USDA: Colorado 9th State To Report HPAI H5 In Cattle - New Guidance Documents

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This afternoon the USDA's (HPAI) Detections in Livestock website added Colorado to the list of states (n=9) reporting confirmed HPAI in cattle, raising the total number of confirmed outbreaks to 34. 

Despite multiple reports of labs finding a significant percentage of contaminated milk products on store shelves, this is only the 2nd herd confirmation over the past 7 days.  

Testing - except prior to interstate transport - remains voluntary, and reports on Wednesday's CDC/HHS/USDA teleconference indicated that the USDA has seen some resistance to testing by members of the dairy industry.  

Today the USDA released two new updated  guidance documents:

4/26/24-APHIS Requirements and Recommendations for Highly Pathogenic Avian Influenza (HPAI) H5N1 Virus in Livestock For State Animal Health Officials, Accredited Veterinarians and Producers 

 4/26/24-Testing Guidance for Labs for Influenza A in Livestock

In addition to testing cattle, the second document recommends:

Testing Wildlife

Sampling dead and dying birds as well as mammals particularly around affected premises is encouraged. Contact the local wildlife agency or call USDA Wildlife Services at 1-866-4USDA-WS (or 1-866-487-3297). They can assist with identification and sampling. Birds are sampled by collecting oropharyngeal and cloacal swabs.

• Recommended samples from mammals include brain (preferred if clinically affected) or oral, nasal, or rectal swabs. After sampling, swabs should be placed in MTM or BHI.
• Wild bird mortality events in and around affected premises should be reported to the State Wildlife Agency or APHIS Wildlife Services at 1-866-4USDA-WS.
• Wildlife samples should be designated as “other” with “wildlife” specified on laboratory submission forms.
• Apparently healthy wildlife should not be euthanized solely for sampling. Nuisance wildlife removed with the appropriate State and Federal permits can be sampled with appropriate coordination with your local WS office or State Wildlife Agency.

Testng Sick or Dead Cats or Other Companion Animals near Affected Premises

Cats are particularly suspectable to H5N1 2.3.4.4b viruses; cats with neurologic disease and dead cats on affected dairies are widely reported.

• Brain swabs from affected cats (or whole carcasses) can be submited to NAHLN laboratories.
• Other domestic animals associated with affected farms showing illness should be tested. Contact your NALHN laboratory for consultation.

Joint FAO/WHO/WOAH Preliminary Assessment of Recent Influenza A(H5N1) Viruses

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This afternoon the WHO, FAO and WOAH have published a joint 8-page preliminary assessment of HPAI H5N1 viruses which have recently spilled over into cattle in the United States, along with many other mammals around the globe.

This is obviously a rapidly evolving situation, and several key findings have been reported since this assessment (dated April 23rd) was generated (see FDA Statement On Investigation Of H5N1 Virus Particles Detected In Finished Milk).

Today's joint assessment pegs the overall public health risk posed by A(H5N1) to be low, but is low-to-moderate for those with exposure to infected birds, animals, or contaminated environments.

First the overview, followed by some excerpts from the full document.  Follow the link to read it in its entirety. 

Overview

During 2020, highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b viruses arose from previously circulating influenza A(H5Nx) viruses and spread predominantly via migratory birds to many parts of Africa, Asia and Europe. The epizootic has led to unprecedented numbers of deaths in wild birds and caused outbreaks in domestic poultry. In late 2021, these viruses crossed to North America and subsequently South America in October 2022.

Additionally, globally, there have been increased detections of A(H5N1) viruses in non-avian species including wild and domestic (including companion and farmed) terrestrial and marine mammals and, more recently in goats and dairy cattle in the United States of America. 

Since the beginning of 2021, 28 detections of A(H5N1) in humans have been reported to WHO, including a case who had exposure to dairy cattle presumed to be infected with A(H5N1) virus. Of these human cases, where the haemagglutinin (HA) H5 clade is known, 13 have been caused by clade 2.3.4.4b viruses. This joint FAO/WHO/WOAH risk assessment focuses on A(H5N1) viruses characterized since 2021 and assesses the public health risk as well as the risk of the virus spread among animals.

Joint FAO/WHO/WOAH preliminary assessment ofrecent influenza A(H5N1) viruses 

23 April 2024 

(Excerpts)

During 2020, highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b viruses arose from previously circulating influenza A(H5Nx) viruses and spread predominantly via migratory birds to many parts of Africa, Asia and Europe. The epizootic has led to unprecedented numbers of deaths in wild birds and caused outbreaks in domestic poultry. 

In late 2021, these viruses crossed to North America and subsequently South America in October 2022. Additionally, globally, there have been increased detections of A(H5N1) viruses in non-avian species including wild and domestic (including companion and farmed) terrestrial and marine mammals and, more recently in goats and dairy cattle in the United States of America. The majority, with some regional exceptions, of the HPAI A(H5N1) viruses characterized genetically since 2020 belong to the 2.3.4.4b clade. 

Since the beginning of 2021, 28 detections of A(H5N1) in humans have been reported to WHO, including a case who had exposure to dairy cattle presumed to be infected with A(H5N1) virus. Of these human cases, where the haemagglutinin (HA) H5 clade is known, 13 have been caused by clade 2.3.4.4b viruses.

This joint FAO/WHO/WOAH risk assessment focuses on A(H5N1) viruses characterized since 2021 and assesses the public health risk as well as the risk of the virus spread among animals. 

Infections in animals

Avian influenza A(H5N1) viruses, especially those of clade 2.3.4.4b, continue to diversify genetically and spread geographically. Since 2022, a broader range of wild bird species has been infected globally which has had deleterious ecological consequences and caused mass die-offs in some species. The situation with wild mammals is also worrying, with some species suffering significant mortality events. Additionally, ongoing circulation in wild and migratory birds and poultry has led to multiple separate incursions into wild carnivorous and scavenging mammals, domestic cats and dogs, and aquatic mammals in a number of countries. 

Spillover of clade 2.3.4.4b viruses from birds to mammals in the Americas and Europe have often resulted in severe infections with neurological signs in some mammals.1 In 2024, A(H5N1) viruses have been detected in neonatal goats on a single premises shared with poultry, and in dairy cattle in the USA. These circumstances have led to increased opportunities for viral reassortment generating new genotypes with varied clinical signs. 

          (SNIP)

Assessment of current risk to humans posed by influenza A(H5N1) viruses 

1. What is the global public health risk of additional human cases of infection with avian influenza A(H5N1) viruses? 

Despite the high number of A(H5N1) clade 2.3.4.4b outbreaks and detections in animals, and human exposures to the virus at the human-animal-environment interface, relatively few human infections have been reported to date. 

Of the 28 human cases of A(H5N1) detections reported since the beginning of 2021, all were sporadic infections in people exposed to A(H5N1) viruses through direct or indirect contact with infected birds, infected mammals or contaminated environments, such as live poultry markets or other premises with infected animals. Among these cases, there has been no reported human-to-human transmission.

While the viruses continue to be detected in animals and related environments, including milk, further sporadic human cases among exposed individuals are expected. Active case finding around reported human cases has been ongoing, and should continue, to determine if there is any human-to-human transmission.

 Individuals with activities that involve exposure to infected animals and/or contaminated environments are at higher risk and should take necessary precautions to prevent infection.18 

At the present time, based on available information, WHO assesses the overall public health risk posed by A(H5N1) to be low, and for those with exposure to infected birds or animals or contaminated environments, the risk of infection is considered low-to-moderate. This risk requires close monitoring and WHO and partners will continue to regularly assess and publish public health risk assessments for avian influenza. 

What is the likelihood of cattle-to-human transmission of influenza A(H5N1) viruses? 

Human cases have followed exposure to avian influenza-infected mammals for other influenza A subtypes, including A(H7N2)19 and A(H7N7)20, but only in a few instances. To date, there has been one reported case of infection with an influenza A(H5N1) virus in the USA in a person who worked at a dairy farm where cattle were presumed to be infected with A(H5N1) viruses. This case presented with conjunctivitis as the only symptom and has since recovered.

Infected lactating cattle have been reported to have high viral loads in their milk and thus could be a source of exposure to persons in close contact with them.21 The potential role of consumption and handling of milk and milk products in transmission, and the role of pasteurization in mitigating the potential risk, is currently being investigated. 

As long as people are in contact with infected cattle without appropriate personal protective equipment, there is a risk for human infections. The risk can be mitigated by measures to reduce exposure to the virus, such as the use of recommended personal protective equipment, appropriate personal hygiene and other risk-based biosecurity measures. 

3. What is the likelihood of human-to-human transmission of avian influenza A(H5N1) viruses? 

There has been no reported human-to-human transmission of A(H5N1) viruses since 2007, although there may be gaps in investigations. Prior to 2007, small clusters of A(H5) virus infections in humans were reported, including some involving health care workers, where limited human-to-human transmission could not be excluded; however, sustained human-to-human transmission was not reported.22

The A(H5N1) viruses detected in mammals, including in human cases, largely retain genomic and biological characteristics of avian influenza viruses and remain well-adapted to spread among birds. Except for in-host obtained amino acid mutations in polymerase proteins, there is still limited evidence for adaptation to mammals and humans even when transmission in mammals has been suspected.23 No changes in receptor binding tropism have been observed that would increase binding to receptors in the human upper respiratory tract which would increase transmission to and among people. Therefore, human-to-human transmission of the currently circulating A(H5N1) viruses is considered unlikely without further genetic changes in the virus.

WHO, together with the Food and Agriculture Organization of the United Nations (FAO) and the World Organisation for Animal Health (WOAH), continues to monitor these viruses and will re-assess the risk associated with the currently spreading A(H5N1) viruses as more information becomes available. Further antigenic characterization of A(H5N1) viruses, including in relation to the existing CVVs, and development of specific reagents are being prioritized at the WHO Collaborating Centres and Essential Regulatory Laboratories of GISRS in collaboration with animal health and veterinary sector colleagues.

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CDC Updated Technical Report On HPAI H5N1 Viruses

 

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The CDC has updated their Technical Report on HPAI H5N1 - last published in December - with details on recent H5N1 cases in Cambodia (n=5), Vietnam (n=1)and the United States (n=1), and the spread of HPAI H5N1 in American cattle. 

While the CDC still believes the overall risk to human health from HPAI H5N1 remains low for the general public: `. . . additional sporadic zoonotic infections are anticipated among people with exposures to infected sick or dead poultry, wild birds, or other infected animals.'

Due to its length, I've only included the summary and the Conclusions/Risk Assessment from a much longer report. Follow the link to read it in its entirety.

Technical Report: Highly Pathogenic Avian Influenza A(H5N1) Viruses
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Updated April 26, 2024

This report provides an update to the December 29, 2023, report to include seven new human cases (5 in Cambodia, 1 in the United States and 1 in Vietnam) and recent activity in wild birds, poultry and other animals, including the multi-state veterinary outbreak in U.S. dairy cattle, and updated information on monitoring for H5N1 virus infections in the United States. Even given these updates, CDC believes the overall risk to human health associated with the ongoing outbreaks of highly pathogenic avian influenza A(H5N1) viruses has not changed and remains low to the U.S. general public at this time.

Executive summary

A small number of sporadic human cases of highly pathogenic avian influenza (HPAI) A(H5N1) have been identified worldwide since 2022, amidst a panzootic of these viruses in wild birds and poultry. Nearly all human cases reported globally since 2022 were associated with poultry exposures, and no cases of human-to-human transmission of HPAI A(H5N1) virus have been identified. One human case of HPAI A(H5N1) virus infection in a farm worker reported in April 2024 in the United States and was attributed to exposure to presumptively infected dairy cattle. One previous human case was reported in the United States in 2022. In a few cases, the source of exposure to HPAI A(H5N1) virus has been unknown.

To date, HPAI A(H5N1) viruses currently circulating most commonly in birds and poultry, with spillover to mammals and humans do not have the ability to easily bind to receptors that predominate in the human upper respiratory tract. This is a major reason why the current risk to the public from HPAI A(H5N1) viruses remains low.

However, because of the potential for influenza viruses to rapidly evolve and the wide global prevalence of HPAI A(H5N1) viruses in wild birds and poultry outbreaks and following the identification and spread among dairy cattle in the United States, additional sporadic human infections are anticipated. Continued comprehensive surveillance of these viruses in wild birds, poultry, mammals, and people worldwide, and frequent reassessments are critical to determine the public health risk, along with ongoing preparedness efforts.

Key Points

• CDC is actively working on the domestic situation with clade 2.3.4.4b HPAI A(H5N1) viruses in wild birds, with outbreaks in poultry and backyard flocks, and infections of other animals, including dairy cattle. These activities include conducting surveillance among people with relevant exposures and preparing for the possibility that contemporary HPAI A(H5N1) viruses gain the ability for increased transmissibility to and among people.
• CDC, along with state and local public health partners, continues to monitor people in the United States who have been exposed to infected birds, poultry, or other animals for 10 days after exposure. To date, more than 8,800 people in 52 jurisdictions have been monitored since 2022, and only two human cases have been identified.
• H5 candidate vaccine viruses (CVV) produced by CDC are expected to provide good protection against current clade 2.3.4.4b HPAI A(H5N1) viruses detected in birds and mammals, including dairy cattle. These H5 CVVs are available and have been shared with vaccine manufacturers.
• Because influenza viruses are constantly changing, CDC performs ongoing analyses of HPAI A(H5N1) viruses to identify genetic changes that might allow for spread more easily to and between people, more serious illness in people, reduce susceptibility to antivirals, affect the sensitivity of diagnostic assays, or reduce neutralization of the virus by vaccine induced antibodies. To date, few genetic changes of public health concern have been identified in HPAI A(H5N1) viruses circulating in wild birds and poultry worldwide and detected in dairy cattle in the United States.
• Currently, HPAI A(H5N1) viruses circulating in birds and U.S. dairy cattle are believed to pose a low risk to the general public in the United States; however, people who have job-related or recreational exposures to infected birds or infected mammals are at higher risk of infection and should take appropriate precautions outlined in CDC guidance.
• Comprehensive surveillance and readiness efforts are ongoing, and CDC continually takes preparedness measures to be ready in case the risk to people from HPAI A(H5N1) virus or from other novel influenza A viruses changes.

(SNIP)

Limitations of the Report

This report is subject to the following limitations. First, the number of reported human infections with HPAI A(H5N1) viruses is small. Conclusions regarding virus characterization analyses, transmissibility from animals to people, transmissibility among people, and clinical spectrum of illness in people should be interpreted in light of this small number. Second, detailed exposure information was not available for all exposed persons or for those being monitored for illness after exposure to HPAI A(H5N1) virus-infected wild birds, poultry, backyard flocks, and other animals, including dairy cattle in the United States. As of the date of this report, understanding of HPAI A(H5N1) virus infections of cattle is very limited. Thus, we are not able to assess the impact of exposure variables such as duration of exposure, nature of exposure (e.g., direct vs. indirect contact), and use of personal protective equipment on infection risk among persons with confirmed HPAI A(H5N1) virus infection or those being monitored after exposures to any animals confirmed or suspected with HPAI A(H5N1) virus infection.

Conclusions

• To date, CDC analyses of clade 2.3.4.4b HPAI A(H5N1) viruses detected in wild birds, poultry, and sporadically in mammals, including in dairy cattle, since late 2021 indicate that these viruses all have a high degree of genetic identity with each other and no significant mammalian adaptive substitutions, insertions, or deletions have been identified, particularly in the HA gene, which is important for zoonotic and subsequent human-to-human transmission.
• Considering the high prevalence of HPAI A(H5N1) viruses detected in wild birds and poultry worldwide, spillover into mammals (including carnivores that may feed on infected animals) and additional sporadic zoonotic infections are anticipated among people with exposures to infected sick or dead poultry, wild birds, or other infected animals.
• HA clade 2.3.4.4b A(H5N1) viruses currently circulating in wild birds and poultry worldwide lack the ability to preferentially bind to the types of sialic acid receptors that are predominant in the upper respiratory tract of humans and therefore do not currently have the ability to easily infect or transmit among people.
• Despite extensive worldwide spread of influenza A(H5N1) viruses in wild birds and poultry in recent years, only a small number of sporadic human infections with 2.3.4.4b or clade 2.3.2.1c H5N1 viruses have been reported since 2022; nearly all cases had recent exposure to poultry and no cases of human-to-human influenza A(H5N1) virus transmission have been identified.

While CDC’s assessment is that the overall threat of HA clade 2.3.4.4b A(H5N1) viruses to public health is currently low, the widespread geographic prevalence of infected birds and poultry raises the potential for exposures and infections of humans and other mammals that could result in viral evolution or reassortment events which might change the current risk assessment. Vigilance and ongoing surveillance of HPAI A(H5N1) viruses circulating in wild birds, poultry, and in sporadic infections of mammals and people worldwide is critical to monitor the public health risk and to detect genetic changes (particularly in the HA gene) that would change CDC’s risk assessment.

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Canada: Food Inspection Agency Not Currently Testing Milk For HPAI

 

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Late yesterday I mentioned that Sky News reported the UK was not planning on testing cows for HPAI, and that I had found no mention of doing so in Mexico.  Although testing remains far less than it should be here in the U.S., elsewhere it appears almost nonexistent. 

Overnight Canada's Food Inspection Agency weighed in (see Twitter/X msg above), stating that they aren't testing milk, but aren't worried because they haven't detected the virus in cattle and `pasteurization kills harmful bacteria and viruses'

It isn't clear from this post whether they are actively testing cattle for HPAI (one hopes so) - and while the sale of unpasteurized milk has been illegal in Canada for more than 30 years -  there is ample evidence that some degree of raw milk consumption continues.  

A quick web search shows numerous groups supporting the legalization of selling raw milk in Canada,  and various forums discussing how to get around the law. You'll also find occasional news reports of farms fined for selling raw milk. 

A 2023 report in the PHAC CCDR (Public health risks of raw milk consumption:Lessons from a case of paediatric hemolytic uremic syndrome) cited:

Between 2005 and 2013, 263 confirmed cases of enteric and zoonotic illnesses in Canada were attributed to the consumption of raw milk products 3. This number is likely an underestimate, as the vast majority of enteric illnesses often do not present to health care or are tested to a confirmatory extent; literature has identified that there may be nearly 25 times the number of unreported cases of illness as compared to confirmed cases in at least one jurisdiction in the United States 4. According to a 2017 study, unpasteurized dairy products cause 840 times more illnesses and 45 times more hospitalizations than pasteurized products, making raw milk a dangerous food 4

Given this illicit trade - even if we assume pasteurization effectively inactivates the virus - it would seem worth knowing if the virus was in the milk supply, if for no other reason than to issue a stronger warnings about the dangers of raw milk consumption. 

Right now, agencies like the USDA and FDA are dealing with the fallout from their initial passive response following the detection of H5N1 in cattle a month ago.  It seems incredible that other countries are willing to follow in their footsteps.

A decade ago, my two favorite risk communications experts Peter Sandman and Jody Lanard wrote about the unprecedented Ebola outbreak in West Central Africa, and the world's Failures Of Imagination in grasping its potential impact. 

While their essay dealt with a specific time, place, and pathogen, it's lessons can be applied to our current - and probably any future - pandemic threat.  We revisited that essay in early 2020, when the world was still in deep denial about the spread of COVID, and it is well worth reading again today.

It seems - no matter how much we may talk about theoretical risks -  when a credible threat actually does emerge, the first `official' instinct is to deny or down play the risk. 

Now would be a very good time for risk communicators to spend a few hours reviewing the sage advice offered on the Sandman Risk Communications Website.  There's a lot to absorb, so pack a lunch.

If you don't have time, at least go read the 2009 essay by Peter Sandman: Swine Flu For Grownups, and the 9 rules that every risk communicator should live by:

1. Don’t feign confidence
2. Don’t over-reassure
3. Don’t worry about panic
4. Don’t obsess over accusations of fear-mongering
5. Don’t fight the adjustment reaction.
6. Don’t oversell what the government is doing
7. Don’t oversell what the public can do
8. Don’t ask the impossible
9. Don’t neglect the teachable moment

Four years ago, I asked what I intended to be a rhetorical question  in this blog about our lack of preparedness for COVID:

The $64 question is whether we'll learn from this, and immediately begin to prepare for the next one. Or if we will we just go back to sleep, and hope the next one doesn't come on our watch. 

Because next time, Nature's laboratory may throw something at us far worse than COVID-19.

Sadly, we seem to have an answer.

An HPAI Cattle Roundup - April 25th

 
A growing, but incomplete, picture of affected States

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It's been a busy day, with a media report by Tyne Morgan writing in the Bovine Veterinarian a report that quotes Andrew Bowman at Ohio State University - who has tested 150 samples of pasteurized milk purchased at the retail level -  as finding 38% (n=58) were PCR positive for H5N1 RNA.

PCR positive does not indicate whether the virus remains infectious (aka `viable'), so samples have been forwarded to St. Jude Children's Research Hospital, where attempts are being made to culture the virus. 

The milk was reportedly purchased from 6 states, but the manufacturing codes on the positive samples came from as many as 10 states.  Since the USDA has only confirmed 8 states with H5N1 in dairy cows, this suggests the problem is more widespread than has been reported. 

The decision announced yesterday that (starting next week) lactating cows must be tested prior to interstate transport should provide more data, but testing remains limited and voluntary for the vast majority of cattle herds. 

Another report by Rhonda Brooks, also in the Bovine Veterinarian called A Message to the Ag Industry about H5N1 warns that agricultural interests must take this threat very seriously, and quotes Texas veterinarian Dr. Barb Petersen as reporting seeing `sick humans' along with `sick cows' at multiple dairy farms.  

While only one mild case has been reported, in yesterday's HHS meeting (as reported by Helen Branswell for STAT),  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.”

At the same meeting, Mike Watson from APHIS confirmed that the USDA had `met some resistance' from some farmers with infected cows, and it is unknown whether orders to discard infected milk are being strictly enforced.  

A week ago the CDC issued recommendations for protective gear to be worn when tending to potentially infected cattle, although it isn't clear how much they are being utilized, particularly when testing for the virus is limited.

Meanwhile, the topic of testing cattle outside of the United States appear to be a third-rail that few officials are willing to touch.  Sky News is reporting the UK has no plans to test local herds with a DEFRA official saying levels of avian flu are so low in birds right now that `it does not consider cattle to be at risk.'

That optimistically assumes that no spillover occurred over the winter, when infected birds were more abundant.  Our spillover to cattle in the appears to have occurred in late 2023, but wasn't detected until cattle were tested in March of this year.

I've found very little from Mexico, which both exports and imports cattle from the United States.  While I suspect (read: hope) some testing is being conducted, no one seems to be talking about it. 

As we discussed a few days ago, the consumption of raw (unpasteurized) milk is far more common in Mexico than in the U.S., and surveillance for potential human infections is arguably less robust than here in the states.  

While there is no way to know how big of a deal this HPAI outbreak in cattle will become, this crisis has demonstrated - once again - how unprepared the world is to deal with an inconvenient, and highly unpredictable, zoonotic threat.

I get it.  

We're all traumatized and weary from the last pandemic, and by all rights we should have a few years before we must deal with another.  But viruses don't read calendars, and all indications are that the time-between-pandemics has grown shorter.  

Which means we need to get better at surveillance and testing, and far more aggressive in responding to threats.   The H5N1 virus has been honing its skills for years, if we hope to be able to cope, we need to do the same. 

As always, the volunteer newshounds on FluTrackers are all over this story, and you'll find expert reporting from Lisa Schnirring at CIDRAP and Helen Branswell at STAT News.  

CDC: Monitoring For Signs Of Human Infection With H5N1

FluView Interactive Novel Influenza

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Depending upon the strain, the method of exposure, viral load, and an individual's immune response and overall health, human influenza A infection can present a wide range of symptoms, ranging from asymptomatic-to-sub-clinical, mild-to-moderate, all the way up to severe and even life threatening..

With seasonal flu, asymptomatic carriage has been estimated to run as high as 35%, while sub-clinical cases may account for > 60% of cases (see EID Journal: Prevalence of Asymptomatic Influenza Virus Infections).

A 2015 study (CID: Viral Detection Increases With Family Size), followed 26 households over the course of one year, testing family members for 16 different respiratory viruses, including influenza, rhinovirus, and RSV on a weekly basis.

While the incidence varied widely by household size (no surprise, the more kids in the house, the more sickness), across the board only about 50% of the PRC positive cases reported cold or flu-like symptoms. 

Understandably, most influenza infections go unreported.  Most people do not consult a doctor unless their symptoms are severe, and even when they do, sub-typing for novel strains is rarely done outside of a sentinel hospital.

Since 2010, the CDC has detected 500 novel flu infections in the United States (see chart below), although this almost certainly represents just the tip of the iceberg.

During a small outbreak of H3N2v (n=13) a dozen years ago, researchers estimated that fewer than 1 in every 200 cases was identified (see CID Journal: Estimates Of Human Infection From H3N2v (Jul 2011-Apr 2012).

Results. We estimate that the median multiplier for children was 200 (90% range, 115–369) and for adults was 255 (90% range, 152–479) and that 2055 (90% range, 1187–3800) illnesses from H3N2v virus infections may have occurred from August 2011 to April 2012, suggesting that the new virus was more widespread than previously thought. 

We've seen similar estimates with H7N9 in China and MERS-CoV in Saudi Arabia.  Quite obviously, there are some regions of the world better equipped to detect novel viruses than others, but even in the UK their Health Security Agency has warned of the difficulties in detecting community spread of HPAI H5N1. 

A little over a year ago, the UKHSA published UK Novel Flu Surveillance: Quantifying TTD) which estimated the TTD (Time To Detect) a novel H5N1 virus in the community via passive surveillance might take 3-10 weeks, and the infection of dozens (or even hundreds) of people, before community spread could be established. 

They present different scenarios based on various levels of testing, but even under the best case scenario, it could take weeks to detect ongoing community transmission of the virus. 

While we can be comforted by the detection of only one mildly symptomatic (conjunctivitis) case in Texas, before the alert to monitor dairy workers went out a month ago, that case would likely have been dismissed as a mild viral infection, and testing would not have been done. 

Mild or sub-clinical cases are obviously less worrisome in the short run, but they are much harder to detect. 

The concern is, they give the virus additional opportunities to adapt to a new species, and potentially spread to their contacts. For a virus that hasn't quite adapted to human hosts, that's quite an advantage.

Yesterday the CDC published the following update on their efforts to detect any spread of the H5N1 virus early.  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.

How CDC is monitoring influenza data among people to better understand the current avian influenza A (H5N1) situation
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Updated April 24, 2024

Weekly Snapshot for Week Ending April 13, 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.

Monitoring for Novel Influenza A Virus Infections among People, including Influenza A(H5N1)

Rapid detection and reporting of human infections with novel influenza A viruses, including influenza A(H5N1), is important to facilitate prompt awareness and an effective public health response. For confirmed cases, the reporting jurisdiction completes a case report form, which is submitted to CDC. The information includes patient demographics, symptoms, the clinical course of illness, and exposure history. The reporting jurisdiction for influenza A(H5N1) cases reported in 2024 are summarized below.

Public Health Laboratory Reporting

Public health laboratories use CDC’s diagnostic tools to detect both seasonal influenza viruses and novel influenza A viruses including influenza A(H5N1). These diagnostic tools are used at more than 100 public health laboratories in all 50 U.S. states. The results of tests performed by these public health laboratories nationwide are summarized below.

Systems Used to Monitor Influenza Activity

Influenza activity is monitored year-round using multiple systems. These systems are used for monitoring seasonal influenza and, because influenza viruses are constantly changing in small, and occasionally more significant ways, these systems are also useful for monitoring signals and trends from novel influenza virus infections. Some examples are provided below.

Monitoring for Changes in Tests Positive for Influenza in Clinical Settings

Approximately 300 clinical laboratories located throughout all 50 states, Puerto Rico, Guam, and the District of Columbia report the results of clinical testing for influenza through either the U.S. WHO Collaborating Laboratories System or the National Respiratory and Enteric Virus Surveillance System (NREVSS). The results of tests performed by clinical laboratories nationwide are summarized below.

While these laboratories don’t test specifically for influenza A(H5N1) virus, by tracking the percentage of specimens tested that are positive for influenza A viruses, we can monitor for unusual increases in influenza activity that may be an early sign of spread of novel influenza A viruses, including H5N1.

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While there is currently no indication of community spread of H5N1 anywhere in the world, the reality is there are many regions of the globe where low-level transmission could go unnoticed for quite some time.  

Even in places with more advanced surveillance capabilities - like the United States, the UK, and Europe - early detection of limited community spread might require a bit of luck. 

A reminder than anything we say about the current threat posed by H5N1, COVID, H5N6,  MERS-CoV, or any other pandemic threat must be tempered by the knowledge that we are always working with incomplete information.