H5N1

Stop H5N1 influenza in US cattle now

An editorial in Science; Stop H5N1 influenza in US cattle now.

The relentless march of a highly pathogenic avian influenza virus (HPAIV) strain, known as H5N1, to become an unprecedented panzootic continues unchecked. The leap of H5N1 clade 2.3.4.4b from Eurasia and Africa to North America in 2021 and its further spread to South America and the Antarctic have exposed new avian and mammalian populations to the virus and led to outbreaks on an unrivaled scale. 

The virus has infected wild birds across vast geographic regions and caused wildlife deaths in some of the world’s most biodiverse ecosystems. Hundreds of millions of poultry have died or been culled, affecting global food security in some of the world’s poorest regions. Numerous mammalian species, including sea lions and fur animals, have been infected. Outbreaks in dairy cows in the United States have been occurring for months, seemingly unchecked in most affected states. Why is there not a greater sense of urgency to control these infections? 

Although the H5 2.3.4.4b virus seems poorly optimized for infection or spread in humans, with fewer than 20 cases since 2016, influenza leaves no room for complacency. The sheer number of infected wild birds and poultry has caused spillover infections to occur in wild carnivores, marine mammals, and farmed animals, providing additional pathways for exposure and perhaps infection in humans. The H5 virus has evolved continuously since 1996 but has never infected so many bird species nor been able to transmit to, and replicate in, cows. 

The more than 140 dairy farms in 12 US states with the virus and the detection of viral RNA in milk products in grocery stores speak for themselves. Infection in cattle creates new possibilities for direct contact between the virus and humans, and also risks the virus evolving the ability to spread in cattle, a new livestock reservoir of around 1.5 billion animals worldwide. 

Until now, human infections with H5 viruses were mainly associated with the keeping of infected poultry. But over the past 3 months, the United States has identified human H5 cases in farmworkers associated with one of the world’s most industrialized dairy production systems. Even difficult viral adaptations can occur if there are enough opportunities for contact and replication in new host species. Adaptation of the virus to cattle must be prevented. The outbreak in cattle in the United States must therefore be brought under control quickly. 

Key measures that should be initiated or intensified immediately include surveillance of all US dairy farms by testing, for example, bulk milk for influenza virus RNA, implementation of strict quarantine for infected cattle, and restriction of within-state transport to stop the circulation of the virus in cows. Only a couple of states are attempting this currently. 

Biosecurity and hygiene measures on US dairy facilities must be enhanced to avoid virus spread and spillover infections. This should include simple and practical steps such as keeping work clothing on the farm, thoroughly decontaminating stock vehicles and equipment, ensuring restricted access and movement of personnel among premises, and providing appropriate personal protective equipment. 

Human influenza surveillance should be bolstered during the summer and before the usual human seasonal influenza wave begins in the fall. The timely development of vaccine candidates for both livestock and humans should be undertaken along with associated policies on their distribution. This is the ultimate insurance against a worst-case scenario in which viral variants emerge that spread more easily in mammals. 

Globally, surveillance of mammalian cases should be intensified and real-time genomic information on the virus should be made publicly available, especially in at-risk populations (such as pig and fur animal farms). There must be increased global awareness of data collection and data sharing on zoonotic influenza. Analyses for incursion risk and pandemic preparedness based on both genetic and phenotypic data (including identifying mammalian adaptive changes, antiviral therapeutic resistance, and diagnostic robustness) in all regions need to be substantially improved, and the detection of human infection clusters needs to be further optimized. 

National and international coordination in the spirit of a modern “One Health” approach is essential, and the quadripartite comprising the Food and Agricultural Organization of the United Nations, United Nations Environment Programme, World Health Organization, and World Organisation for Animal Health should step up to take a leading role.

H5N1: International failures and uncomfortable truths

An editorial in The Lancet: H5N1: international failures and uncomfortable truths.

If you ask an infectious diseases specialist whether we should start worrying about influenza A H5N1, they will probably tell you that we should always be worrying about it. An influenza pandemic has long topped the list of global threats to health, and avian influenza poses a particularly serious concern. 

H5N1 has infected over 800 people since its identification in 1996, with a mortality rate exceeding 50%. Since 2020, it has become endemic in bird populations, triggering an unparalleled animal pandemic, affecting at least 26 mammal species. There is nothing new in influenza strains evolving, shifting their epidemiological habits, and causing infections in people, although human-to-human transmission of H5N1 is rare. 

Nonetheless, although developments over the past 3 months may or may not signal the start of a global pandemic, they are at the very least a pressing and unwelcome reminder of the caprices of zoonotic influenza and our continued collective complacency about it. 

An unprecedented outbreak of highly pathogenic avian influenza A(H5N1), the first documented infection in dairy cows, was reported on March 25, 2024 in Texas, Kansas, and New Mexico, raising the potential of cow-to-human transmission. Three confirmed human cases in the USA, all farm workers, have been reported so far, with the third person presenting with respiratory symptoms. 

Genetic analysis shows that the virus lacks changes that would make it better adapted to transmit between people and the risk to human health remains low, but it did detect adaptation to mammalian hosts. 

Despite calls for increased surveillance, the US response has been slow, with many cases likely going undetected. There has been resistance from the farming industry around testing and prevention, driven by a lack of awareness or understanding around changing practice and fear of trade restrictions and product loss. The US Department of Agriculture (USDA) and the US Centers for Disease Control and Prevention are incentivising dairy producers to supply personal protective equipment and offer laundering services for employees, but the USDA has been accused of being slow in sharing crucial virus sequence data, complicating our understanding of the outbreak. 

In Canada, early warning systems have been implemented to screen for H5N1 in milk. The UK says it has intensified its response to the US outbreak, but according to a report last month, it is not yet testing cows for the virus.

Action to curb this outbreak is needed urgently, including improving testing, surveillance, and reporting of infected animals and food products; vaccinating animal populations; transparent information sharing; developing and stockpiling human vaccine; and promoting protective measures among farm workers. All countries should build capacities to test, detect, and report infections, cases, and deaths above expected levels and share this information. Countries in need of external assistance to bolster their capacity should receive support.

 

The need for a robust and coordinated response to highly pathogenic avian influenza A(H5N1), as described in a Comment by Kojima and colleagues, serves to highlight the scale of the failure of countries to secure an international agreement on the pandemic accord. The 77th World Health Assembly, which closed on June 1, was meant to see a finalised draft of an international instrument on pandemic prevention, preparedness, and response. As The Lancet has noted, negotiations have been mired in disagreement and draft provisions have been unjust and inequitable (although changes to the International Health Regulations have been agreed). The process is not over yet—discussions continue with the hope of securing an agreement by May, 2025. Until then, the continued absence of a meaningful and effective accord undermines the ability to respond appropriately to international health threats, such as H5N1. Despite COVID-19, most countries are not prepared for a new pandemic.

 

Beyond the proximal drivers of outbreaks and potential interventions though, there is a need to confront an uncomfortable truth that the US H5N1 outbreak once again raises. Spillover of zoonoses into human populations stems ultimately from our ways of life and how they shape the human–animal interface. Our diets, our intensive farming practices, our livelihoods, our behaviours, and our cultures. Our exploitation of the natural world and our destruction of the environment. These issues are tractable through interdisciplinary education, intersectoral collaboration, adequate funding, and integrated policies. The concept of One Health, although often acknowledged, is rarely prioritised and operationalised. The result is a missed opportunity to not just respond to pandemic threats, but to prevent them altogether.

 

WHO: Dengue - Global situation

WHO has published a DON: Dengue - Global situation. The situation at a glance:

As of 30 April 2024, over 7.6 million dengue cases have been reported to WHO in 2024, including 3.4 million confirmed cases, over 16 000 severe cases, and over 3000 deaths. 

While a substantial increase in dengue cases has been reported globally in the last five years, this increase has been particularly pronounced in the Region of the Americas, where the number of cases has already exceeded seven million by the end of April 2024, surpassing the annual high of 4.6 million cases in 2023. Currently, 90 countries have known active dengue transmission in 2024, not all of which have been captured in formal reporting. 

In addition, many endemic countries do not have strong detection and reporting mechanisms, so the true burden of dengue globally is underestimated. In order to control transmission more effectively, real-time robust dengue surveillance is needed to address concerns about potential undetected cases, co-circulation and misdiagnosis as other arboviruses, and unrecorded travel movements. These factors could contribute to unrecognized disease spread and establish a potential risk for local transmission in non-endemic countries. 

Dengue virus is transmitted to humans through the bite of infected mosquitoes. Cases are most commonly asymptomatic or result in mild febrile illness. However, some cases will develop severe dengue, which may involve shock, severe bleeding or severe organ impairment. 

To strengthen global surveillance, and monitor temporal trends and disease incidence, WHO has established a global dengue surveillance system with monthly reporting across all WHO regions with a new dashboard now live (https://worldhealthorg.shinyapps.io/dengue_global/). 

The overall capacity for countries to respond to multiple, concurrent outbreaks continues to be strained due to the global lack of resources, including shortages of good quality dengue diagnostic kits for early disease detection, lack of trained clinical and vector control staff and community awareness. 

Emergency response mechanisms have been established, and WHO supports high-risk countries across affected regions. Given the current scale of the dengue outbreaks, the potential risk of further international spread and the complexity of factors impacting transmission, the overall risk at the global level is still assessed as High and thus dengue remains a global threat to public health.

A message to the agriculture industry about H5N1

Via Bovine Veterinarian, an important article: A Message to the Ag Industry about H5N1. Excerpt from the long report:

So far, H5N1 has been officially confirmed in only 32 herds in eight states, according to data from USDA’s Animal and Plant Health Inspection Service (APHIS).    

Some veterinarians working with dairies in Texas believe the virus is more active than current data suggest. Nick Schneider, a consulting dairy practitioner, is one of them.      

“The thing is, when you get into the Panhandle of Texas, I’m not sure there’s anybody (dairy farms) that did not have it,” says Schneider.  

Texas is home to 335 Grade A dairies with an estimated 625,00 cows, according to information on the Texas Association of Dairymen website. More than 100 of those operations are in the Panhandle.  

The virus likely is being under-reported by the dairy industry because the presence of the virus in dairy cows is new, and there are no reporting requirements, Russo says.  

“It's not a foreign animal disease like it's considered in poultry, where there are reporting requirements,” she explains. “This is considered an emerging disease (in dairy cattle).”  

The dairy industry needs to be “very forward looking” now and address the virus, advises Schneider, the Texas dairy consultant.  

“Looking at what happened in the rearview mirror is great, but if you're not looking at where you're going, it's really just a pointless endeavor,” he says.  

To that end, he advises gaining  insights and expertise in preparation for whatever new information emerges next.  

“We need to think about this potentially being something we have to live with as being a part of the industry in the future,” Schneider says. “I hope I'm wrong. I would love to be wrong about that. But it's something that we definitely need to consider when we're thinking of how we're going to manage it.”

WHO: Weekly epidemiological update on COVID-19 - 3 August 2023

WHO has published Weekly epidemiological update on COVID-19 - 3 August 2023. Click or tap through to download the complete report. The overview:

Globally, over one million new COVID-19 cases and over 3100 deaths were reported in the last 28 days (3 to 30 July 2023). While five WHO regions have reported decreases in the number of both cases and deaths, the Western Pacific Region has reported an increase in the number of cases and a decrease in the number of deaths. 

As of 30 July 2023, over 768 million confirmed cases and over 6.9 million deaths have been reported globally. Currently, reported cases do not accurately represent infection rates due to the reduction in testing and reporting globally. 

During this 28-day period, 46% (107 of 234) of countries and territories reported at least one case to WHO – a proportion that has been declining since mid-2022. 

In this edition, we include:  

• The COVID-19 epidemiological update at the global and the regional levels  

• An update on hospitalizations and ICU admissions  

• An update on the SARS-CoV-2 variants of interest (VOI) and variants under monitoring (VUM)  

• An update on the vaccine effectiveness of primary series and booster vaccination against the Omicron and its descendant lineages

WHO: Influenza A(H1N2)v-United States of America

A WHO DON: Influenza A(H1N2)v-United States of America. Excerpt:

Situation at a glance:  

On 4 August 2023, the United States International Health Regulations (IHR) National Focal Point informed PAHO/WHO of a human infection with a novel influenza A(H1N2) variant virus identified in the State of Michigan. This was confirmed by Reverse Transcription Polymerase Chain Reaction at the United States (US) Centers for Disease Control and Prevention (CDC) on August 2.  

The case was not hospitalized and is recovering from the illness. Investigations by local public health officials identified swine exposure by the patient at an agricultural fair.  

Additional public health response efforts including enhanced surveillance for cases is undergoing. Given the potential impact on public health, human infections with these viruses need to be monitored closely. In this event, there was no reported evidence of sustained human-to-human transmission, the illness was mild and no further influenza variant virus transmission in the community has been identified.  

Description of the case:  

On 4 August 2023, the United States IHR National Focal Point informed PAHO/WHO of a human infection with a novel influenza A(H1N2) variant virus identified in the State of Michigan and confirmed by the US CDC.   

According to the report, the case is under 18 years old, with no comorbidities, resident in the State of Michigan, who developed respiratory illness on 29 July 2023. The case presented with fever, cough, sore throat, muscle aches, headache, shortness of breath, diarrhea, nausea, dizziness, and lethargy. On 29 July, the case sought medical care at an emergency department, and an upper respiratory tract specimen was collected on 30 July. The specimen tested positive for influenza A virus on the same day. On 1 August, the patient received influenza antiviral treatment (Oseltamivir).  

On 31 July, the specimen was tested at the Michigan Department of Health and Human Services (MDHHS), and RT-PCR results were positive for influenza A virus but lacked reactivity with diagnostic tests for contemporary human influenza viruses representing either (H1) pdm09 or (H3) subtypes. The specimen was then sent to the US CDC for further testing and received on 2 August. On the same day, RT-PCR analysis of the specimen indicated an influenza A(H1N2) variant (v) virus. The virus was isolated and subsequent analysis including genetic sequencing is underway.  

The case was not hospitalized. Investigation by local public health officials identified swine exposure by the patient at an agricultural fair, that took place between 23 and 29 July, within 10 days prior to illness onset. Additional investigation did not identify respiratory illness in any of the patient’s close contacts or household contacts. No additional cases were identified related to this agriculture fair. No person-to-person transmission of influenza A(H1N2)v virus associated with this case has been identified. No additional cases of human infection with A(H1N2)v virus have been identified as of 10 August 2023.  

This is the first influenza A(H1N2)v virus infection identified in the United States this year. Since 2005, there have been 512 influenza A variant virus infections (all subtypes), including 37 (human infections with influenza A (H1N2)v viruses reported in the United States.

WHO: Weekly epidemiological update on COVID-19 - 3 August 2023

WHO has published Weekly epidemiological update on COVID-19 - 3 August 2023. Click or tap through to download the full report. The overview:

Globally, over one million new COVID-19 cases and over 3100 deaths were reported in the last 28 days (3 to 30 July 2023). While five WHO regions have reported decreases in the number of both cases and deaths, the Western Pacific Region has reported an increase in the number of cases and a decrease in the number of deaths. 

As of 30 July 2023, over 768 million confirmed cases and over 6.9 million deaths have been reported globally. Currently, reported cases do not accurately represent infection rates due to the reduction in testing and reporting globally. 

During this 28-day period, 46% (107 of 234) of countries and territories reported at least one case to WHO – a proportion that has been declining since mid-2022. 

In this edition, we include:  

• The COVID-19 epidemiological update at the global and the regional levels  

• An update on hospitalizations and ICU admissions  

• An update on the SARS-CoV-2 variants of interest (VOI) and variants under monitoring (VUM)   

• An update on the vaccine effectiveness of primary series and booster vaccination against the Omicron and its descendant lineages

How we used machine learning to look where Ebola may strike

Via ProPublica: How We Used Machine Learning to Look Where Ebola May Strike. Excerpt:

ProPublica spent months teaching a computer to analyze past Ebola outbreaks linked to deforestation. What we found reveals a weakness in the way that governments and public health experts are preparing for future pandemics. 

The bright spots on the map struck us like a lightning bolt. 

We had spent months teaching a computer about the Ebola virus –– feeding it information about the landscapes and populations in places where the disease had previously emerged, showing it how to analyze those outbreaks for patterns, and then instructing it to flag other areas that looked similarly perilous.   

Some of the highlighted spots were predictable; the virus had repeatedly ravaged one of those countries.  

But we didn’t expect our model to light up Nigeria, the most populous country in Africa. The West African nation and international travel hub has never seeded an Ebola outbreak, but just a year ago, it served as the springboard for another virus to travel into Europe and the Americas and spread across the globe. However that virus, mpox, originally known as monkeypox, is rarely fatal.  

What if it had been Ebola, which kills about half of the people it infects?  

We asked Nigerian public health officials whether they were concerned.  

“Ebola is not part of our top concerns any more,” said Oyeladun Okunromade, the director of surveillance and epidemiology at the Nigeria Centre for Disease Control.  

In the aftermath of the 2014 West African Ebola epidemic, the worst on record, Nigerian officials were on high alert. But last year, they took the virus off the list of the top infectious diseases the country needed to prepare for, downgrading Ebola in relation to threats like mpox, which Nigeria was actively fighting.  

The disjoint between how our model sees Nigeria’s risk and how the nation’s health officials view it reveals a weakness in the way that governments and public health experts are preparing for future pandemics. The methods many countries use to rank threats focus mainly on factors that occur after an outbreak has already begun, such as the potential economic impact of an epidemic. Or they rely on past cases, looking at where a pathogen has previously struck.  

Neither approach considers the root causes.  

We’ve spent more than a year digging into the question of what causes outbreaks and what the world can do to prevent them. And we’ve learned that while science has advanced so we’re starting to understand the complex factors that trigger an outbreak, the world is not doing nearly enough to try to head off the next big one.

UK almost ‘flying blind’ on Covid this autumn, experts say

Via The Guardian: UK almost ‘flying blind’ on Covid this autumn, experts say. Excerpt:

The UK is nearly “flying blind” when it comes to Covid this autumn, experts have said, amid an increase in cases.  

While the UK Health Security Agency (UKHSA) continues to track some metrics of Covid, including hospitalisation numbers, many of the community surveillance studies tracking infection levels have finished.  

Now experts have said the situation is leaving the country in the dark about how Covid may play out in the months ahead.  

Christina Pagel, a professor of operational research at University College London, said a new wave of Covid appeared to be under way – possibly driven by waning immunity, new variants of Omicron, and factors including poor weather keeping people inside.  

With the autumn coming on and people returning to school and work, Covid pressures may increase, Pagel added.  

“We might see the wave continue to grow, and grow faster, in September,” she said.  

As well as public health measures including reintroducing high-quality masks within healthcare settings, Pagel said she would support bringing back the nationwide infection survey published by the Office for National Statistics for autumn and winter, as well as expanding it to cover flu and RSV.  

Failing that, she said, wastewater monitoring should be reinstated across the UK as a cheaper alternative that is used in many countries to track Covid prevalence and variants. Such schemes have recently been cut in England and Wales.  

“What worries me most is if we get a repeat of the last winter NHS crisis this winter again, with Covid, flu and RSV all hitting around the same time,” said Pagel. “We are definitely flying near blind.”  

Prof Rowland Kao, an epidemiologist at the University of Edinburgh, also highlighted the decline in surveillance.  

“With seasonal flu, we have of course a certain amount of predictability with the many years of data. However, with Covid, now that we don’t have those multiple data streams to rely on, it’s harder to say what is happening [in the general population],” he said.  

Kao added that the variant emergence patterns for Covid were largely unknown and Covid was not simply following seasonal patterns.

WHO: Weekly epidemiological update on COVID-19 - 3 August 2023

Via WHO: Weekly epidemiological update on COVID-19 - 3 August 2023. Click or tap through to download the full report. The overview:

Globally, over one million new COVID-19 cases and over 3100 deaths were reported in the last 28 days (3 to 30 July 2023). While five WHO regions have reported decreases in the number of both cases and deaths, the Western Pacific Region has reported an increase in the number of cases and a decrease in the number of deaths. 

As of 30 July 2023, over 768 million confirmed cases and over 6.9 million deaths have been reported globally. Currently, reported cases do not accurately represent infection rates due to the reduction in testing and reporting globally. During this 28-day period, 46% (107 of 234) of countries and territories reported at least one case to WHO – a proportion that has been declining since mid-2022.