Sci Repts: Blowflies As Potential Vectors Of Avian Influenza

 

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A little over 17 years ago in this blog - in Cats and Dogs and Flies, Oh My! - we looked at a 2006 study (see Detection and isolation of highly pathogenic H5N1 avian influenza A viruses from blow flies collected in the vicinity of an infected poultry farm in Kyoto, Japan, 2004 by Kyoko Sawabe et al.) that found that at least 2 types of flies could carry the H5N1 virus.

While flies weren't believed infected with the virus, they could ingest (and subsequently regurgitate or defecate) infected material, or potentially spread it mechanically by their feet or body, thereby spreading the disease.

The authors wrote:

The H5 influenza A virus genes were detected from the intestinal organs, crop, and gut of the two blow fly species, Calliphora nigribarbis and Aldrichina grahami, by reverse transcription-polymerase chain reaction for the matrix protein (M) and hemagglutinin (HA) genes. The HA gene encoding multiple basic amino acids at the HA cleavage site indicated that this virus is a highly pathogenic strain. . . . . Our results suggest it is possible that blow flies could become a mechanical transmitter of H5N1 influenza virus.

Four years later Dr. Sawabe and his team would publish (Blow Flies Were One of the Possible Candidates for Transmission of Highly Pathogenic H5N1 Avian Influenza Virus during the 2004 Outbreaks in Japan) where they conclude:

We have suggested here that blow flies are likely candidates for mechanical transmission of HPAI because of their ecological and physiological characteristics as reviewed here. In fact, blow flies have already been recognized as important vectors for mechanical transmission of several serious infectious diseases, that is, poxvirus [28], rabbit hemorrhagic disease [29], and paratuberculosis [30]. Recently, it has been reported that the H5N1 viral gene was detected in house flies [31] and engorged mosquitoes [32]. 

Last December, we looked at a brief synopsis of an upcoming study (see Kyushu University: The Return Of The Fly), which revisited this topic; testing blowflies for HPAI at the national wildlife reserve in Izumi City, Kagoshima Prefecture, which is the overwintering home for thousands of endangered Hooded Cranes. 

That study got a lot of attention in the Japanese press, with Dr. Ryusuke Fujita quoted as saying,

`Until now, countermeasures have been taken based on the assumption that small animals and people will bring the virus. There was no improvement, and when we suspected it was a fly, a virus was detected.

We will conduct a more detailed investigation, take measures to prevent fly intrusion, and verify their effectiveness."

Given that American dairy farmers are now having to worry about HPAI biosecurity, and flies tend to be abundant around both cows and poultry, this research is certainly timely. We now have the full, English language version, which was published today in Science Reports. 

I've only posted some excerpts, so follow the link to read it in its entirety. 

Article
Open access
Published: 04 May 2024

Blowflies are potential vector for avian influenza virus at enzootic area in Japan
Ryosuke Fujita, Takuji Tachi, Masato Hino, Kosuke Nagata, Masahiro Saiki, Mizue Inumaru, Yukiko Higa, Kentaro Itokawa, Nozomi Uemura, Ryo Matsumura, Izumi Kai, Kyoko Sawabe, Mutsuo Kobayashi, Haruhiko Isawa, Takahiro Kusakabe, Kazunori Matsuo & Shinji Kasai

Scientific Reports volume 14, Article number: 10285 (2024) Cite this article

Abstract

High pathogenicity avian influenza (HPAI) poses a significant threat to both domestic and wild birds globally. The avian influenza virus, known for environmental contamination and subsequent oral infection in birds, necessitates careful consideration of alternative introduction routes during HPAI outbreaks.

This study focuses on blowflies (genus Calliphora), in particular Calliphora nigribarbis, attracted to decaying animals and feces, which migrate to lowland areas of Japan from northern or mountainous regions in early winter, coinciding with HPAI season. Our investigation aims to delineate the role of blowflies as HPAI vectors by conducting a virus prevalence survey in a wild bird HPAI-enzootic area. 

In December 2022, 648 Calliphora nigribarbis were collected. Influenza virus RT-PCR testing identified 14 virus-positive samples (2.2% prevalence), with the highest occurrence observed near the crane colony (14.9%). Subtyping revealed the presence of H5N1 and HxN1 in some samples. Subsequent collections in December 2023 identified one HPAI virus-positive specimen from 608 collected flies in total, underscoring the potential involvement of blowflies in HPAI transmission.

Our observations suggest C. nigribarbis may acquire the HPAI virus from deceased wild birds directly or from fecal materials from infected birds, highlighting the need to add blowflies as a target of HPAI vector control.

          (SNIP)

Blowflies represent a potential vector of HPAI, particularly in enzootic regions. The effectiveness of virus detection from flies relies heavily on the prevalence of infected and deceased wild birds. C. nigribarbis is widespread in human-populated areas across Japan, including semi-rural regions with poultry farms.

Like other insects, C. nigribarbis intermittently disperses its feces, leading to environmental contamination. In this study, we focused on C. nigribarbis because it was the dominant blowfly species in our study field and the season, but we could not exclude the contribution of other necrophagous blowflies in HPAI propagation, especially in geographical areas.

Although the extent of blowfly intrusion into poultry houses and their role as infection sources has not been extensively studied, it is important to pay equal attention not only to the intrusion of small animals or birds but also to the entry of flies into poultry houses15. Unfortunately, due to the lack of comparable data on virus prevalence in each vector and their invasion rates into poultry farms, we could not determine which vector poses a higher risk for HPAI transmission on poultry farms.

Unlike house flies, which often originate within poultry houses and are visibly active, C. nigribarbis does not exhibit such behavior. While they may appear elusive, they can be readily captured in winter using baits or traps. Considering the possible involvement of blowflies in HPAI transmission, it would be advisable to implement fly control measures in poultry settings, such as utilizing fine mesh nets, fly traps, or insecticides.

(Continue . . .)

 

Gen. Virology: Iceland: An Underestimated Hub for the Spread of HPAI Viruses in the North Atlantic

 

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Despite nearly 30 years of dealing with H5N1, we have an unfortunate habit of underestimating what the HPAI H5Nx virus is capable of.  In the early 2000s, the virus was believed to be restricted to Southeast Asia, since the nearly everybody `knew' that sick migratory birds don't fly. 

Even after the virus winged its way to Europe, the Middle East, and Africa (following the 2005 Qinghai Lake event ) many experts still doubted the ability of the virus to spread efficiently via migratory birds (see 2014's Bird Flu Spread: The Flyway Or The Highway?).

This peculiar bit of self-delusion persisted until December of 2014 when HPAI H5Nx crossed the relatively narrow Bering Straits and began spreading across Canada and the United States, sparking the biggest avian epizootic (to that time) in North American history.

 

By the time it finally burned itself out in the summer of 2015, avian flu had affected 15 states and several provinces in Canada, and resulted in the loss of over 50 million commercially raised birds (see map above).

Luckily, HPAI wasn't sustained in North American birds (see PNAS: The Enigma Of Disappearing HPAI H5 In North American Migratory Waterfowl) and the outbreak did not resume the following fall.

While another Pacific crossing was always possible, most (but not all) experts believed the Atlantic was simply too vast to allow the virus to spread from Europe. A few contrarian studies from the last decade, with an emphasis on the potential role of both  Iceland and Greenland, included:

PLoS One: North Atlantic Flyways Provide Opportunities For Spread Of Avian Influenza Viruses

H5Nx: Why North America Must Remain Alert

Iceland Warns On Bird Flu 

In late 2021, the inevitable happened, and HPAI H5 arrived in Eastern Canada and Western Canada via two different routes; across the Pacific and the Atlantic (Multiple Introductions of H5 HPAI Viruses into Canada Via both East Asia-Australasia/Pacific & Atlantic Flyways).

Unlike older versions of HPAI H5, this reinvented avian flu was able to persist in a wide array of avian (and a few mammalian) hosts. Meaning it no longer requires re-introduction of the virus every year.  

While we've seen no evidence of west-to-east spread of North American HPAI viruses to Europe, we have seen evidence that some North American LPAI viruses  have crossed over into Asia.

According to the Icelandic Institute of Natural History, birds from both Canada and Europe regularly visit Iceland, making an exchange of avian viruses plausible (see below).

A total of 75 bird species regularly nest in Iceland, and a number of others occasionally choose to breed here, although they have been slow to establish themselves permanently. Some Arctic birds spend the winter in Iceland but nest at more northerly latitudes. Iceland is an extremely important stopover for geese and waders migrating between breeding grounds in Greenland and Canada and wintering grounds in Europe.

In late 2022, in Iceland as Stepping Stone for Spread of Highly Pathogenic Avian Influenza Virus between Europe and North America, we looked at an EID Journal Synopsis on the role Iceland, and migratory birds, played in introducing HPAI H5Nx to the North America. 

All of which brings us to a new study, by many of the same authors, that identifies Iceland as a likely, but underestimated, hub for the intercontinental spread of HPAI viruses. 

I've only included a few excerpts, so follow the link to read the full report. 

Iceland: an underestimated hub for the spread of high-pathogenicity avian influenza viruses in the North Atlantic

Ann Kathrin Ahrens1​, Stefán Ragnar Jónsson2​, Vilhjálmur Svansson2​, Brigitte Brugger3​, Martin Beer1​, Timm C. Harder1​ and Anne Pohlmann1​
 
Published: 02 May 2024 https://doi.org/10.1099/jgv.0.001985

High-pathogenicity avian influenza viruses (HPAIVs) of the goose/Guangdong lineage are enzootically circulating in wild bird populations worldwide. This increases the risk of entry into poultry production and spill-over to mammalian species, including humans. Better understanding of the ecological and epizootiological networks of these viruses is essential to optimize mitigation measures. 

Based on full genome sequences of 26 HPAIV samples from Iceland, which were collected between spring and autumn 2022, as well as 1 sample from the 2023 summer period, we show that 3 different genotypes of HPAIV H5N1 clade 2.3.4.4b were circulating within the wild bird population in Iceland in 2022.

Furthermore, in 2023 we observed a novel introduction of HPAIV H5N5 of the same clade to Iceland. The data support the role of Iceland as an utmost northwestern distribution area in Europe that might act also as a potential bridging point for intercontinental spread of HPAIV across the North Atlantic.

         (SNIP)

 

In conclusion, our data confirm that Iceland is involved in the circulation of clade 2.3.4.4b HPAI H5N1 viruses both as a sink for viruses from continental European and as a source for North America. It is therefore reasonable to assume that Iceland could act as a gateway for avian influenza in the transatlantic transmission pathway.

However, to date there is no evidence of west-to-east transmission.

Nevertheless, Iceland remains an important sampling area for the detection of novel avian influenza incursions. Iceland also remains a focal point for ongoing monitoring with regard to the potential impact of the HPAI epidemic in seabirds on biodiversity and the protection of endangered species.

         (Continue . . .).

While HPAI H5 has yet to crack the code on how to infect and spread efficiently in humans, it continues to exceed most other expectations.

Our focus today is understandably on the recent spillover into American cattle, but we need to remember that the virus is following hundreds of divergent evolutionary pathways around the globe, most of which are occurring outside of our view. 

Most will result in failure, but the virus only has to get `lucky' once.  

Which is why we need to cast a wide net, be prepared for surprises, and the strong likelihood that some will come from out of left field. 

Upcoming WHO EPI-WIN Webinar (May 6th) on Public Health Risk of H5N1 in Cattle

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On Monday, May 6th,  the World Health Organization will hold a new live Epi-Win Webinar on the public health risk of H5N1 recently found in American Cattle. A little over a year ago they held a webinar on H5N1 which you can view at this link. 

Although this is a rapidly evolving situation, and everyone is working with limited data, this should be an illuminating presentation. 

The time of the webcast (13:00 CET) works out to 7am EDT in the United States. Registration is required for the Zoom call, but the video will be posted on the WHO's YouTube Channel sometime after the broadcast.

WHO EPI-WIN Webinar: Public health risk of avian influenza A(H5N1) detected recently in dairy cattle
6 May 2024 13:00 – 14:00 CET

Background:

The highly pathogenic avian influenza (HPAI) A(H5N1) clade of viruses which arose in 2020 from previously circulating influenza A(H5Nx) viruses led to unprecedented numbers of deaths in wild birds and in domestic poultry. It spread globally and has been reported in non-avian species including, and most recently in dairy cattle. This has led to widespread concern. On 24th April 2024, WHO, FAO and WOAH published a joint risk assessment. This EPI-WIN webinar will explain the public health risks of the recent avian influenza detected in dairy cattle.

Tentative agenda:


Moderator: Dr Wenqing Zhang, Head, Global Influenza Programme (GIP), WHO
Opening remarks: Dr Maria Van Kerkhove, Director a.i., Epidemic and Pandemic Prevention and Preparedness (EPP), WHO

Speakers:
Dr Aspen Hammond, Technical Officer, GIP
Dr Moez Sanaa, Unit Head, Standard and Scientific Advice on Food Nutrition, WHO

Panel:
Dr Charles(Todd) Davis, CDC, USA
Dr Magdi Samaan, GIP, WHO
Dr David Swayne, Influenza Veterinarian, USA
Dr Mia Torchetti, USDA, USA
Dr Richard Webby, WHO CC, St Jude Children’s Hospital, USA


To register, please click here.

Participants will be able to submit questions during the webinar by using Zoom's "Q&A" feature. You may also submit questions in advance by sending them to epi-win@who.int.

CDC Update On Monitoring People For H5 Infection

 

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On a number of occasions we've discussed how difficult it would be for even a well-equipped western nation to monitor for - and detect - novel influenza cases in the community.    

A year ago, in UK Novel Flu Surveillance: Quantifying TTD, health authorities estimated the TTD (Time To Detect) a novel H5N1 virus in the community - with aggressive testing - to take several weeks. 

We are now more than a month since the first human H5N1 infection linked to infected dairy cattle was reported (see CDC Statement & Risk Assessment On The Texas H5N1 Case) - and instead of an aggressive and widespread testing testing campaign - only about 30 people appear to have been tested for H5 over the past 5 weeks. 

Today, Helen Branswell of STAT news has an extensive and illuminating interview with Vivien Dugan, Director of the CDC’s influenza division, on some of the challenges that agency is facing, including a lack of cooperation by states where HPAI outbreaks have been reported. 

According to Dugan, the CDC doesn't have the authority to go into a state without an invite. And so far, no state has requested their assistance.  

Some of this was telegraphed last week. In An HPAI Cattle Roundup - April 25th we looked anecdotal reports (by a veterinarian) of numerous `sick people' working in dairy farms next to sick cows. 

During a joint agency teleconference 9 days ago, CDC Deputy Director Nirav Shah  acknowledged there have been obstacles to testing farm workers. 

“We’ve had a diversity of levels of engagement with farms,” Shah said. “These situations are challenging. There may be owners that are reluctant to work with public health to say nothing of individual workers who may be reluctant to sit down with somebody who identifies themself as being from the government in some way.”

Mike Watson from APHIS confirmed that the USDA had `met some resistance' from some farmers with infected cows, and they are unable to determine whether orders to discard infected milk are being strictly followed. 

If the point is to keep a potentially bad situation from getting worse, this is not the way to go about it.  I have to believe the frustration levels at the CDC and APHIS over this lack of cooperation are running sky high.

First, the weekly update from the CDC, after which I'll have a postscript.

How CDC is monitoring influenza data to better understand the current avian influenza A (H5N1) situation in people
Español | Other Languages Print

Updated May 3, 2024

Weekly Snapshot for Week Ending April 27, 2024

CDC influenza (flu) surveillance systems show no indicators of unusual influenza activity in people, including avian influenza A(H5N1).

This page provides information on how CDC systems that monitor national, state, and local level influenza data are being used during the current avian influenza A(H5N1) situation

• Influenza virus and illness activity are monitored year-round through a collaborative effort between CDC and many partners, including state, local, and territorial health departments; public health and clinical laboratories; clinics; and emergency departments.
• Human cases of novel influenza, which are human infections with non-human influenza A viruses that are different from currently spreading seasonal human influenza viruses, are nationally notifiable. Every identified case is investigated and reported to CDC.
• CDC is actively looking at multiple flu indicators during the current situation to monitor for influenza A(H5N1) viruses, including looking for spread of the virus to, or among people, in jurisdictions where the virus has been identified in people or animals.

          (Continue . . . )

While I'm not in the camp that believes the H5N1 virus is certain to spark a pandemic, it is high on my list of contenders.  We've certainly seen it threaten before, only to recede.  But this time it `feels' different, since we are seeing scores of mammalian species infected, and things could go from 0 to 60 in hurry. 

I have a hard time envisioning any novel flu scenario where a full-blown public health response and epidemiological investigation wouldn't be appropriate, so I'm at a loss to explain why this one should be treated any different. 

One thing is certain, we better hope we get lucky again and H5 fizzles.  Because we aren't anywhere nearly as well prepared for severe influenza pandemic as we need to be. 

Preprint: Virological Characteristics of the SARS-CoV-2 KP.2 variant

 

CDC Nowcast

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While COVID has taken a back seat to other infectious disease concerns the past few weeks, and rates of infection appear to be currently low in the United States, it continues to evolve into new, and potentially worrisome variants. 

Despite this ongoing evolution, over the past 2 years the world has intentionally dismantled the bulk of their global surveillance, testing, and reporting system in order to `move on' from the pandemic emergency (see No News Is . . . Now Commonplace).

The most recent WHO Update (Apr 12th) indicates:

Globally, the number of new cases decreased by 11% during the past 28-day period of 4-31 March 2024 compared to the previous 28-day period (5 February to 3 March 2024), with over two hundred and seven-five thousand new cases reported. The number of new deaths decreased by 41% as compared to the previous 28-day period, with over 4200 new fatalities reported

But these numbers are admittedly incomplete, with only about 20% of the world's nations still reporting hospitalizations and deaths, and the quality of that data is unknown. 

The latest CDC Nowcast map of the United States (see below) is blank.  Not enough samples were collected over the previous 2 weeks to generate a graphic, and while the Nowcast pegs the new KP.2 variant as the new leader in the United States, their estimate is unusually vague (range 12.9% - 42.1%).

This `don't test, don't tell' policy extends far beyond COVID, with novel flu infections in some countries often going weeks or months before being reported (assuming they are reported at all).   

A year ago, in Lancet Preprint: National Surveillance for Novel Diseases - A Systematic Analysis of 195 Countries, we looked at an independent analysis which suggested that many nations have substantially overstated their compliance with the 2005 IHR regulations, and that surveillance and reporting are far less robust than advertised.

It is against this backdrop that we look at a recent preprint from the Sato Lab on the rapidly emerging KP.2 variant, which appears to have - compared to the JN.1 variant - increased transmissibility and immune resistance.

This variant has been dubbed a FLiRT variant, due to two substitutions (S:F456L and S:R346T), which appear to give it an epidemiological advantage over earlier variants.  

First, the link and Abstract from the preprint, after which I'll have more.

Virological characteristics of the SARS-CoV-2 KP.2 variant

Yu Kaku, Keiya Uriu, Yusuke Kosugi, Kaho Okumura, Daichi Yamasoba, Yoshifumi Uwamino, Jin Kuramochi, Kenji Sadamasu, Kazuhisa Yoshimura, Hiroyuki Asakura, Mami Nagashima, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Jumpei Ito, Kei Sato
doi: https://doi.org/10.1101/2024.04.24.590786

Preview PDF

Abstract

The JN.1 variant (BA.2.86.1.1), arising from BA.2.86(.1) with the S:L455S substitution, exhibited increased fitness and outcompeted the previous dominant XBB lineage by the biggening of 2024. JN.1 subsequently diversified, leading to the emergence of descendants with spike (S) protein substitutions such as S:R346T and S:F456L.

Particularly, the KP.2 (JN.1.11.1.2) variant, a descendant of JN.1 bearing both S:R346T and S:F456L, is rapidly spreading in multiple regions as of April 2024.

Here, we investigated the virological properties of KP.2. KP.2 has three substitutions in the S protein including the two above and additional one substitution in non-S protein compared with JN.1. We estimated the relative effective reproduction number (Re) of KP.2 based on the genome surveillance data from the USA, United Kingdom, and Canada where >30 sequences of KP.2 has been reported, using a Bayesian multinomial logistic model.

 

The Re of KP.2 is 1.22-, 1.32-, and 1.26-times higher than that of JN.1 in USA, United Kingdom, and Canada, respectively. These results suggest that KP.2 has higher viral fitness and potentially becomes the predominant lineage worldwide. Indeed, as of the beginning of April 2024, the estimated variant frequency of KP.2 has already reached 20% in United Kingdom.

The pseudovirus assay showed that the infectivity of KP.2 is significantly (10.5-fold) lower than that of JN.1. We then performed a neutralization assay using monovalent XBB.1.5 vaccine sera and breakthrough infection (BTI) sera with XBB.1.5, EG.5, HK.3 and JN.1 infections. In all cases, the 50% neutralization titer (NT50) against KP.2 was significantly lower than that against JN.1.

Particularly, KP.2 shows the most significant resistance to the sera of monovalent XBB.1.5 vaccinee without infection (3.1-fold) as well as those who with infection (1.8-fold). Altogether, these results suggest that the increased immune resistance ability of KP.2 partially contributes to the higher Re more than previous variants including JN.1.

         (Continue . . . )

KP.2 appears poised to become the dominant COVID variant in the short-term, but whether it will spark more serious illness - or a significant summer wave - is unknown.  

If we had better global surveillance and reporting, we might know more  . . .  but we don't.

Ignorance may be bliss, but that happy state of affairs only lasts until we get blindsided by the next global health crisis.  A least, when that  inevitably happens, our leaders will be able to honestly say:

`Nobody saw it coming.'

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.