H5N1

Animal health body urges bird flu vaccination to avoid pandemic

Via Reuters: Animal health body urges bird flu vaccination to avoid pandemic. Excerpt:

PARIS, May 21 (Reuters) - Governments should consider vaccinating birds against bird flu to avoid the virus - which has already killed hundreds of millions of birds and infected mammals worldwide - turning into a new pandemic, the head of the World Animal Health Organisation (WOAH) said.  

The severity of the current outbreak of avian influenza, commonly called bird flu, and the economic and personal damage it has caused, has led governments to reconsider vaccinating poultry. However, some, like the United States, remain reluctant mainly because of the trade curbs this would entail.

"We are coming out of a COVID crisis where every country realised the hypothesis of a pandemic was real," WOAH Director General Monique Eloit told Reuters in an interview.  

"Since almost every country that does international trade has now been infected, maybe it's time to discuss vaccination, in addition to systematic culling which remains the main tool (to control the disease)," she said.  

The WOAH is holding a five-day general session from Sunday, and will be focus on global control of highly pathogenic avian influenza, or HPAI. 

A WOAH survey showed only 25% of its member states would accept imports of products from poultry vaccinated against HPAI.  

The European Union's 27 member states agreed last year to implement a bird flu vaccine strategy. France is set to be the first one, starting with ducks in the autumn.  

"If a bloc like the EU, which is a large exporter, starts moving in that direction, it will have a ricochet impact," Eloit said.  

The U.S. department of Agriculture (USDA) told Reuters on Friday that "in the interest of leaving no stone unturned in the fight against HPAI, USDA continues to research vaccine options that can protect poultry from this persistent threat".  

However, it still considers biosecurity measures to be the most effective tool for mitigating the virus in commercial flocks, it said in emailed answers.

8 dead skunks found in Vancouver and Richmond test positive for H5N1 avian flu

Via CBC News, a story that's getting close to home: 8 dead skunks found in Vancouver and Richmond test positive for avian flu. Excerpt:

Eight skunks found dead last month in Vancouver and nearby Richmond, B.C., have tested positive for avian flu. 

The B.C. government says it is the same strain of avian influenza associated with the outbreak that began in April 2022.  

The skunks were found in residential areas in both cities and were taken to B.C.'s Animal Health Centre over concerns they may have been deliberately poisoned.  

British Columbia's Ministry of Agriculture says the skunks were infected with the same H5N1 strain that has caused the deaths of millions of domestic poultry since the outbreak began in April last year.  

The ministry says in a statement the skunks may have contracted H5N1 by scavenging on infected wild birds.  

The statement says while avian flu in skunks is considered to be a low risk to human health, there are always risks when people or pets come into contact with sick or dead wild animals.

Avian influenza overview December 2022 – March 2023

ECDC has published Avian influenza overview December 2022 – March 2023. The abstract:

Between 3 December 2022 and 1 March 2023 highly pathogenic avian influenza (HPAI) A(H5N1) virus, clade 2.3.4.4b, was reported in Europe in domestic (522) and wild (1,138) birds over 24 countries. An unexpected number of HPAI virus detections in sea birds were observed, mainly in gull species and particularly in black-headed gulls (large mortality events were observed in France, Belgium, the Netherlands, and Italy). The close genetic relationship among viruses collected from black-headed gulls suggests a southward spread of the virus. Moreover, the genetic analyses indicate that the virus persisted in Europe in residential wild birds during and after the summer months. 

Although the virus retained a preferential binding for avian-like receptors, several mutations associated to increased zoonotic potential were detected. The risk of HPAI virus infection for poultry due to the virus circulating in black-headed gulls and other gull species might increase during the coming months, as breeding bird colonies move inland with possible overlap with poultry production areas. 

Worldwide, HPAI A(H5N1) virus continued to spread southward in the Americas, from Mexico to southern Chile. The Peruvian pelican was the most frequently reported infected species with thousands of deaths being reported. The reporting of HPAI A(H5N1) in mammals also continued probably linked to feeding on infected wild birds. 

In Peru, a mass mortality event of sea lions was observed in January and February 2023. Since October 2022, six A(H5N1) detections in humans were reported from Cambodia (a family cluster with 2 people, clade 2.3.2.1c), China (2, clade 2.3.4.4b), Ecuador (1, clade 2.3.4.4b), and Vietnam (1, clade 2.3.4.4b), as well as two A(H5N6) human infections from China. 

The risk of infection with currently circulating avian H5 influenza viruses of clade 2.3.4.4b in Europe is assessed as low for the general population in the EU/EEA, and low to moderate for occupationally or otherwise exposed people.

Deaths of thousands of wild birds from H5N1 avian flu is ‘new Silent Spring’

Via The Guardian: Deaths of thousands of wild birds from avian flu is ‘new Silent Spring’. Excerpt:

The planet is experiencing a new “Silent Spring” of wildlife destruction because so many wild birds have died from avian flu, according to a leading scientist, who said the past year has seen the most significant and sudden loss of birds in decades.  

James Pearce-Higgins, director of science at the British Trust for Ornithology, said: “The last time we experienced such large-scale and rapid losses of wild birds in the UK would be the impacts of DDT on birds of prey in the 1950s and 1960s associated with the Silent Spring narrative, or the widespread declines of farmland birds during the 1970s and 80s as a result of agricultural intensification.”  

The Silent Spring narrative refers to the seminal 1962 book by Rachel Carson about how pesticides, particularly DDT, were killing birds. DDT caused egg shells to become so thin that adults crushed them during incubation, leading to nest failure and the deaths of thousands of birds.  

The World Organisation for Animal Health estimates that more than 50,000 wild birds have died of the highly pathogenic avian influenza H5N1 since October 2021, mainly in Europe and America. But experts say this is likely to be a huge underestimate. In the UK alone, numbers could be in the hundreds of thousands, although conservationists say the true impact is still unknown, and most are unwilling to speculate.  

In the UK, the effects of avian flu started in the northernmost islands of Scotland in spring, spreading south down the east coast of England reaching as far south as Sussex, with colonies of nesting seabirds the worst hit. 

Already there are more than a dozen outbreaks dotted across the country among wintering waterbirds. This suggests it is already widespread and will be found in breeding seabird colonies again next year, said Pearce-Higgins.  

There were more than 3,500 virus detections in wild birds across Europe in the 2021-2022 season, with reports from 37 countries that it was being seen in 63 wild bird species, according to an avian influenza overview published by the European Food Safety Authority. For wild birds, Germany, France, the Netherlands and the UK had the most reported cases, with most coming from coastal areas because seabirds were the worst affected.  

The first US case in this current outbreak was in an American wigeon duck in South Carolina on 14 January 2022. Since then, there have been 3,700 positive tests in 47 states, according to the US Centers for Disease Control and Prevention.  

Yet testing should not be taken as an indicator of impact, because only a fraction of birds that die will be collected and sent for laboratory testing, researchers say. “Reported numbers are likely a vast underestimate,” said Michelle Wille from the University of Sydney.

BC wildlife rescue centres say they're overrun with calls for birds sick with suspected avian flu

Via CBC News: B.C. wildlife rescue centres say they're overrun with calls for birds sick with suspected avian flu. Excerpt:

The provincial and federal governments advise people not to handle sick birds, as wildlife rehabilitation centres say they are seeing increased calls from the public who want to try and help the animals suspected of having avian influenza.  

"It's been exceptional in my almost 37 years of doing this," said Elizabeth Melnick, who for decades has worked to rehabilitate injured or orphaned animals at her centre in Abbotsford.  

She said her centre, which runs on donations, is unable to keep up with calls, and even people bringing her sick birds such as wild geese and crows they've observed in distress, mostly in the Fraser Valley where avian flu has been detected.  

"It's really taken a toll," she said. "It's not a good situation at all."  

Seven commercial poultry farms have been quarantined with avian flu since Nov. 16 in Abbotsford and Chilliwack, the same area where 17 million birds were culled in 2004 to prevent the flu's spread. 

Officials in the industry say, so far, there has not been farm-to-farm transmission, but wild birds are spreading the disease as they can easily access poultry farms in the Fraser Valley, which are close together.  

The first poultry infection in B.C. this year was confirmed in mid-April. There have now been 57 confirmed cases, with the majority discovered this fall as wild birds migrate.

Iceland as stepping stone for spread of highly pathogenic avian influenza virus between Europe and North America

Via Emerging Infectious Diseases: Iceland as Stepping Stone for Spread of Highly Pathogenic Avian Influenza Virus between Europe and North America. The abstract:

Highly pathogenic avian influenza viruses (HPAIVs) of hemagglutinin type H5 and clade 2.3.4.4b have widely spread within the northern hemisphere since 2020 and threaten wild bird populations, as well as poultry production. 

We present phylogeographic evidence that Iceland has been used as a stepping stone for HPAIV translocation from northern Europe to North America by infected but mobile wild birds. At least 2 independent incursions of HPAIV H5N1 clade 2.3.4.4b assigned to 2 hemagglutinin clusters, B1 and B2, are documented for summer‒autumn 2021 and spring 2022. Spread of HPAIV H5N1 to and among colony-breeding pelagic avian species in Iceland is ongoing. 

Potentially devastating effects (i.e., local losses >25%) on these species caused by extended HPAIV circulation in space and time are being observed at several affected breeding sites throughout the North Atlantic.

H5N1 bird flu kills close to a record number of poultry in the US

In the old days, we worried about H5N1 reaching the Americas. Now, without much fanfare, it's very much here. Via Reuters: Bird flu kills close to a record number of poultry in the U.S. Excerpt:

A near-record number of U.S. chickens and turkeys have died in this year's outbreak of avian flu, as a different form of the virus than farmers battled before has infected more wild birds that then transmit the disease, officials said.  

More than 47 million birds have died due to infections and cullings. This has spurred export bans, lowered egg and turkey production, and contributed to record prices of the staples ahead of the U.S. holiday season. The outbreak exacerbates economic pain for consumers grappling with soaring inflation.

In 2015, 50.5 million birds died in the deadliest U.S. outbreak, the nation's worst animal-health event to date.  

Farmers are fighting a subtype of the H5N1 strain of the virus that survived over the summer, when rising temperatures typically reduce avian flu, said Rosemary Sifford, chief veterinary officer for the U.S. Department of Agriculture (USDA).  

The same subtype, known as the goose/Guangdong lineage, is spreading in Europe, she said in an interview. Europe is already suffering its worst avian flu crisis, with nearly 50 million poultry culled.  

Officials are finding the subtype in a broader range of wild birds, such as ducks, than in the past and it seems to live in the birds longer, Sifford said. An elevated threat for infections may persist until summer 2023 as they migrate, she said.  

The United States is monitoring wild birds for avian flu in four migration paths known as flyways, up from two previously, and plans to do the same next year.

"This virus could be present in wild birds for the foreseeable future," Sifford said. "This one is certainly different."  

The outbreak has infected flocks in 42 states since February, twice as many as in 2015, USDA records show. Infections slowed over the summer this year but did not stop as they did in 2015.  

The tenacity of the virus surprised some producers, who have boosted cleaning and security in barns since the 2015 outbreak.  

"Unfortunately what we've done probably hasn't been enough to protect us from this high load of virus in the wild bird population," Sifford said.

Climate change increases cross-species viral transmission risk

Via Nature, an important new study: Climate change increases cross-species viral transmission risk. The abstract:

At least 10,000 virus species have the capacity to infect humans, but at present, the vast majority are circulating silently in wild mammals. However, climate and land use change will produce novel opportunities for viral sharing among previously geographically-isolated species of wildlife. In some cases, this will facilitate zoonotic spillover—a mechanistic link between global environmental change and disease emergence.  

 

Here, we simulate potential hotspots of future viral sharing, using a phylogeographic model of the mammal-virus network, and projections of geographic range shifts for 3,139 mammal species under climate change and land use scenarios for the year 2070.  

 

We predict that species will aggregate in new combinations at high elevations, in biodiversity hotspots, and in areas of high human population density in Asia and Africa, driving the novel cross-species transmission of their viruses an estimated 4,000 times.  

 

Because of their unique dispersal capacity, bats account for the majority of novel viral sharing, and are likely to share viruses along evolutionary pathways that will facilitate future emergence in humans. Surprisingly, we find that this ecological transition may already be underway, and holding warming under 2°C within the century will not reduce future viral sharing.  

 

Our findings highlight an urgent need to pair viral surveillance and discovery efforts with biodiversity surveys tracking species’ range shifts, especially in tropical regions that harbor the most zoonoses and are experiencing rapid warming.

Timing the SARS-CoV-2 index case in Hubei province

Published in Science on March 18: Timing the SARS-CoV-2 index case in Hubei province. The abstract:

Understanding when SARS-CoV-2 emerged is critical to evaluating our current approach to monitoring novel zoonotic pathogens and understanding the failure of early containment and mitigation efforts for COVID-19. We employed a coalescent framework to combine retrospective molecular clock inference with forward epidemiological simulations to determine how long SARS-CoV-2 could have circulated prior to the time of the most recent common ancestor. 

Our results define the period between mid-October and mid-November 2019 as the plausible interval when the first case of SARS-CoV-2 emerged in Hubei province. By characterizing the likely dynamics of the virus before it was discovered, we show that over two-thirds of SARS-CoV-2-like zoonotic events would be self-limited, dying out without igniting a pandemic. 

Our findings highlight the shortcomings of zoonosis surveillance approaches for detecting highly contagious pathogens with moderate mortality rates.

Deadly pig disease could have led to Covid-19 spillover to humans, analysis suggests

Via The Guardian:, an intriguing hypothesis: Deadly pig disease could have led to Covid spillover to humans, analysis suggests. Excerpt:

An outbreak of a deadly pig disease may have set the stage for Covid-19 to take hold in humans, a new analysis has suggested. African swine fever (ASF), which first swept through China in 2018, disrupted pork supplies increasing the potential for human-virus contact as people sought out alternative meats. 

Pork is the main meat source in the Chinese diet, and the country produces half of the world’s pigs, which generate roughly 55m tonnes of pork annually, forming an industry worth more than $128bn (£98bn). The ASF outbreak had spread across most of China by the fourth quarter of 2019. The disease is untreatable and incurable. Once it takes hold, the only solution is to kill infected animals. 

The dramatic drop in pork supply, after restrictions on movement of pigs and culling led to price rises, escalated demand for alternative sources of meat to be transported nationwide. These sources included wild animals, thus greatly increasing opportunities for human-coronavirus contact, a team of researchers from China and the UK have suggested in a yet to be peer-reviewed analysis. 

“If more wildlife enters the human food chain, either through [individuals] hunting … or going to market and getting different meat sources. If that increases, it could just increase the contact opportunity,” said the author of the study, David Robertson, professor of viral genomics and bioinformatics at Glasgow University. “You’re just increasing the opportunity for the [Sars-CoV-2] virus to get into humans.”