H5N1

Colorado reports three presumptive positive H5 cases in poultry workers

A CDC news release: Colorado Reports Three Presumptive Positive H5 Cases in Poultry Workers. Excerpt and then a comment:

July 12, 2024 – The state of Colorado has announced that three people have tested presumptive positive for highly pathogenic avian influenza (HPAI) A(H5) (“H5 bird flu”) virus infection. Specimens have been sent to CDC for confirmatory testing. All of the people who tested presumptive positive experienced mild symptoms and were workers who were involved in the depopulation of poultry at a poultry facility experiencing an outbreak of the H5N1 virus that is circulating in wild birds and has been causing multistate outbreaks in dairy cows and poultry. At the state’s request, CDC is sending a team to Colorado to support their investigation, which is ongoing.  

CDC’s current risk assessment for the general public remains low. As we learn more, we will continue to assess the situation and provide updates. These preliminary results again underscore the risk of exposure to infected animals. There are no signs of unexpected increases in flu activity otherwise in Colorado, or in other states affected by H5 bird flu outbreaks in cows and poultry.

Similar cases occurred when H5N1 was spreading in Asia 20 years ago. South Korea had several such cases after poultry culls. I seem to recall that, like the American cases, they were relatively minor; most serious cases followed consumption of infected poultry meat.

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.

Neolithic population collapse may have been caused by plague, researchers say

Via The Guardian: Neolithic population collapse may have been caused by plague, researchers say. Excerpt:

A devastating population collapse that decimated stone age farming communities across northern Europe 5,000 years ago may have been driven by an outbreak of the plague, according to research.  

The cause of the calamity, known as the Neolithic collapse, has long been a matter of debate.  

Studies based on DNA from human bones and teeth excavated from ancient burial tombs in Scandinavia – seven from an area in Sweden called Falbygden, one from coastal Sweden close to Gothenburg and one from Denmark – now suggest that disease played a central role.  

The remains of 108 people – 62 males, 45 females and one undetermined – were studied. Eighteen of them, or 17%, were infected with plague at the time of death.  

The researchers were able to chart the family tree of 38 people from Falbygden across six generations, spanning about 120 years. Twelve of them, or 32%, were infected with plague. Genomic findings indicated that their community experienced three distinct waves of an early form of plague.  

The researchers reconstructed full genomes of the different strains of the plague-causing bacterium Yersinia pestis responsible for these waves. They determined that the last one may have been more virulent than the others, and they identified traits indicating the disease could have spread from person to person to cause an epidemic.  

“We learned that the Neolithic plague is an ancestor to all later plague forms,” said Frederik Seersholm, a geneticist at the University of Copenhagen and lead author of the research, published in the journal Science.  

A later form of this same pathogen caused the Justinian Plague of the sixth century AD and the 14th-century Black Death that ravaged Europe, north Africa and the Middle East. Because the strains circulating during the Neolithic decline were much earlier versions, the plague may have produced different symptoms than those in the epidemics millennia later.  

The study demonstrated that the plague was abundant and widespread in the area examined.  

Martin Sikora, who is also a geneticist at the University of Copenhagen and a co-author of the report, said: “This high prevalence of plague indicates that plague epidemics played a substantial role in the Neolithic decline in this region. 

“Indeed, it seems plausible that the decline seen in other parts of Europe was also in some way affected by plague. We do already have evidence for plague in other megalithic sites in different parts of northern Europe. And seeing how prevalent it was in Scandinavia, I would expect a similar picture to emerge once we study these other megaliths with the same resolution.”

Cambodia: Two Takeo boys confirmed infected by H5N1 bird flu

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Thanks to Peter O'Meagher for alerting me to this Khmer Times report: Two Takeo boys confirmed infected by H5N1 bird flu. Takeo is a province south of the capital, Phnom Penh. The 3-year-old case was reported yesterday, but not the 5-year-old. Excerpt:

The Takeo Health Department said two boys, ages three and five, have been confirmed to be infected with the H5N1 bird flu, while 29 others are still waiting for test results from the National Institute of Public Health (NIPH) and the Pasteur Institute (PI) of Cambodia.  

H5N1 is a subtype of influenza that predominantly infects birds. However, the H5N1 virus can also infect mammals that have been exposed to infected birds in some cases. In these cases, symptoms are frequently severe or fatal.  

Takeo Health Director Nhea Sithan said yesterday that two children have been diagnosed with the H5N1 bird flu virus, while 29 people were waiting on results of blood tests from the NIPH and PI. He said that the Takeo Provincial Health Department has asked experts to cooperate with the relevant ministries to identify everyone who ate chickens that are suspected of having been infected with the H5N1 bird flu virus.  

“We have dealt with the situation in a timely manner and we’ve sent 29 people who may have been exposed to H5N1 to analyse their blood to see whether they have contracted bird flu or not,” he said.  

The director of the Takeo Provincial Production and Veterinary Office, Thai Ly, said yesterday that more than 600 chickens that were thought to be at high risk of being infected with the H5N1 virus were destroyed after the Takeo Provincial Department of Agriculture, Forestry, and Fisheries identified a case of bird flu in Por village.  

He added that according to past studies of the bird flu virus, this level of infection is unlikely to spread to other villages. However, he urged people not to eat sick or already-dead birds to avoid H5N1 infection.  

“We are calling on people to be vigilant against infection by bird flu by not eating and cooking the chickens and ducks that are sick or die from unknown causes due to the danger caused by H5N1,” he said.

Counting the dead in Gaza: difficult but essential

Via The Lancet: Counting the dead in Gaza: difficult but essential. Excerpt, with my bolding:

By June 19, 2024, 37 396 people had been killed in the Gaza Strip since the attack by Hamas and the Israeli invasion in October, 2023, according to the Gaza Health Ministry, as reported by the UN Office for the Coordination of Humanitarian Affairs. The Ministry's figures have been contested by the Israeli authorities, although they have been accepted as accurate by Israeli intelligence services, the UN, and WHO. These data are supported by independent analyses, comparing changes in the number of deaths of UN Relief and Works Agency (UNRWA) staff with those reported by the Ministry, which found claims of data fabrication implausible. 

Collecting data is becoming increasingly difficult for the Gaza Health Ministry due to the destruction of much of the infrastructure. The Ministry has had to augment its usual reporting, based on people dying in its hospitals or brought in dead, with information from reliable media sources and first responders. This change has inevitably degraded the detailed data recorded previously. Consequently, the Gaza Health Ministry now reports separately the number of unidentified bodies among the total death toll. As of May 10, 2024, 30% of the 35 091 deaths were unidentified. 

Some officials and news agencies have used this development, designed to improve data quality, to undermine the veracity of the data. However, the number of reported deaths is likely an underestimate. The non-governmental organisation Airwars undertakes detailed assessments of incidents in the Gaza Strip and often finds that not all names of identifiable victims are included in the Ministry's list. Furthermore, the UN estimates that, by Feb 29, 2024, 35% of buildings in the Gaza Strip had been destroyed, so the number of bodies still buried in the rubble is likely substantial, with estimates of more than 10 000. 

Armed conflicts have indirect health implications beyond the direct harm from violence. Even if the conflict ends immediately, there will continue to be many indirect deaths in the coming months and years from causes such as reproductive, communicable, and non-communicable diseases. The total death toll is expected to be large given the intensity of this conflict; destroyed health-care infrastructure; severe shortages of food, water, and shelter; the population's inability to flee to safe places; and the loss of funding to UNRWA, one of the very few humanitarian organisations still active in the Gaza Strip. 

In recent conflicts, such indirect deaths range from three to 15 times the number of direct deaths. Applying a conservative estimate of four indirect deaths per one direct death to the 37 396 deaths reported, it is not implausible to estimate that up to 186 000 or even more deaths could be attributable to the current conflict in Gaza. Using the 2022 Gaza Strip population estimate of 2 375 259, this would translate to 7·9% of the total population in the Gaza Strip. 

A report from Feb 7, 2024, at the time when the direct death toll was 28 000, estimated that without a ceasefire there would be between 58 260 deaths (without an epidemic or escalation) and 85 750 deaths (if both occurred) by Aug 6, 2024.

An immediate and urgent ceasefire in the Gaza Strip is essential, accompanied by measures to enable the distribution of medical supplies, food, clean water, and other resources for basic human needs. At the same time, there is a need to record the scale and nature of suffering in this conflict. Documenting the true scale is crucial for ensuring historical accountability and acknowledging the full cost of the war. 

It is also a legal requirement. The interim measures set out by the International Court of Justice in January, 2024, require Israel to “take effective measures to prevent the destruction and ensure the preservation of evidence related to allegations of acts within the scope of … the Genocide Convention”. The Gaza Health Ministry is the only organisation counting the dead. Furthermore, these data will be crucial for post-war recovery, restoring infrastructure, and planning humanitarian aid.