedia.org/wiki/Influenza_A_virus_subtype_H5N1#cite_note-pmid38158694-40 - [40]}  The segmentation of its  https://en.wikipedia.org/wiki/Genome - genome  facilitates  https://en.wikipedia.org/wiki/Genetic_recombination - genetic recombination  by segment  https://en.wikipedia.org/wiki/Reassortment - reassortment  in hosts infected with two different strains of influenza viruses at the same time. ^{https://en.wikipedia.org/wiki/Influenza_A_virus_subtype_H5N1#cite_note-Kou-41 - [41] https://en.wikipedia.org/wiki/Influenza_A_virus_subtype_H5N1#cite_note-WHOinfluenza-42 - [42]}  Through a combination of  https://en.wikipedia.org/wiki/Mutation - mutation  and genetic  https://en.wikipedia.org/wiki/Reassortment - reassortment  the virus can evolve to acquire new characteristics, enabling it to evade host immunity and occasionally to jump from one species of host to another. ^{https://en.wikipedia.org/wiki/Influenza_A_virus_subtype_H5N1#cite_note-43 - [43] https://en.wikipedia.org/wiki/Influenza_A_virus_subtype_H5N1#cite_note-Eisfeld2-44 - [44]}