Preprint: Emergence and Interstate Spread of HPAI A(H5N1) in Dairy Cattle

 

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As we have discussed repeatedly over the years, the superpower of influenza viruses is its ability to reinvent itself via reassortment; the swapping of genetic material between two influenza viruses co-infecting a single host. 

Since HPAI H5N1 arrived in North America in late 2021, it has reassorted repeatedly with other avian viruses which are native to this part of the world. As a result, instead of having one H5N1 virus to contend with, we have scores of genotypes circulating in the wild.

Each genotype can have different capabilities, with some being more pathogenic in birds, while others may be more transmissible to mammals. Each genotype, however, is on its own, distinct evolutionary path. 

Some will thrive, while others may fail. And every once in a while, one comes along that does something completely unexpected. 

Up until six weeks ago, cattle were thought unlikely hosts for influenza A infection.  While cattle had been experimentally infected with H5N1 more than 15 years ago and a few studies had hinted at prior influenza outbreaks in cattle (see A Brief History Of Influenza A In Cattle/Ruminants), no one expected to see a multi-state outbreak of H5N1 in cattle.

But the emergence of a new genotype - B3.13 - changed all that.  Demonstrating that HPAI H5 still has a few tricks to show us. 

According to the following report, this virus likely spilled over into cattle in late 2023, and circulated for 4 months before it was detected in March of this year.  

During that time, it spilled back into wild birds, poultry, cats, other peridomestic mammals, and at least 1 human.  

Today we've a detailed preprint from U.S. Government researchers and from several Universities that describes the emergence, spread, and potential threat from this new genotype. Due to its length I've only posted some excerpts, so follow the link to read it in its entirety. 

I'll have a brief postscript after the break. 

Emergence and interstate spread of highly pathogenic avian influenza A(H5N1) in dairy cattle

Thao-Quyen Nguyen, Carl Hutter, Alexey Markin, Megan N Thomas, Kristina Lantz, Mary Lea Killian, Garrett M Janzen, Sriram Vijendran, Sanket Wagle, Blake Inderski, Drew R Magstadt, Ganwu Li, Diego G Diel, Elisha Anne Frye, Kiril M Dimitrov, Amy K Swinford, Alexis C Thompson, Kevin R Snevik, David L Suarez, Erica Spackman, Steven M Lakin, Sara C Ahola, Kammy R Johnson, Amy L Baker, Suelee Robbe-Austerman,Mia Kim Torchetti, Tavis K Anderson
doi: https://doi.org/10.1101/2024.05.01.591751

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Abstract

Highly pathogenic avian influenza (HPAI) viruses cross species barriers and have the potential to cause pandemics. In North America, HPAI A(H5N1) viruses related to the goose/Guangdong 2.3.4.4b hemagglutinin phylogenetic clade have infected wild birds, poultry, and mammals. 

Our genomic analysis and epidemiological investigation showed that a reassortment event in wild bird populations preceded a single wild bird-to-cattle transmission episode. The movement of asymptomatic cattle has likely played a role in the spread of HPAI within the United States dairy herd. 

Some molecular markers in virus populations were detected at low frequency that may lead to changes in transmission efficiency and phenotype after evolution in dairy cattle. Continued transmission of H5N1 HPAI within dairy cattle increases the risk for infection and subsequent spread of the virus to human populations.

(SNIP)

Our Bayesian discrete state analysis (Fig. 3) that quantified the movement of HPAIV between six different host categories (poultry, wild bird, cattle, wild mammal, domestic cat, and 20 humans) demonstrated sufficient evidence to support the proposition of HPAI in cattle resulted in infections in other hosts. 

We cannot exclude the possibility that this genotype is circulating in unsampled locations and hosts as the existing analysis suggests that data are missing and undersurveillance may obscure transmission inferred using phylogenetic methods (31). 

The gap in data is highlighted by the human infection with genotype B3.13 HPAIV where the HA gene sequence was not nested within cattle HA gene 25 sequences. This could indicate that HPAIV in unsampled cows were the source of infection or within-host evolution resulted in divergence sufficient to result in a different phylogenetic grouping. 

It is most likely, however, that asymptomatic transmission and undersurveillance in epidemiologically important populations drove this pattern. Our analysis of transmission chains within the cattle B3.13 clade using a phylogenomic approach suggested unsampled transmission in late 2023 and early 2024 (Fig. S8), and the 30 TMRCA indicates there may have been 4 months of circulation prior to confirmation by USDA. However, given the decline in milk production in highly monitored dairy herds, it is unlikely that the spillover occurred significantly outside of the described TMRCA ranges.

Discussion 

The potential for HPAI H5N1 to become endemic in cattle will shape the zoonotic risk of the B3.13 genotype. There may be low levels of immunity against H5N1 viruses (36-39) and the immunological landscape in the human population affects disease severity (40). Genetically similar viruses do have the potential to cross the species barrier as there has already been a clade 2.3.4.4b B3.13 virus infection in a person with conjunctivitis in March of 2024. 

The existing prepandemic candidate vaccine viruses (CVV) do retain cross-reactivity with currently circulating clade 2.3.4.4b HPAI H5N1 (41). These CVVs are coordinated and shared among the WHO Global Influenza Surveillance and Response Network for use by academic, government, and industry partners for research and development (42). 

However, recent viruses collected in the US had reduced reactivity with the A/Astrakhan/3212/2020 candidate vaccine virus and 15 based on these data and other genetic and epidemiologic measures, a new CVV for the clade 2.3.4.4b viruses was proposed (41).

The HPAI H5N1 genotype B3.13 viruses circulating in cattle represent a potential zoonotic threat based on the evidence we present for transmission in a mammalian host. Based upon current information, it appears that once infected, a cow may shed virus for 2-3 weeks.

We detected some amino acid mutations at sites associated with mammalian adaptation that had already become fixed in the virus population that likely reflect the ~4 months of evolution and limited local circulation in dairy cattle.

Notably, important low frequency sequence variants within cattle were also detected, even within the limited time following the first spillover. If these low-frequency variants become dominant, they may have phenotypes that increase the probability of interspecies transmission. 

Further studies are needed to understand the pathobiology and evolution of the virus in dairy cattle. In addition, there is the potential for multiple animal species to be colocated on agricultural premises, each species may be infected with endemic IAV strains, and an IAV coinfection with HPAI could result in reassortment and the emergence of new strains that increase zoonotic risk (43, 44).

Monitoring of cattle for HPAI will inform epidemiological risk and provide an early warning 30 for whether this interspecies transmission event and dissemination of the viruses throughout the US dairy cattle herd represents a future threat to human health. 

          (Continue . . . )

Even if cattle don't turn out to be the right jumping off point for HPAI to spill over into humans, it is another important - and unexpected - stepping stone for the virus.  

From cattle, the virus could easily continue to take a more circuitous route, passing through dogs and cats, or other peridomestic mammals, where it can pick up additional mammalian adaptations.

Obviously, the growing diversity of HPAI H5 viruses doesn't guarantee we'll see a more humanized virus, but it certainly increases the chances. 

FDA Update On HPAI In Pasteurized Milk Products

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The news on the safety of pasteurized dairy products following the detection of H5N1 in dairy cattle continues to be reassuring, with the FDA reporting yesterday that after analyzing nearly 300 retail mild samples they were unable to culture the virus in any of them. 

Additionally the FDA reports being unable to detect H5N1 RNA in retail powdered infant formula and powdered milk products. 

The big concern continues to be the consumption of `raw milk' or unpasteurized dairy products.  And while there are laws on the books in most states to discourage the practice, there are enough loopholes that if someone really wants raw milk, they can generally find it.  

Colorado was set to relax their strict laws on the sale of raw milk this week, but according to Food Safety News (see Colorado raw milk bill laid over to next year), the recent outbreak of H5N1 in dairy cattle has at least temporarily derailed those plans. 

The `raw milk' movement in the United States continues to grow.  A 2022 study published in the Journal of Food Protection reported that:

Results show that 4.4% of U.S. adults reported consuming raw milk at least once in the past year, with 1.6% reporting frequent consumption of raw milk (once per month or more often) and 1.0% reporting consumption once per week or more often. 

Which suggests that several million people in the United States regularly consume raw milk, a practice that even without avian flu, carries a number of health risks.  

First, the latest from the FDA, after which I'll have a bit more.

Ongoing Work to Ensure Continued Effectiveness of Federal-State Milk Safety System

What's New

May 1, 2024

The FDA is announcing an additional set of results from our national commercial milk sampling study underway in coordination with USDA. The study includes 297 total retail dairy samples. New preliminary results of egg inoculation tests on a second set of 201 quantitative polymerase chain reaction (qPCR)-positive retail dairy samples, including cottage cheese and sour cream, in addition to fluid milk, show that pasteurization is effective in inactivating HPAI.

This additional preliminary testing did not detect any live, infectious virus.

In addition to preliminary results released late last week on an initial set of 96 retail milk samples, these results reaffirm our assessment that the commercial milk supply is safe.

To ensure the safety of milk-derived products for our youngest populations, the FDA also tested samples of retail powdered infant formula and powdered milk products marketed as toddler formula. All qPCR results of formula testing were negative, indicating no detection of HPAI viral fragments or virus in powdered formula products so no further testing was required for these samples. The FDA is continuing to identify additional products that may be tested.

The FDA is also continuing to test samples of pooled raw milk that has been routed to pasteurization and processing for commercial use. This will be used as a basis to characterize potential virus levels that pasteurization may encounter – and will be used to inform studies to further validate pasteurization.

As this situation evolves, the FDA will continue to consider all ongoing scientific research related to the effectiveness of pasteurization for HPAI in bovine milk. We are also committed to continued surveillance of milk production, processing and pasteurization to help ensure the safety of the milk supply. Our state partners are integral to this process, and we are working with them on a continual basis. We will also continue working with our state co-regulators on managing this emerging disease.

The FDA continues to advise strongly against the consumption of raw milk and recommends that industry does not manufacture or sell raw milk or raw milk products.

To date the HPAI H5N1 in dairy cattle (and goats) has only been reported in the United States, but the B3.13 genotype has also been detected in wild birds, and has the potential to expand its geographic range via the major migratory flyways (see below).

 

Although these are primarily north-south conduits, and the most immediate threat would appear to be to  Canada and Mexico, there are enough overlaps that lateral east and west movements are possible given enough time.

Canada has much stricter laws regarding unpasteurized dairy products, but in Mexico the consumption of raw milk (`leche bronca') is far more common than in the United States.  In 2019 the USDA reported unpasteurized, raw milk accounts for between 5-10% of consumption in Mexico.

SENISICA published last week that (at least in commercial poultry) Mexico is free of avian influenza AH5N1 and AH5N2, but I'm seeing very little about testing of cattle, and milk in Mexico.  Hopefully they are taking a more proactive stance than it appears on the surface. 

While there are no guarantees that HPAI H5 will ever spark a pandemic, with each spillover into a mammalian host, the virus gets another chance the roll the genetic dice.  

Something it does often enough without us giving it a helping hand.

Another Brief Hiatus

 

Today (Weds May 1st) I'll be away from my desk having 3 small skin cancers (the result of living under the Florida sun for much of my 70 years) removed from my scalp and face by Mohs surgery. Depending on what they find, this could be an all-day affair.

 All three are squamous cell, so the prognosis is excellent. 

In any event, I don't expect to be able to blog today, but I hope to be back tomorrow. In the meantime, you can check in with FluTrackers and with CIDRAP or Crof for the latest infectious disease news. 

Cheers, and thanks again for all the visits to this humble blog over the years.

DEFRA Risk Assessment Of HPAI H5N1 Occurring in Cattle In the UK

 

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Other than a story in Sky News last week which reported the UK was not planning on testing cows for HPAI, we've seen very little comment outside of North America on the detection of HPAI H5N1 in dairy cattle in the United States.  

Yesterday, however, the UK's DEFRA (Department for Environment, Food & Rural Affairs) published a risk assessment (below), which finds the risks of something similar affecting UK cattle very low. 

They base their assessment on the fact that the B3.13 genotype found in US cattle was created from the European H5 virus reassorting with North American birds.  

As a segmented virus with 8 largely interchangeable parts, the flu virus is like a viral LEGO (TM) set which allows for the creation of hundreds of unique variants (via reassortment) called genotypes.

As as result, there are scores of different genotypes of H5N1 in circulation around the world, and they can have significant differences in their pathogenicity, transmissibility, and host range.  

The ability of genotype B3.13 to infect cows - thus far - appears to be a rare skill set for H5N1. 

Whether it is truly unique, has yet to be established.  

They also reassure that the B3.13 genotype - which may spread north and south via the North American Flyways (see graphic below), are far less likely to spread east across the Atlantic to the UK. 

That said, HPAI H5 crossing the Atlantic to North America in late 2021 was once considered a long-shot, as was H5N1's arrival in the Antarctic last fall. 

When discussing the spread of HPAI via migratory birds, one never likes to say `never'. 

First, some excerpts from the DEFRA risk assessment, then I'll return with a brief postscript.

Preliminary Outbreak Assessment 

Influenza A (H5N1) of Avian origin in domestic livestock in the United States of America

 25 April 2024 

Disease report 

On 26 March 2024, the United States of America (USA) made an immediate notification to the World Organisation for Animal Health (WOAH) of an outbreak of Influenza A (H5N1) of avian origin (Influenza A (H5N1)) affecting dairy cattle in Texas. Milk samples and oropharyngeal swabs tested positive for viral RNA after cows showed clinical signs including decreased lactation, thickened discoloured milk, fever, and low appetite.

 The material detected has been sequenced and shown to belong to clade 2.3.4.4b strain B3.13, a viral reassortant between Eurasian High Pathogenicity Avian Influenza (HPAI) H5N1 and North American Low Pathogenicity Avian Influenza (LPAI) strains.

This strain has not been detected in the UK, and none of the viruses detected in the UK over the 2020 to 2024 HPAI outbreak period have contained genetic material originating from North or South American viruses. 

Additional testing of cattle was carried out on farms where clinical signs have been observed, with deceased wild birds noted on the Texas farm, and since then, and as of 24 April 2024, there have been 32 further reports of Influenza A(H5N1) in dairy cattle in 8 states (USDA). There have also been further reports of the same strain in domestic and wild mammals, including 6 cats showing signs of neurological illness in dairy farm settings where the cattle were also positive (at least 3 of which were reported to have died) and a skunk in North America. There has been one infection in a person exposed to infected dairy cattle, who showed symptoms of conjunctivitis prior to recovery following isolation and anti-viral treatment.

 The risk to GB of H5N1 in livestock is assessed at very low. 

(SNIP)

The emergence of a strain of H5N1 capable of infecting cattle, or any other domestic mammal, is thought to be a rare event, which is made even less likely by implementing biosecurity practices and disease control measures. The full genome of the virus affecting cattle has been made publicly available, and the virus is different to, and distinguishable from, H5N1 that has been circulating in Great Britain and Europe.

This is also the case for other H5N1 viruses circulating in poultry and wild birds in North America since they have been evolving independently from European viruses since 2022. Therefore, the likelihood of the same sequence of events occurring in Great Britain resulting in an identical virus emerging in cattle is highly improbable.

While a similar event could be possible with a UK virus adapting to more mammalian livestock species, this would still be very rare, and would likely require a high initial introductory dose as well as close proximity between mammalian livestock and poultry.

Whole Genome Sequencing (WGS) of H5N1 viruses detected on poultry farms in Great Britain has taken place throughout the HPAI H5 epizootic and pigs present on the same premises as poultry outbreaks have been sampled for avian influenza (with negative results). The avian influenza surveillance carried out to date in Great Britain gives a very high level of confidence that this strain has not been detected in Great Britain. 

Conclusion 

Available trade data shows that only a small proportion of consignments of dairy products could contain H5N1 virus, and given the low prevalence of disease in dairy cattle in the USA so far, it is very unlikely that these would come from infected farms. Additionally, the mitigation measures that are currently in place in the USA, along with the mandatory testing and reporting that are soon to be implemented will reduce this likelihood further. Migratory birds could be a plausible route of introduction of H5N1 virus affecting dairy cattle to Great Britain, although not directly and would be considered rare events. Therefore, the risk of entry of H5N1 virus capable of infecting domestic livestock is very low. We will continue to monitor the situation as it evolves.

There are always concerns around infected products entering the UK in passenger luggage and the subsequent waste being discarded in areas where livestock or wildlife could access them. We would like to highlight to all cattle keepers, dairy producers, smallholders and general public that it is illegal to feed cattle catering waste, kitchen scraps or dairy products, and to adhere to the swill feeding ban.

All dairy keepers should remain vigilant and ensure that any visitors to their premises have not had any recent contact with dairy cattle or cattle premises in the affected regions. People who have been working on farms or with animals returning from any affected areas should avoid any contact with domestic cattle or domestic poultry in commercial holdings and smallholdings. All clothing, footwear or equipment should be disinfected before entering dairy cattle or other livestock areas. Any suspect cases must be reported promptly. 

If you suspect a notifiable disease in your animals, you must report it immediately by calling the Defra Rural Services Helpline on 03000 200 301. In Wales, call 0300 303 8268. In Scotland, contact your local Field Services Office. Failure to do so is an offence. We will continue to monitor the situation. 

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While it seems reasonable that the B3.13 genotype is unlikely to infect UK cattle anytime soon, the assumption that another cattle-affecting genotype won't evolve elsewhere in the world (including in the UK or Europe) is a tad optimistic. 

Nature continues to conduct countless GOF (Gain of Function) experiments with HPAI around the globe, and B3.13 should be viewed as a proof-of-concept.  If it happened once, it can presumably happen again. 

While we might not like what we find, our best strategy is to greatly increase testing and surveillance around the world; to start looking for the virus in previously presumed unlikely places, like in cows, pigs, goats, cats, and anyone who works with them. 

Otherwise, we're just basically waiting and praying the virus goes away.

EID Journal: HPAI A(H5N1) Clade 2.3.4.4b Virus Infection in Domestic Dairy Cattle and Cats, United States, 2024

A growing, but incomplete, picture of affected States

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The CDC's EID Journal published an expedited research paper today on preliminary findings into the infection and spread of HPAI H5N1 clade 2.3.4.4b among both cattle and domestic cats in the United States.   

Infected cattle appear to suffer relatively mild, nonspecific illness, but shed copious amounts of the virus in their milk.

Cats, however, often develop severe neurological manifestations leading to rapid death , similar to what we've seen with other mammals (see PrePrint: HPAI H5N1 Infections in Wild Red Foxes Show Neurotropism and Adaptive Virus Mutations ).

The authors note a number of antemortem clinical signs observed in affected cats, including: `. . . depressed mental state, stiff body movements, ataxia, blindness, circling, and copious oculonasal discharge. Neurologic exams of affected cats revealed the absence of menace reflexes and pupillary light responses with a weak blink response.'

Due to its length, I've only posted the link, abstract, and some excerpts.  Follow the link to read the report in its entirety.  I'll have brief postscript after the break.

Research
Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus Infection in Domestic Dairy Cattle and Cats, United States, 2024

Eric R. Burrough , Drew R. Magstadt, Barbara Petersen, Simon J. Timmermans, Phillip C. Gauger, Jianqiang Zhang, Chris Siepker, Marta Mainenti, Ganwu Li, Alexis C. Thompson, Patrick J. Gorden, Paul J. Plummer, and Rodger Main

Abstract

We report highly pathogenic avian influenza A(H5N1) virus in dairy cattle and cats in Kansas and Texas, United States, which reflects the continued spread of clade 2.3.4.4b viruses that entered the country in late 2021. Infected cattle experienced nonspecific illness, reduced feed intake and rumination, and an abrupt drop in milk production, but fatal systemic influenza infection developed in domestic cats fed raw (unpasteurized) colostrum and milk from affected cows. 

Cow-to-cow transmission appears to have occurred because infections were observed in cattle on Michigan, Idaho, and Ohio farms where avian influenza virus–infected cows were transported. Although the US Food and Drug Administration has indicated the commercial milk supply remains safe, the detection of influenza virus in unpasteurized bovine milk is a concern because of potential cross-species transmission. Continued surveillance of highly pathogenic avian influenza viruses in domestic production animals is needed to prevent cross-species and mammal-to-mammal transmission. 

Highly pathogenic avian influenza (HPAI) viruses pose a threat to wild birds and poultry globally, and HPAI H5N1 viruses are of even greater concern because of their frequent spillover into mammals. In late 2021, the Eurasian strain of H5N1 (clade 2.3.4.4b) was detected in North America (1,2) and initiated an outbreak that continued into 2024. Spillover detections and deaths from this clade have been reported in both terrestrial and marine mammals in the United States (3,4). The detection of HPAI H5N1 clade 2.3.4.4b virus in severe cases of human disease in Ecuador (5) and Chile (6) raises further concerns regarding the pandemic potential of specific HPAI viruses.

In February 2024, veterinarians were alerted to a syndrome occurring in lactating dairy cattle in the panhandle region of northern Texas. Nonspecific illness accompanied by reduced feed intake and rumination and an abrupt drop in milk production developed in affected animals. The milk from most affected cows had a thickened, creamy yellow appearance similar to colostrum. On affected farms, incidence appeared to peak 4–6 days after the first animals were affected and then tapered off within 10–14 days; afterward, most animals were slowly returned to regular milking. Clinical signs were commonly reported in multiparous cows during middle to late lactation; ≈10%–15% illness and minimal death of cattle were observed on affected farms. Initial submissions of blood, urine, feces, milk, and nasal swab samples and postmortem tissues to regional diagnostic laboratories did not reveal a consistent, specific cause for reduced milk production. Milk cultures were often negative, and serum chemistry testing showed mildly increased aspartate aminotransferase, gamma-glutamyl transferase, creatinine kinase, and bilirubin values, whereas complete blood counts showed variable anemia and leukocytopenia.

In early March 2024, similar clinical cases were reported in dairy cattle in southwestern Kansas and northeastern New Mexico; deaths of wild birds and domestic cats were also observed within affected sites in the Texas panhandle. In >1 dairy farms in Texas, deaths occurred in domestic cats fed raw colostrum and milk from sick cows that were in the hospital parlor. Antemortem clinical signs in affected cats were depressed mental state, stiff body movements, ataxia, blindness, circling, and copious oculonasal discharge. Neurologic exams of affected cats revealed the absence of menace reflexes and pupillary light responses with a weak blink response.

(SNIP)

Discussion

This case series differs from most previous reports of IAV infection in bovids, which indicated cattle were inapparently infected or resistant to infection (9). We describe an H5N1 strain of IAV in dairy cattle that resulted in apparent systemic illness, reduced milk production, and abundant virus shedding in milk. The magnitude of this finding is further emphasized by the high death rate (≈50%) of cats on farm premises that were fed raw colostrum and milk from affected cows; clinical disease and lesions developed that were consistent with previous reports of H5N1 infection in cats presumably derived from consuming infected wild birds (10–12). 

Although exposure to and consumption of dead wild birds cannot be completely ruled out for the cats described in this report, the known consumption of unpasteurized milk and colostrum from infected cows and the high amount of virus nucleic acid within the milk make milk and colostrum consumption a likely route of exposure. 

Therefore, our findings suggest cross-species mammal-to-mammal transmission of HPAI H5N1 virus and raise new concerns regarding the potential for virus spread within mammal populations.

Horizontal transmission of HPAI H5N1 virus has been previously demonstrated in experimentally infected cats (13) and ferrets (14) and is suspected to account for large dieoffs observed during natural outbreaks in mink (15) and sea lions (16). Future experimental studies of HPAI H5N1 virus in dairy cattle should seek to confirm cross-species transmission to cats and potentially other mammals.

(SNIP)

The susceptibility of domestic cats to HPAI H5N1 is well-documented globally (10–12,25–28), and infection often results in neurologic signs in affected felids and other terrestrial mammals (4). Most cases in cats result from consuming infected wild birds or contaminated poultry products (12,27). The incubation period in cats is short; clinical disease is often observed 2–3 days after infection (28). Brain tissue has been suggested as the best diagnostic sample to confirm HPAI virus infection in cats (10), and our results support that finding. One unique finding in the cats from this report is the presence of blindness and microscopic lesions of chorioretinitis. Those results suggest that further investigation into potential ocular manifestations of HPAI H5N1 virus infection in cats might be warranted.

The genomic sequencing and subsequent analysis of clinical samples from both bovine and feline sources provided considerable insights. The HA and NA sequences derived from both bovine milk and cat tissue samples from different Texas farms had a notable degree of similarity. Those findings strongly suggest a shared origin for the viruses detected in the dairy cattle and cat tissues.

Further research, case series investigations, and surveillance data are needed to better understand and inform measures to curtail the clinical effects, shedding, and spread of HPAI viruses among mammals. Although pasteurization of commercial milk mitigates risks for transmission to humans, a 2019 US consumer study showed that 4.4% of adults consumed raw milk >1 time during the previous year (29), indicating a need for public awareness of the potential presence of HPAI H5N1 viruses in raw milk.

Ingestion of feed contaminated with feces from wild birds infected with HPAI virus is presumed to be the most likely initial source of infection in the dairy farms. Although the exact source of the virus is unknown, migratory birds (Anseriformes and Charadriiformes) are likely sources because the Texas panhandle region lies in the Central Flyway, and those birds are the main natural reservoir for avian influenza viruses (30). HPAI H5N1 viruses are well adapted to domestic ducks and geese, and ducks appear to be a major reservoir (31); however, terns have also emerged as an important source of virus spread (32). The mode of transmission among infected cattle is also unknown; however, horizontal transmission has been suggested because disease developed in resident cattle herds in Michigan, Idaho, and Ohio farms that received infected cattle from the affected regions, and those cattle tested positive for HPAI H5N1 (33). Experimental studies are needed to decipher the transmission routes and pathogenesis (e.g., replication sites and movement) of the virus within infected cattle.

In conclusion, we showed that dairy cattle are susceptible to infection with HPAI H5N1 virus and can shed virus in milk and, therefore, might potentially transmit infection to other mammals via unpasteurized milk. A reduction in milk production and vague systemic illness were the most commonly reported clinical signs in affected cows, but neurologic signs and death rapidly developed in affected domestic cats. 

HPAI virus infection should be considered in dairy cattle when an unexpected and unexplained abrupt drop in feed intake and milk production occurs and for cats when rapid onset of neurologic signs and blindness develop. The recurring nature of global HPAI H5N1 virus outbreaks and detection of spillover events in a broad host range is concerning and suggests increasing virus adaptation in mammals. Surveillance of HPAI viruses in domestic production animals, including cattle, is needed to elucidate influenza virus evolution and ecology and prevent cross-species transmission.

Dr. Burrough is a professor and diagnostic pathologist at the Iowa State University College of Veterinary Medicine and Veterinary Diagnostic Laboratory. His research focuses on infectious diseases of livestock with an emphasis on swine.

Since 2020 we've seen increased HPAI H5Nx spillover into mammalian species, with many displaying severe neurological symptoms prior to death.

Travel Med. & Inf. Dis.: Pacific and Atlantic Sea Lion Mortality Caused by HPAI A(H5N1) in South America

Emerging Microbes & Inf.: Neurotropic HPAI H5N1 Viruses with Mammalian Adaptive Mutations in Free-living Mesocarnivores in Canada 

EID Journal: HPAI A(H5N1) Virus Clade 2.3.4.4b Infections in Wild Terrestrial Mammals, United States, 2022

While HPAI H5N1 has most often been a respiratory infection in humans, we have seen several case reports over the years describing severe neurological presentations.   

A 2009 PNAS study (Highly pathogenic H5N1 influenza virus can enter the central nervous system and induce neuroinflammation and neurodegeneration) found that the H5N1 virus was highly neurotropic in lab mice, and in the words of the authors `could initiate CNS disorders of protein aggregation including Parkinson's and Alzheimer's diseases’.

Six years later - following the 2014 death of the first imported H5N1 case in Canada - we saw a study (see CJ ID & MM: Case Study Of A Neurotropic H5N1 Infection - Canada), where the authors wrote: `These reports suggest the H5N1 virus is becoming more neurologically virulent and adapting to mammals'. 

In a 2015 Scientific Reports study on the genetics of the H5N1 clade 2.3.2.1c virus - Highly Pathogenic Avian Influenza A(H5N1) Virus Struck Migratory Birds in China in 2015 – the authors described its neurotropic effects, and warned that it could pose a ` . . . significant threat to humans if these viruses develop the ability to bind human-type receptors more effectively.'

While clinical details of many H5Nx human infections have gone unpublished, almost 18 months ago, in Clinical Features of the First Critical Case of Acute Encephalitis Caused by Avian Influenza A (H5N6) Virus, we learned of the severe neurological impact of the virus on a 6 year-old girl in China.  

While certainly not the typical presentation of H5Nx infection in humans, the authors wrote:

In view of the fact that the clinical manifestations of this novel H5N6 reassortant are acute encephalitis, rather than previous respiratory symptoms, once these reassortants obtained the ability of human-to-human transmission through reassortment or mutations, it will bring great health threat for humans.

While we can't really know what H5Nx pandemic would look like, last September we looked at a study (see Cell: The Neuropathogenesis of HPAI H5Nx Viruses in Mammalian Species Including Humans) that warned:

• Highly pathogenic avian influenza (HPAI) H5Nx viruses can cause neurological complications in many mammalian species, including humans.
• Neurological disease induced by HPAI H5Nx viruses in mammals can manifest without clinical respiratory disease.
• HPAI H5Nx viruses are more neuropathogenic than other influenza A viruses in mammals.
• Severe neurological disease in mammals is related to the neuroinvasive and neurotropic potential of HPAI H5Nx viruses.
• Cranial nerves, especially the olfactory nerve, are important routes of neuroinvasion for HPAI H5Nx viruses.
• HPAI H5Nx viruses have a broad neurotropic potential and can efficiently infect and replicate in various CNS cell types.
• Vaccination and/or antiviral therapy might in part prevent neuroinvasion and neurological disease following HPAI H5Nx virus infection, although comprehensive studies in this area are lacking.

But even without a neurological component, HPAI H5Nx has an impressive record of causing severe illness and death, and is not to be taken lightly. 

  

Other Potential Flash Points For Pandemic Influenza

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While the world is understandably focused on the discovery of HPAI H5N1 in U.S. cattle, it is worth remembering that this isn't the only potential flash point for avian flu.  A few (of many) examples include:

• In October of 2022, we learned of a mink farm in Spain where H5N1 had spread rapidly, generating rare mutations (see Eurosurveillance: HPAI A(H5N1) Virus Infection in Farmed Minks, Spain, October 2022), which resulted in a new risk analysis from the CDC.
• Last summer and fall we were focused on outbreaks in cats in Poland and South Korea, along with dozens of fur farms infected with H5N1 in Finland.
• Also last summer, in PNAS: Mink Farming Poses Risks for Future Viral Pandemics, we looked at an excellent opinion piece penned by two well known virologists from the UK (Professor Wendy Barclay & Tom Peacock) on why fur farms - and mink farms in particular - are high risk venues for flu.
• Over the past year we've seen reports of tens of thousands of marine mammals killed by H5N1 (see here, here, and here) in North America, South America, and Europe.

While only a small percentage are ever reported, there are spillovers into mammals occurring all over the world (see USDA map below).  Most are presumed to be dead-end infections, but we've seen the impact of California Condors feeding on infected carrion. 

Not only are there several clades of H5N1 in circulation around the world, there are literally dozens of genotypes within these clades. And within each genotype, there may be variants.  Meaning we aren't dealing with one threat, but rather an array of similar viruses all pursuing different evolutionary paths. 

If we get lucky, and HPAI H5N1 somehow fizzles in cattle, we aren't in the clear.  HPAI H5Nx is firmly entrenched in birds around the globe, expanding its mammalian host range, and it is continually running GOF (Gain of Function) experiments. 

Since the HPAI in cattle story has overshadowed nearly everything else, today a couple of recent studies showing the expanding diversity, and growing capabilities, of HPAI H5N1 outside of the United States.  

First stop, a report in  Virologica Sinica on the growing threat from H5 clade 2.3.4.4b viruses in China as they transitioned from H5N8 to H5N1 during 2021 and 2022.

Evolutionary dynamics and comparative pathogenicity of clade 2.3.4.4b H5 subtype avian influenza viruses, China, 2021–2022
Siru Lin a 1, Junhong Chen a 1, Ke Li d 1, Yang Liu a 1, Siyuan Fu a, Shumin Xie a, Aimin Zha a, Aiguo Xin a, Xinyu Han a, Yuting Shi a, Lingyu Xu a, Ming Liao a b c, Weixin Jia a b cShow more

https://doi.org/10.1016/j.virs.2024.04.004Get rights and content
Under a Creative Commons license
 

Highlights

• The evolutionary and biological properties of major pandemic H5 AIVs isolated from China in 2021–2022 were analyzed.
• H5Nx isolates originated from H5N8, with high evolutionary rate in H5N1 and H5N8 and a declining trend in H5N6 in 2015–2022.
• HI assay suggests that A(H5N1) viruses may be antigenically distinct from the circulating H5N6 and H5N8 strains.
• Representative viruses of three H5 AIVs isolates exhibit variable tissue tropism and pathogenicity in mice.
• A(H5N1) viruses have a higher risk of emergence in the future.

Abstract

The recent concurrent emergence of H5N1, H5N6, and H5N8 avian influenza viruses (AIVs) has caused significant avian mortality globally. Since 2020, frequent human-animal interactions have been documented. To gain insight into the novel H5 subtype AIVs (i.e., H5N1, H5N6 and H5N8), we conducted a comparative analysis on phylogenetic evolutionary and biological properties of H5 subtype AIVs strains isolated from China between January 2021 and September 2022. 

Phylogenetic analysis revealed that the 41 H5Nx strains belonged to clade 2.3.4.4b, with 13 related to H5N1, 19 to H5N6, and 9 to H5N8. The genetic relatedness analysis based on global 2.3.4.4b viruses showed that all the viruses described in this study was likely originated from H5N8, exhibiting a heterogeneous evolutionary history between H5N1 and H5N6 during 2015–2022 worldwide. 

In this context, we further estimated that H5N1, characterized by higher evolutionary rates in 2021–2022 and more sites under positive selection pressure in 2015–2022. The antigenic profiles of novel H5N1 and H5N6 exhibited notable variations. Further hemagglutination inhibition assay suggest that some A(H5N1) viruses may be antigenically distinct from the circulating H5N6 and H5N8 strains.

Mammalian challenge assays demonstrated that the H5N8 virus (21GD001_H5N8) displayed the highest pathogenicity in mice, followed by the H5N1 virus (B1557_H5N1) and then the H5N6 virus (220086_H5N6), suggesting a heterogeneous virulence profile of H5 AIVs in the mammalian hosts.

Based on the above results, we consider that A(H5N1) viruses have a higher risk of emergence in the future. Collectively, these findings unveil a new landscape of different evolutionary history and biological characteristics of novel H5 AIVs in clade 2.3.4.4b, contributing to a better understanding for designing more effective strategies for the prevention and control of novel H5 AIVs.

Half a world away, in South America, researchers tracking the spread of HPAI H5N1 through marine mammals continue to find mammalian adaptations, and have reasons to believe mammal-to-mammal transmission may be occurring. 

Highly pathogenic avian influenza H5N1 virus infections in pinnipeds and seabirds in Uruguay: implications for bird-mammal transmission in South America

Gonzalo Tomás, Ana Marandino, Yanina Panzera, Sirley Rodríguez, Gabriel Luz Wallau, Filipe Zimmer Dezordi, Ramiro Pérez, Lucía Bassetti, Raúl Negro, Joaquín Williman ... Show more

Virus Evolution, veae031, https://doi.org/10.1093/ve/veae031

Published:13 April 2024 Article history

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ABSTRACT

The highly pathogenic avian influenza viruses of the clade 2.3.4.4b have caused unprecedented deaths in South American wild birds, poultry, and marine mammals. In September 2023, pinnipeds and seabirds appeared dead on the Uruguayan Atlantic coast.

Sixteen influenza virus strains were characterized by real-time reverse transcription PCR and genome sequencing in samples from sea lions (Otaria flavescens), fur seals (Arctocephalus australis), and terns (Sterna hirundinacea). Phylogenetic and ancestral reconstruction analysis showed that these strains have pinnipeds as the most likely ancestral host, representing a recent introduction of the clade 2.3.4.4b in Uruguay.

The Uruguayan and closely related strains from Peru (sea lions) and Chile (sea lions and a human case) carry mammalian adaptative residues 591K and 701N in the viral polymerase basic protein 2 (PB2). Our findings suggest that the clade 2.3.4.4b strains in South America may have spread from mammals to mammals and seabirds, revealing a new transmission route.

          (Continue . . . .)

A reminder that the rapid growth and evolution of HPAI H5 was a threat long before it was detected in American cattle, and will remain so, even if we dodge this bovine bullet.