#Disruption of seasonal #influenza #circulation and #evolution during the 2009 #H1N1 and #COVID19 #pandemics in Southeastern #Asia

Abstract

East, South, and Southeast Asia (together referred to as Southeastern Asia hereafter) have been recognized as critical areas fuelling the global circulation of seasonal influenza. However, the seasonal influenza migration network within Southeastern Asia remains unclear, including how pandemic-related disruptions altered this network. We leveraged genetic, epidemiological, and airline travel data between 2007-2023 to characterise the dispersal patterns of influenza A/H3N2 and B/Victoria viruses both out of and within Southeastern Asia, including during perturbations by the 2009 A/H1N1 and COVID-19 pandemics. During the COVID-19 pandemic, consistent autumn-winter movement waves from Southeastern Asia to temperate regions were interrupted for both subtype/lineages, however the A/H1N1 pandemic only disrupted A/H3N2 spread. We find a higher persistence of A/H3N2 than B/Victoria circulation in Southeastern Asia and identify distinct pandemic-related disruptions in A/H3N2 antigenic evolution between two pandemics, compared to interpandemic levels; similar patterns are observed in B/Victoria using genetic distance. The internal movement structure within Southeastern Asia markedly diverged during the COVID-19 pandemic season, and to a lesser extent, during the 2009 A/H1N1 pandemic season. Our findings provide insights into the heterogeneous impact of two distinct pandemic-related disruptions on influenza circulation, which can help anticipate the effects of future pandemics and potential mitigation strategies on influenza dynamics.

Source: Nature Communications, https://www.nature.com/articles/s41467-025-55840-y

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#Trends of acute respiratory #infection, including human #metapneumovirus, in the Northern Hemisphere

Situation at a glance

In many countries of the Northern Hemisphere, trends in acute respiratory infections increase at this time of year. 

These increases are typically caused by seasonal epidemics of respiratory pathogens such as seasonal influenza, respiratory syncytial virus (RSV), and other common respiratory viruses, including human metapneumovirus (hMPV), as well as mycoplasma pneumoniae. 

Many countries conduct routine surveillance for acute respiratory infections and common respiratory pathogens. 

Currently, in some countries in the temperate Northern hemisphere, influenza-like illness (ILI) and/or acute respiratory infection (ARI) rates have increased in recent weeks and are above baseline levels, following usual seasonal trends. 

Seasonal influenza activity is elevated in many countries in the Northern hemisphere. 

Where surveillance data is available, trends in RSV detections currently vary by region with decreases reported in most regions except in North America. 

Recently, there has been interest in hMPV cases in China including suggestions of hospitals being overwhelmed. 

hMPV is a common respiratory virus found to circulate in many countries in winter through to spring, although not all countries routinely test and publish data on trends in hMPV . 

While some cases can be hospitalized with bronchitis or pneumonia, most people infected with hMPV have mild upper respiratory symptoms similar to the common cold and recover after a few days. 

Based on data published by China, covering the period up to 29 December 2024, acute respiratory infections have increased during recent weeks and detections of seasonal influenza, rhinovirus, RSV, and hMPV, particularly in northern provinces of China have also increased. 

The observed increase in respiratory pathogen detections is within the range expected for this time of year during the Northern hemisphere winter. 

In China, influenza is the most commonly detected respiratory pathogen currently affecting people with acute respiratory infections. 

WHO is in contact with Chinese health officials and has not received any reports of unusual outbreak patterns. 

Chinese authorities report that the health care system is not overwhelmed and there have been no emergency declarations or responses triggered. 

WHO continues to monitor respiratory illnesses at global, regional and country levels through collaborative surveillance systems, and provides updates as needed.

Description of the situation

In many countries of the Northern Hemisphere, trends in acute respiratory infections increase at this time of year. These increases are typically caused by seasonal epidemics of respiratory pathogens such as seasonal influenza, RSV, and other common respiratory viruses, including hMPV, as well as mycoplasma pneumoniae. The co-circulation of multiple respiratory pathogens during the winter season can sometimes cause an increased burden on health care systems treating sick persons.

Currently, in some countries in the temperate Northern hemisphere, influenza-like illness (ILI) and/or acute respiratory infection (ARI) rates have increased in recent weeks and are above baseline levels, following usual seasonal trends. 

Influenza activity is elevated in many countries in Europe, Central America and the Caribbean, Western Africa, Middle Africa, and many countries across Asia, with the predominant seasonal influenza type and subtype varying by location, typical for this time of year, except during most of 2020 and 2021, when there was little influenza activity during the COVID-19 pandemic (...). 

SARS-CoV-2 activity as detected in sentinel surveillance and reported to Global Influenza Surveillance and Response System (GISRS), along with wastewater monitoring from the reporting countries, is currently low in countries in the Northern hemisphere following prolonged high level activity during summer months in the Northern hemisphere. 

Where surveillance data is available, trends in RSV activity are variable by region with downward trends observed in most subregions of the Americas, except in North America where RSV activity has increased, and decreases have been observed in the European region in recent weeks. Some countries conduct routine surveillance and report trends for other commonly circulating respiratory pathogens, such as hMPV, and report such information on a routine basis. Some countries in the Northern hemisphere have reported increased trends, varying by virus, in recent weeks, typical for this time of year.  

There has been international interest in a potential increase of respiratory virus transmission in China, particularly hMPV, including suggestions of hospitals being overwhelmed. China has an established sentinel surveillance system for ILI and severe acute respiratory infections (SARI), including hMPV, and conducts routine virological surveillance for common respiratory pathogens with detailed reports published weekly on the China Center for Disease Control and Prevention (CDC) website.[1] Surveillance and laboratory data for hMPV is not available routinely from all countries.

According to the most recent surveillance data on acute respiratory infections shared by the China CDC with data up to 29 December 2024, there has been an upward trend of common acute respiratory infections, including those due to seasonal influenza viruses, RSV and hMPV – as expected for this time of year during the Northern Hemisphere winter. 

Influenza is currently the most reported cause of respiratory disease, with the highest positivity rate among all monitored pathogens for all age groups except children aged 5-14 years for whom mycoplasma pneumoniae had the highest positivity rate. SARS-CoV-2 activity remains low however with an increase in reported severe COVID-19 cases. 

The predominant circulating SARS-CoV-2 variant in the country is XDV and its sublineages accounting for  59.1% detection among sequenced samples. ILI activity in China’s northern and southern provinces have been increasing since late 2024, following the previous year’s trends. Current ILI activity in the southern provinces remains below that of the previous two years, while current ILI activity in the northern provinces is similar to levels seen at this time in the previous two years.

China’s reported levels of acute respiratory infections, including hMPV, are within the expected range for the winter season with no unusual outbreak patterns reported. Chinese authorities confirmed that the health care system is not overwhelmed, hospital utilization is currently lower than this time last year, and there have been no emergency declarations or responses triggered. Since the expected seasonal increase was observed, health messages have been provided to the public on how to prevent the spread of respiratory infections and reduce the impact of these diseases.

Public health response

Based on the expected increase in respiratory infections during the winter season, countries, including China, have been providing health messages to the public on how to prevent the spread of respiratory infections and reduce the impact of disease.

WHO risk assessment

In temperate climates, seasonal epidemics of common respiratory pathogens, including influenza, occur often during winter periods. The observed increases in acute respiratory infections and associated pathogen detections in many countries in the Northern hemisphere in recent weeks is expected at this time of year and is not unusual. The co-circulation of respiratory pathogens may pose a burden to health facilities. 

WHO advice

WHO recommends that individuals in areas where it is winter take normal precautions to prevent the spread and reduce risks posed by respiratory pathogens, especially to the most vulnerable. People with mild symptoms should stay home to avoid infecting other people and rest. 

People at high risk or with complicated or severe symptoms should seek medical care as soon as possible. 

Individuals should also consider wearing a mask in crowded or poorly ventilated spaces, cover coughs and sneezes with a tissue or bent elbow, practice regular handwashing, and get recommended vaccines as per physician and local public health authorities’ advice.[2]

WHO advises Member States to maintain surveillance for respiratory pathogens through an integrated approach, considering country context, priorities, resources and capacities. WHO has published guidance on integrated surveillance here. WHO has also updated guidance on assessing influenza epidemic and pandemic severity, including the impact on healthcare facilities, here.

Based on the current risk assessment, WHO advises against any travel or trade restrictions related to current trends in acute respiratory infections.

Further information

-- World Health Organization (WHO). Implementing the integrated sentinel surveillance of influenza and other respiratory viruses of epidemic and pandemic potential by the Global Influenza Surveillance and Response System. Available at: https://iris.who.int/handle/10665/379678

-- WHO fact sheet for Influenza (Seasonal): https://www.who.int/news-room/fact-sheets/detail/influenza-(seasonal)

-- WHO Routine influenza weekly updates. Available at:https://www.who.int/teams/global-influenza-programme/surveillance-and-monitoring/influenza-updates

-- WHO Influenza surveillance outputs. Available at: https://www.who.int/teams/global-influenza-programme/surveillance-and-monitoring/influenza-surveillance-outputs

-- WHO Global COVID-19 Dashboard. Available at:  https://data.who.int/dashboards/covid19/cases

-- WHO Coronavirus disease (COVID-19) Epidemiological Updates. Available at: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports

-- WHO Clinical practice guidelines for influenza. Available at: https://www.who.int/publications/i/item/9789240097759

-- WHO Respiratory Syncytial Virus (RSV) disease. Available at: https://www.who.int/teams/health-product-policy-and-standards/standards-and-specifications/norms-and-standards/vaccine-standardization/respiratory-syncytial-virus-disease https://www.chinacdc.cn/jksj/jksj04_14249/

-- US CDC Human Metapneumovirus. Available at: https://www.cdc.gov/human-metapneumovirus/about/index.html

-- American Lung Association. Human Metapneumovirus (hMPV) Symptoms and Diagnosis. Available at: https://www.lung.org/lung-health-diseases/lung-disease-lookup/human-metapneumovirus-hmpv/symptoms-diagnosis

[1] China CDC Weekly Influenza Surveillance Report. Available at: https://www.chinacdc.cn/jksj/jksj04_14249/   

[2] WHO Clinical practice guidelines for influenza. Available at: https://www.who.int/publications/i/item/9789240097759

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Source: World Health Organization, https://www.who.int/emergencies/disease-outbreak-news/item/2025-DON550

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#Avian #flu #risk still ‘low’ after first #US #patient dies from #H5N1 virus: #WHO

7 January 2025 

A day after the United States reported its first human death from avian flu, the UN World Health Organization (WHO) insisted on Tuesday that the risk to the wider population remains “low”. 

WHO spokesperson Dr. Margaret Harris told reporters in Geneva that the H5N1 virus causing the disease is “not circulating in humans but jumping into humans” who are exposed to poultry or dairy cattle. “We’re not seeing sustained circulation,” she insisted.

Underlying conditions

The man who died of the disease in Louisiana was over 65 and reportedly had underlying medical conditions, Dr. Harris said. 

According to the health authorities, he had been exposed to chickens and wild birds. Several dozen people in the US have contracted avian influenza – commonly referred to as bird flu – during the current outbreak, mainly farmworkers in close contact with poultry flocks and cattle herds.

Dr. Harris stressed that WHO’s assessment of the risk to the general population “is still low and remains set”. The main concern is for people who work in animal industries because they need to be better protected from infection.

The WHO spokesperson added that the United States was continuing to carry out “a lot of surveillance” in the human and animal population, “in the methods we use for farming, for our food production…all those things need to be combined because indeed it always does pose a risk”.

China respiratory virus is not new

Meanwhile, a respiratory virus gaining ground in China, known as the human metapneumovirus, or hMPV, has been sparking media attention in recent weeks, but it does not represent a new or major threat, Dr. Harris insisted.

The UN health agency spokesperson said that such infections are on the rise in China “as expected during winter”, with seasonal influenza being “by far the most common among them”, as reported by the Chinese Center for Disease Control and Prevention.

“China’s reported levels of respiratory infections are within the usual range for the winter season,” Dr. Harris explained. “Authorities report that hospital utilization is currently lower than this time last year, and there have been no emergency declarations or responses triggered,” she added.

As for hMPV, it was first identified in 2001 and “has been in the human population for a long time”, Dr. Harris clarified. 

‘Very, very low’ risk

She added that it is a common virus that circulates in winter and spring and usually “causes respiratory symptoms similar to the common cold”. 

Like any of the hundreds of common cold viruses known to exist, it can lead to more serious disease in patients with low immunity, particularly but not limited to newborns and the elderly.

Asked about hMPV’s mortality rate, Dr. Harris described it as “very, very low”. It is not a pathogen that normally leads to deaths in humans, save for the most vulnerable, she concluded, recommending “simple” prevention measures, such as wearing a mask, improving ventilation of closed spaces and handwashing.

Source: United Nations, https://news.un.org/en/story/2025/01/1158776

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Social Media #Memes and Early Public #Opinion #Formation Regarding Highly Pathogenic Avian #Influenza (HPAI) as a Public Health #Threat in the #USA

 {Summary}

Misinformation, disinformation, and conspiracy theories gain traction in times of uncertainty when little is known about a disease and when trust in government and public institutions is low. Amidst uncertainty, public health-related memes act as a sort of coping mechanism. Memes images, text, or video that serve as a shorthand form of communication—have the potential to spread quickly and widely on social media. While memes can be humorous, perhaps harmless, they can have serious effects at other times, as during the COVID-19 pandemic. One thing they have in common, however, is their transportability from user to user and platform to platform.  Frame analysis of Internet memes is useful for categorizing what we call frames of meaning in digital space. Unlike the agenda-setting function of mass media, in which gatekeepers (e.g., news editors) set the agenda regarding public issues, framing theory in the digital age is more dynamic, as content may take on different forms or formats, change over time, and the digital frame may traverse media platforms. Consumer-generated content (CGC) plays a significant role in setting the agenda or framing the event. Based onthe fluid nature of social networks and changes in the hierarchy of agenda setting, the model of connective action applied to public discourse on digital media can be visualized and analyzed through topic modeling to understand the role that memes play in shaping emergent public issues. In this study, we focused on memes shared in response to the current Highly Pathogenic Avian Influenza (HPAI), specifically the H5N1 outbreak in the United States, to get a glimpse into the early stages of public opinion formation around a potential public health issue. We present this approach to study the situational awareness of this public health issue through analysis of memes as a form of public discourse and as a cost-effective tool for resource challenged public health agencies to scan the environment for emergent issues.

(...)

Source: Disaster Medicine and Public Health Preparedness, https://www.cambridge.org/core/journals/disaster-medicine-and-public-health-preparedness/article/social-media-memes-and-early-public-opinion-formation-regarding-highly-pathogenic-avian-influenza-hpai-as-a-public-health-threat-in-the-united-states/5119C8A5DA2152D4392FC93BDCE575A8

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#Polymerase #mutations underlie #adaptation of #H5N1 #influenza virus to dairy #cattle and other #mammals.

Abstract

In early 2024, an unprecedented outbreak of H5N1 high pathogenicity avian influenza was detected in dairy cattle in the USA. The epidemic remains uncontrolled, with spillbacks into poultry, wild birds and other mammals including humans. Here, we present molecular and virological evidence that the cattle B3.13 genotype H5N1 viruses rapidly accumulated adaptations in polymerase genes that enabled better replication in bovine cells, as well as cells of other mammalian species including humans and pigs. We find evidence of several mammalian adaptations gained early in the evolution of these viruses in cattle including PB2 M631L, which is found in all cattle sequences, and PA K497R, which is found in the majority. Structurally, PB2 M631L maps to the polymerase-ANP32 interface, an essential host factor for viral genome replication. We show this mutation adapts the virus to co-opt bovine ANP32 proteins and thereby enhances virus replication in bovine and primary human airway cells. Importantly, we show that ongoing evolution during 2024 in the PB2 gene, including a convergently arising D740N substitution, further increases polymerase activity in a range of mammalian cells. Thus, the continued circulation of H5N1 in dairy cattle allows virus adaption improving replicative ability in cattle and increasing zoonotic spillover risk.

Source: BioRxIV, https://www.biorxiv.org/content/10.1101/2025.01.06.631435v1?rss=1

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First #H5N1 #Birdflu #Death Reported in #USA

January 6, 2025 -- CDC is saddened by Louisiana's report that a person previously hospitalized with severe avian influenza A(H5N1) illness ("H5N1 bird flu") has passed away. 

While tragic, a death from H5N1 bird flu in the United States is not unexpected because of the known potential for infection with these viruses to cause severe illness and death. 

As of January 6, 2025, there have been 66 confirmed human cases of H5N1 bird flu in the United States since 2024 and 67 since 2022. 

This is the first person in the United States who has died as a result of an H5 infection. 

Outside the United States, more than 950 cases of H5N1 bird flu have been reported to the World Health Organization; about half of those have resulted in death.

CDC has carefully studied the available information about the person who died in Louisiana and continues to assess that the risk to the general public remains low. 

Most importantly, no person-to-person transmission spread has been identified. 

As with the case in Louisiana, most H5 bird flu infections are related to animal-to-human exposures. 

Additionally, there are no concerning virologic changes actively spreading in wild birds, poultry, or cows that would raise the risk to human health. (CDC reported previously on its analysis of the viruses isolated from the patient in Louisiana.) 

However, people with job-related or recreational exposures to infected birds or other animals are at greater risk of infection. For these and others, CDC has developed prevention resources about how to protect yourself.

CDC is continually:

-- Supporting critical epidemiologic investigations with state and local partners to assess the public health impact of each H5 case.

-- Working closely with state and local partners to conduct active surveillance for H5 cases.

-- Monitoring for changes that might suggest H5 viruses are becoming better adapted to mammals and therefore might spread more easily from animals-to-humans or human-to-human or cause more severe disease.

-- Monitoring for any viral changes that could make these viruses less responsive to flu antiviral medications or the available candidate vaccine viruses.

-- Additional information about H5 bird flu is available on the CDC website.

Source: US Centers for Disease Control and Prevention, https://www.cdc.gov/media/releases/2025/m0106-h5-birdflu-death.html

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#USA, #Louisiana Department of Health reports first U.S. #H5N1-related #human #death

{Edited}

January 06, 2025

The Louisiana Department of Health reports the patient who had been hospitalized with the first human case of highly pathogenic avian influenza (HPAI), or H5N1, in Louisiana and the U.S. has died. 

The patient was over the age of 65 and was reported to have underlying medical conditions. 

The patient contracted H5N1 after exposure to a combination of a non-commercial backyard flock and wild birds. 

LDH’s extensive public health investigation has identified no additional H5N1 cases nor evidence of person-to-person transmission. This patient remains the only human case of H5N1 in Louisiana. 

The Department expresses its deepest condolences to the patient’s family and friends as they mourn the loss of their loved one. Due to patient confidentiality and respect for the family, this will be the final update about the patient. 

While the current public health risk for the general public remains low, people who work with birds, poultry or cows, or have recreational exposure to them, are at higher risk.

The best way to protect yourself and your family from H5N1 is to avoid sources of exposure. That means avoiding direct contact with wild birds and other animals infected with or suspected to be infected with bird flu viruses. 

Protecting yourself and others from H5N1 infection

-- Do not touch sick or dead animals or their droppings and do not bring sick wild animals into your home.

-- Keep your pets away from sick or dead animals and their feces.

-- Do not eat uncooked or undercooked food. Cook poultry, eggs and other animal products to the proper temperature and prevent cross-contamination between raw and cooked food.

-- Avoid uncooked food products such as unpasteurized raw milk or cheeses from animals that have a suspected or confirmed infection.

-- If you work on poultry or dairy farms, talk to your provider about getting your seasonal flu vaccination. It will not prevent infection with avian influenza viruses, but it can reduce the risk of coinfection with avian and flu viruses.

-- Report dead or sick birds or animals to the USDA toll-free at 1-866-536-7593 or the Louisiana Department of Agriculture and Forestry Diagnostic Lab at 318-927-3441.

-- If you have been exposed to sick or dead birds or other animals or work on a farm where avian influenza has been detected, watch for respiratory symptoms or conjunctivitis. If you develop symptoms within 10 days after exposure to sick or dead animals, tell your healthcare provider that you have been in contact with sick animals and are concerned about avian influenza. This will help them give you appropriate advice on testing and treatment. Stay home and away from others while you have symptoms.

Source: Department of Health, https://ldh.la.gov/news/H5N1-death

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#USA reports its first #human fatal case of #H5N1 #birdflu virus

 {Excerpt, edited, original article in Bahasan}

KOMPAS.com - The United States recorded its first death from bird flu ( H5N1 ), as recorded by the Louisiana Department of Health (LDH), Monday (6/1/2025) local time. Quoted from the Washington Post , Tuesday (7/1/2025), this case occurred in Louisiana, involving a patient over 65 years old who had comorbidities.

(...)

Source: Kompas, https://health.kompas.com/read/25A07073728468/as-laporkan-kasus-kematian-pertama-flu-burung-pada-manusia#

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#USA, #Genetic #Sequences of Highly Pathogenic Avian #Influenza A(#H5N1) Viruses Identified in a Person in #Louisiana

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

What to know

-- CDC has sequenced the influenza viruses in specimens collected from the patient in Louisiana who was infected with, and became severely ill from HPAI A(H5N1) virus. 

-- The genomic sequences were compared to other HPAI A(H5N1) sequences from dairy cows, wild birds and poultry, as well as previous human cases and were identified as the D1.1 genotype. 

-- The analysis identified low frequency mutations in the hemagglutinin gene of a sample sequenced from the patient, which were not found in virus sequences from poultry samples collected on the patient’s property, suggesting the changes emerged in the patient after infection.

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.

Follow Up Actions

Overall, CDC considers the risk to the general public associated with the ongoing U.S. HPAI A(H5N1) outbreak has not changed and remains low. The detection of a severe human case with genetic changes in a clinical specimen underscores the importance of ongoing genomic surveillance in people and animals, containment of avian influenza A(H5) outbreaks in dairy cattle and poultry, and prevention measures among people with exposure to infected animals or environments.

Source: US Centers for Disease Control and Prevention, https://www.cdc.gov/bird-flu/spotlights/h5n1-response-12232024.html

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#Zoonotic #transmission of novel #Influenza A #variant viruses detected in #Brazil during 2020 to 2023

Abstract

Zoonotic infections (swine-human) caused by influenza A viruses (IAVs) have been reported and linked to close contact between these species. Here, we describe eight human IAV variant infections (6 mild and 2 severe cases, including 1 death) detected in Paraná, Brazil, during 2020–2023. Genomes recovered were closely related to Brazilian swIAVs of three major lineages (1 A.3.3.2/pdm09, 1B/human-like, and H3.1990.5), including three H1N1v, two H1N2v, two H3N2v and one H1v. Five H1v were closely related to pdm09 lineage, one H1v (H1N2v) grouped within 1B.2.3 clade, and the two H3v grouped within a clade composed exclusively of Brazilian H3 swIAV (clade H3.1990.5.1). Internal gene segments were closely related to H1N1pdm09 isolated from pigs. IAV variant rarely result in sustained transmission between people, however the potential to develop such ability is of concern and must not be underestimated. This study brings into focus the need for continuous influenza surveillance and timely risk assessment.

Source: Nature Communications, https://www.nature.com/articles/s41467-024-53815-z

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#Portugal - High pathogenicity avian #influenza #H5N1 viruses (#poultry) (Inf. with) - Immediate notification

 A poultry farm in Lisboa Region.

Source: WOAH, https://wahis.woah.org/#/in-review/6164

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#Hungary - High pathogenicity avian #influenza #H5N1 viruses (#poultry) (Inf. with) - Immediate notification

 A poultry farm in Szabolcs-Szatmár-Bereg Region.

Source: WOAH, https://wahis.woah.org/#/in-review/6165

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#Germany - #Influenza A #H5N1 viruses of high pathogenicity (Inf. with) (non-poultry including wild birds) (2017-) - Immediate notification

 Wild Anatidae birds in Hessen Region, Frankfurt am Main.

Source: WOAH, https://wahis.woah.org/#/in-review/6166

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Anti- #neuraminidase and anti- #hemagglutinin #stalk responses to different #influenza A(#H7N9) #vaccine regimens

Abstract

Introduction

Pandemic influenza vaccine development focuses on the hemagglutinin (HA) antigen for potency and immunogenicity. Antibody responses targeting the neuraminidase (NA) antigen, or the HA stalk domain have been implicated in protection against influenza. Responses to the NA and HA-stalk domain following pandemic inactivated influenza are not well characterized in humans.

Material and methods

In a series of clinical trials, we determine the vaccines' NA content and demonstrate that NA inhibition (NAI) antibody responses increase in a dose-dependent manner following a 2-dose priming series with AS03-adjuvanted influenza A(H7N9) inactivated vaccine (A(H7N9) IIV). NAI antibody responses also increase with interval extension of the 2-dose priming series or following a 5-year delayed boost with a heterologous adjuvanted A(H7N9) IIV. Neither concomitant seasonal influenza vaccination given simultaneously or sequentially, nor use of heterologous A(H7N9) IIVs in the 2-dose priming series had an appreciable effect on NAI antibody responses. Anti-HA stalk antibody responses were minimal and not durable.

Conclusions

We provide evidence for strategies to improve anti-neuraminidase responses which can be further standardized for pandemic preparedness.

Source: Vaccine, https://www.sciencedirect.com/science/article/abs/pii/S0264410X24013719?via%3Dihub

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Evidence of #Influenza A(#H5N1) #Spillover #Infections in #Horses, #Mongolia

Abstract

Recent outbreaks of influenza A(H5N1) have affected many mammal species. We report serologic evidence of H5N1 virus infection in horses in Mongolia. Because H3N8 equine influenza virus is endemic in many countries, horses should be monitored to prevent reassortment between equine and avian influenza viruses with unknown consequences.

Source: Emerging Infectious Diseases Journal, https://wwwnc.cdc.gov/eid/article/31/1/24-1266_article

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#USA, #Update on #Delaware #H5 Avian #Influenza Case on Kent County #Farm

DOVER, Del. (January 5, 2025)—The U.S. Department of Agriculture’s National Veterinary Services Laboratory (NVSL) has returned results from the Kent County, Del. poultry farm that was announced presumptive positive for H5 avian influenza on January 3, 2025. The poultry affected had highly pathogenic H5 avian influenza (HPAI) of the Eurasian lineage 2.3.4.4b with early indications that the virus is the D1.1 genotype found in wild birds; however, confirmation of the genotype is determined by sequencing. There is currently no timeline for the receipt of this data by the Delaware Department of Agriculture.

All poultry farms in the state should be monitoring flocks for any signs of increased mortality. Producers should pay particular attention to whether birds show signs of respiratory illness or distress, such as sneezing, gasping for air, coughing, and/or runny nose. Other signs of HPAI in poultry can include swelling around the eyes, neck, and head; purple discoloration of the wattles, combs, and legs; tremors, drooping wings, circling, twisting of the head and neck, or any combination; watery, green diarrhea; lack of energy, poor appetite; and a drop in egg production, or soft or thin-shelled, misshapen eggs.

Commercial poultry producers should follow the protocol of notifying the company they grow for when they see any signs of HPAI.

Backyard flock owners who notice any of the signs of HPAI or experience increased mortality in their flock should email the Delaware Poultry Health Hotline at poultry.health@delaware.gov or call 302-698-4507 and provide your contact information, flock size, location, and concerns. Backyard flock owners will be contacted if a sample needs to be taken. Do not take dead or sick birds to a lab to be tested or move them off-site.

Backyard flock owners should keep their flock from commingling with wild birds and keep them under cover to protect them from coming into contact with infected wild bird droppings. The H5N1 virus has infected a small number of people across the U.S., and there has been no documented transmission between people in the U.S. to date. While continuing testing of people in close contact with animals infected with HPAI indicates a low risk to the general public’s health, backyard flock owners should keep birds in outdoor coops and not bring birds that have been living outside into the home. Children and pets should be kept away from wild birds and bird droppings.

When adding birds to your flock, make sure to purchase them from a reputable source. The baby chicks purchased at local farm stores come from NPIP-certified flocks tested and shown to be free from avian influenza. When they are between two days and two weeks old, these chicks will typically leave the store with their new owner, so they are considered low-risk for having the disease. However, once they are about three weeks old, they are more susceptible to contracting the virus from their new environment. Make sure to keep new birds or returning show birds separated from the established home flocks for 30 days.

The Delaware Department of Agriculture requires the registration of all locations where live poultry is kept, which allows timely information on disease incidents to be sent to all poultry producers. Registration forms are available online at https://de.gov/poultry.

Delawareans are reminded not to touch or handle injured, sick, or dead birds and to use the DNREC Division of Fish and Wildlife’s Sick and Dead Wildlife Reporting Form should they encounter dead or sick birds. Wild birds should not be reported to the Delaware Poultry Health Hotline, as that reporting hotline is reserved for backyard flocks and farms with poultry.

(...)

Source: Government of Delaware State, https://news.delaware.gov/2025/01/05/update-on-delaware-h5-avian-influenza-case-on-kent-county-farm/

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#China, National sentinel #surveillance of acute #respiratory infectious #diseases (Week 52, 2024)

{Excerpt}

In the 52nd week of 2024 ( December 23rd to December 29th ), respiratory samples from outpatient influenza-like cases and hospitalized severe acute respiratory infection cases collected in sentinel hospitals across the country (excluding Hong Kong, Macao and Taiwan) were tested for 10 viruses including the new coronavirus, influenza virus, respiratory syncytial virus, adenovirus, human metapneumovirus, parainfluenza virus, common coronavirus, bocavirus, rhinovirus and enterovirus, as well as multiple respiratory pathogens including Mycoplasma pneumoniae.

1. Test results

The pathogens detected positive in respiratory samples of influenza-like cases in outpatient and emergency departments of sentinel hospitals were mainly influenza virus, human metapneumovirus, and rhinovirus; the pathogens detected positive in respiratory samples of hospitalized severe acute respiratory infection cases were mainly influenza virus, Mycoplasma pneumoniae, and human metapneumovirus. The specific results are shown in Table 1 , Figure 1 , and Figure 2. The test results showed differences between the north and south regions and between different age groups, as shown in Table 2 and Table 3 .

2. Analysis and health tips

The results showed that the overall acute respiratory infectious diseases are showing a continuous upward trend, and the trends of infections caused by different pathogens are different. Influenza is generally in the seasonal epidemic period, and the influenza virus positive rate is rising rapidly. Among them, the influenza virus positive rate of outpatient influenza-like cases nationwide increased by 6.2% compared with last week ; the level of influenza activity varies among provinces, and the increase in northern provinces is slightly obvious, but still lower than the same period last year. Recently, the positive rate of respiratory syncytial virus in cases aged 0 to 4 years and the positive rate of human metapneumovirus in cases aged 14 years and below have fluctuated upward, and the upward trend is more obvious in northern provinces. The positive rate of rhinovirus continues to decline; the positive rate of Mycoplasma pneumoniae in northern provinces continues to decline, and Mycoplasma pneumoniae infection in southern provinces is still at a low level. The positive rate of adenovirus fluctuates and declines. Other respiratory pathogens such as the new coronavirus are at a low epidemic level.

We are still in the season of high incidence of respiratory infectious diseases. In order to reduce the spread of diseases and reduce the harm of diseases, the public is advised to take the following protective measures:

( 1 ) Maintain good hygiene habits: cover your mouth and nose with a tissue, towel or elbow when coughing or sneezing; wash your hands frequently with soap and water for at least 20 seconds, or use alcohol-based hand sanitizer; avoid touching your eyes, nose, and mouth with your hands to reduce the risk of pathogen transmission.

( 2 ) Promote a healthy lifestyle: A balanced diet, moderate exercise and adequate rest can help enhance immunity. If you have a fever, cough or other respiratory infection symptoms, it is recommended to rest at home, avoid going to work or school while sick, wear a mask when in contact with family members, and keep the room well ventilated.

( 3 ) Wear a mask scientifically: Wear a mask throughout the medical treatment process; it is recommended to wear a mask in crowded places or when taking public transportation (such as airplanes, trains, subways, etc.).

( 4 ) Actively vaccinate: People with weak immunity (such as pregnant women, young children, the elderly and patients with chronic diseases) should be vaccinated with relevant vaccines to prevent respiratory infectious diseases in a timely manner according to vaccination guidelines, including influenza vaccine, new coronavirus vaccine and pneumococcal vaccine. In particular, as the level of influenza activity has increased recently, people of appropriate age who have not received influenza vaccination should be vaccinated as soon as possible. 

(...)

Source: China Centers for Disease Control and Prevention, https://www.chinacdc.cn/jksj/jksj04_14275/202501/t20250102_303654.html

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#Detection of #Hemagglutinin #H5 #influenza A virus #RNA and model of potential inputs in an #urban #California #sewershed

Abstract

In 2024, the highly pathogenic avian influenza A H5N1 caused outbreaks in wild birds, poultry, cows, and other mammals in the United States with 61 human cases also reported by the CDC. Detection of influenza A H5 RNA in wastewater has been previously reported in sewersheds in Texas and North Carolina with nearby impacted dairy herds following the emergence of H5N1 in dairy cows. Here, we conduct retrospective testing of total influenza A and H5 hemagglutinin genes in wastewater as well presenting and applying new assays for detection of H1 and H3 genes across a respiratory virus season in an urban California sewershed from September 2023-May 2024. Total influenza A, H1, and H3 were regularly detected, while H5 was first detected in March. We developed a model that uses Monte Carlo simulations and previously published parameters to estimate numbers of infected people, poultry, wild birds, or liters of H5-contaminated milk required to result in measured H5 concentrations in wastewater. Our findings demonstrate that in this California sewershed, contaminated milk or infected poultry were the most likely sources of H5 to wastewater. We created a publicly available tool to apply the H5 input model in other sewersheds estimate required inputs.

Source: MedRxIV, https://www.medrxiv.org/content/10.1101/2024.12.31.24319823v1

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