Are we at the edge of another pandemic? H5N1

Post Reply New Topic

H5 is on the move, but much more rapidly then in ages past. This is due to the rapid ability of humans to travel around the world.

A team of Australian scientists has recently identified highly pathogenic avian influenza A(H5N1) virus clade 2.3.2.1a in a child who traveled back to Australia from India.

Highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b has emerged from goose/Guangdong lineage HPAI H5N1 viruses after decades of evolution. This viral clade circulates dominantly worldwide and causes infection in wild and domestic birds and mammals.

Despite the global predominance of clade 2.3.4.4b, a diversity of HPAI H5N1 clades currently circulate in poultry in Asia. Since 2005, more than 900 zoonotic infections have been recorded. Contact with infected poultry is the primary cause of these infections. However, human-to-human transmission has yet to be detected.

Various HPAI H5N1 clades have been found to cause human infections in Asia. Eleven human infections caused by HPAI H5N1 clade 2.3.2.1c have been reported in Cambodia in the past two years. In China, 91 human infections caused by HPAI H5N6 and two infections caused by clade 2.3.4.4b H5N1 have been recorded since 2014.

Highly pathogenic avian influenza A(H5N1) virus clade 2.3.2.1a persistently circulates in South Asia, especially in India and Bangladesh. Although this clade rarely infects humans, two cases have been detected in these regions so far. However, poultry-related outbreaks of H5N1 were reported in Ranchi, India, in 2023 and 2024, approximately 400 km from Kolkata, where the child in this study visited.

Source: Scientists detect rare H5N1 avian flu strain in Australian child after travel to India

A rare and complex avian flu strain in a child traveler reveals how globally circulating viruses are reshaping local outbreaks—and highlights critical surveillance gaps in South Asia.

Add another state to the list of U.S. states that have human cases of the H5N1 virus. This time Wisconsin.

This virus has been found in California, Colorado, Louisiana, Michigan, Missouri, Oregon, Texas and Washington.

The Wisconsin Department of Health Services (DHS) has detected the first presumptive positive human case of Highly Pathogenic Avian Influenza A (H5N1), also known as bird flu, in Barron County. The human case follows an infected flock of commercial poultry identified in Barron County. The person had exposure to the infected flock. The case was identified through testing at the Wisconsin State Lab of Hygiene (WSLH) and is pending confirmation at CDC (Centers for Disease Control and Prevention).

Source: DHS Reports Presumptive Positive Human Case of Highly Pathogenic Avian Influenza (HPAI) in Wisconsin

This week, health officials confirmed the first known case of severe illness in the U.S. All the previous U.S. cases — there have been about 60 — were generally mild. The patient in Louisiana, who is older than 65 and had underlying medical problems, is in critical condition. Officials said the person developed severe respiratory symptoms after exposure to a backyard flock of sick birds.

Tests showed that the strain that caused the person’s illness is one found in wild birds, but not in cattle. Last month, health officials in Canada reported that a teen in British Columbia was hospitalized with a severe case of bird flu, also with the virus strain found in wild birds.

Worldwide, nearly 1,000 cases of illnesses caused by H5N1 have been reported since 2003, and more than half of people infected have died, according to the World Health Organization.

Source: California declared an emergency. How serious is bird flu?

This is an interesting discussion on H5N1 by Henry I. Miller, MS, MD.

The Media and I: H5N1 'Bird Flu'

It contains a 9:26 minute podcast about Bird Flu.

When H5N1 first began to appear in cows in the U.S. in the beginning of 2024, many cows became sick but generally recovered. But now in California around 15 percent are dying. This is having a very destructive effect on the cattle industry in California, primarily affecting dairy cows.

So why is this happening? H5N1 has been detected in very high levels in the udders of sick Dairy Cows. But in California when one cow gets H5N1, it is now leading to a swarm of dairy cows becoming infected. I have been discussing how H5N1 is transmitted for almost 6 months on this thread. I have come to the conclusion that it is being transmitted by insects. An insect drinks the blood of an infected animal and then bites an uninfected animal and spreads the diseases. Cows are very large animals and a dead cow cannot be disposed of quickly. They are being left along the sides of roads. In California when one cow dies, it is left on the ground for a day or two until it is collected and disposed of. This allows many insects to feed off the animal and carry the infection to other dairy cows.

All you have to do is collect the insects attacking the dead cow and measure the levels of H5N1 they are carrying. One way in my humble opinion to slow down the spread is to immediately treat all dead cows and other animals with a very deadly insect spray to minimize the spread of H5N1 in dairy cows.

The number of cases of H5N1 is on the rise. Add the state of Iowa to the list.

In a statement, Iowa HHS officials said the patient had mild symptoms, received treatment, and is recovering. The case was identified through testing at Iowa’s State Hygienic Laboratory and was confirmed by the Centers for Disease Control and Prevention (CDC). The new case pushes the national total since the first of the year to 65 cases from 10 states.

The farm where the patient was exposed is in the northwestern part of the state. Over the past several weeks, H5N1 has struck several Iowa commercial farms. Iowa is the nation’s top egg-producing state.

Source: H5N1 sickens Iowa poultry worker, virus strikes more cats, wild birds, and poultry

If my count is right, the human cases of Bird Flu has been observed in California, Colorado, Iowa, Louisiana, Michigan, Missouri, Oregon, Texas, Washington, Wisconsin.

More evidence of the spread of H5N1 in the U.S. This time in geese.

Shane Hesting with the Kansas Department of Wildlife and Parks who gave a rough estimate that around 14,000 sick and dead Ross’s geese, snow geese and Canada geese have reportedly been sickened or died due to the spread of bird flu in early December.

Source: K-State won’t take poultry or wild birds with bird flu

H5N1 was first identified in wild geese in China in 1996 and soon spread among birds in Asia, jumping to people on hundreds of occasions along the way. More than half of those known infections were fatal.

Source: Why scientists say we are fighting H5N1 bird flu with one hand tied behind our backs

Australia is taking the threat seriously.

I came across an analysis that was beyond my skill level of knowledge. It contains significant depth so I decided to provide this analysis. There are several strains of H5N1 in humans in the U.S. and Canada. This variant is the most deadly.

USCDC: Genetic Sequences of Highly Pathogenic Avian Influenza A(H5N1) Viruses Identified in a Person in Louisiana

Background
This is a technical summary of an analysis of the genomic sequences of the viruses identified in two upper respiratory tract specimens from the patient who was severely ill from an infection with highly pathogenic avian influenza (HPAI) A(H5N1) virus in Louisiana. The patient was infected with A(H5N1) virus of the D1.1 genotype virus that is closely related to other D1.1 viruses recently detected in wild birds and poultry in the United States and in recent human cases in British Columbia, Canada, and Washington State. This avian influenza A(H5N1) virus genotype is different from the B3.13 genotype spreading widely and causing outbreaks in dairy cows, poultry, and other animals, with sporadic human cases in the United States. Deep sequencing of the genetic sequences from two clinical specimens from the patient in Louisiana was performed to look for changes associated with adaptation to mammals. There were some low frequency changes in the hemagglutinin (HA) gene segment of one of the specimens that are rare in people but have been reported in previous cases of A(H5N1) in other countries and most often during severe infections. One of the changes found was also identified in a specimen collected from the human case with severe illness detected in British Columbia, Canada, suggesting they emerged during the clinical course as the virus replicated in the patient. Analysis of the N1 neuraminidase (NA), matrix (M) and polymerase acid (PA) genes from the specimens showed no changes associated with known or suspected markers of reduced susceptibility to antiviral drugs.

CDC Update
December 26, 2024 – CDC has sequenced the HPAI A(H5N1) avian influenza viruses in two respiratory specimens collected from the patient in Louisiana who was severely ill from an A(H5N1) virus infection. CDC received two specimens collected at the same time from the patient while they were hospitalized for severe respiratory illness: a nasopharyngeal (NP) and combined NP/oropharyngeal (OP) swab specimens. Initial attempts to sequence the virus from the patient´s clinical respiratory specimens using standard RNA extraction and multisegment-RTPCR (M-RTPCR)1 techniques yielded only partial genomic data and virus isolation was not successful. Nucleic acid enrichment was needed to sequence complete genomes with sufficient coverage depth to meet quality thresholds. CDC compared the influenza gene segments from each specimen with A(H5N1) virus sequences from dairy cows, wild birds, poultry and other human cases in the U.S. and Canada. The genomes of the virus (A/Louisiana/12/2024) from each clinical specimen are publicly posted in GISAID (EPI_ISL_19634827 and EPI_ISL_19634828) and GenBank (PQ809549-PQ809564).

Summary of amino acid mixtures identified in the hemagglutinin (HA) of clinical specimens from the patient.

Overall, the hemagglutinin (HA) sequences from the two clinical specimens were closely related to HA sequences detected in other D1.1 genotype viruses, including viruses sequenced from samples collected in November and December 2024 in wild birds and poultry in Louisiana. The HA genes of these viruses also were closely related to the A/Ezo red fox/Hokkaido/1/2022 candidate vaccine virus (CVV) with 2 or 3 amino acid changes detected. These viruses have, on average, 3 or 4 amino acid changes in the HA when compared directly to the A/Astrakhan/3212/2020 CVV sequence. These data indicate the viruses detected in respiratory specimens from this patient are closely related to existing HPAI A(H5N1) CVVs that are already available to manufacturers, and which could be used to make vaccines if needed.

There were some differences detected between the NP/OP and the NP specimens. Despite the very close similarity of the D1.1 sequences from the Louisiana human case to bird viruses, deep sequence analysis of the HA gene segment from the combined NP/OP sample detected low frequency mixed nucleotides corresponding to notable amino acid residues (using mature HA sequence numbering):

A134A/V [Alanine 88%, Valine 12%];
N182N/K [Asparagine 65%, Lysine 35%]; and
E186E/D [Glutamic acid 92%, Aspartic Acid 8%].
The NP specimen, notably, did not have these low frequency changes indicating they may have been detected from swabbing the oropharyngeal cavity of the patient. While these low frequency changes are rare in humans, they have been reported in previous cases of A(H5N1) in other countries and most often during severe disease2345. The E186E/D mixture, for example, was also identified in a specimen collected from the severe human case detected in British Columbia, Canada67.

This summary analysis focuses on mixed nucleotide detections at residues A134V, N182K, E186D as these changes may result in increased virus binding to α2-6 cell receptors found in the upper respiratory tract of humans. It is important to note that these changes represent a small proportion of the total virus population identified in the sample analyzed (i.e., the virus still maintains a majority of ´avian´ amino acids at the residues associated with receptor binding). The changes observed were likely generated by replication of this virus in the patient with advanced disease rather than primarily transmitted at the time of infection. Comparison of influenza A(H5) sequence data from viruses identified in wild birds and poultry in Louisiana, including poultry identified on the property of the patient, and other regions of the United States did not identify these changes. Of note, virus sequences from poultry sampled on the patient´s property were nearly identical to the virus sequences from the patient but did not have the mixed nucleotides identified in the patient´s clinical sample, strongly suggesting that the changes emerged during infection as virus replicated in the patient. Although concerning, and a reminder that A(H5N1) viruses can develop changes during the clinical course of a human infection, these changes would be more concerning if found in animal hosts or in early stages of infection (e.g., within a few days of symptom onset) when these changes might be more likely to facilitate spread to close contacts. Notably, in this case, no transmission from the patient in Louisiana to other persons has been identified. The Louisiana Department of Public Health and CDC are collaborating to generate additional sequence data from sequential patient specimens to facilitate further genetic and virologic analysis.

Additional genomic analysis

The genetic sequences of the A(H5N1) viruses from the patient in Louisiana did not have the PB2 E627K change or other changes in polymerase genes associated with adaptation to mammals and no evidence of low frequency changes at critical positions. And, like other D1.1 genotype viruses found in birds, the sequences lack PB2 M631L, which is associated with viral adaptation to mammalian hosts, and which has been detected in >99% of dairy cow sequences but is only sporadically found in birds. Analysis of the N1 neuraminidase (NA), matrix (M) and polymerase acid (PA) genes from the specimens showed no changes associated with known or suspected markers of reduced susceptibility to antiviral drugs. The remainder of the genetic sequences of A/Louisiana/12/2024 were closely related to sequences detected in wild bird and poultry D1.1 genotype viruses, including poultry identified on the property of the patient, providing further evidence that the human case was most likely infected following exposure to birds infected with D1.1 genotype virus.

The above article mentioned Washington State. Did I miss something? I will look a little deeper.

Bird Flu (Highly Pathogenic Avian Influenza H5N1)

The Washington State Department of Health (DOH) reported that 4 people have tested presumptive positive for highly pathogenic avian influenza (HPAI H5N1), commonly known as bird flu, in Washington state. These agricultural workers tested positive after working with infected poultry at a commercial farm in Franklin County.

At the same time Bird Flu is killing off many large cats in a sanctuary in the state.

Bird flu roars through sanctuary in Washington, kills 20 wild cats: ‘We are heartbroken’

A Washington state wildlife sanctuary is mourning the deaths of 20 wild cats amid a bird flu outbreak. The center said a variety of cats have died from the outbreak, including cougars, bobcats and African servals. "Cats are particularly vulnerable to this virus, which can cause subtle initial symptoms but progress rapidly, often resulting in death within 24 hours due to pneumonia-like conditions," the nonprofit said.

The Wild Felid Advocacy Center of Washington in Shelton, about 36 miles southwest of Bremerton, announced it is under quarantine and will be closed to the public until further notice to protect the remaining animals and stop the spread.

This is not the only large cat sanctuary affected.

Earlier this month, officials in Arizona said nearly a half-dozen animals died including a cheetah and a mountain lion at a Phoenix-area zoo died and others were sick after being exposed to the bird flu. Two big cats and three large birds − a cheetah, a mountain lion, a swamphen, a kookaburra and an Indian goose − died after contracting the virus, Jolene Westerling of the Wildlife World Zoo