Born from the COVID-19 pandemic, a viral-agnostic approach blends sequencing research and public health to get ahead of bird flu transmission.

Farmscape for November 7, 2024

Animal health officials are responding to the first case of a pig in the United States testing positive for high path H5N1 avian influenza.
On October 30th USDA confirmed that the first detection in a pig of highly pathogenic H5N1 avian influenza had occurred on a small backyard mixed farm in Oregon that housed poultry, swine, sheep and goats.
Swine Health Information Center Executive Director Dr. Megan Niederwerder notes the investigation was triggered when birds on the farm started showing clinical signs of infection.

Quote-Dr. Megan Niederwerder-Swine Health Information Center:
We know that H5N1 is a specific highly pathogenic avian influenza strain that has really increased with regards to circulation over the last two years.
This is primarily maintained in migratory waterfowl but the virus has spilled over into other mammalian species such as seals and sea lions as well as domestic livestock including dairy cattle, first detected in March of 2024 and now in the first pig in October of 2024.
These pigs that were housed on this farm, there were five pigs, none of these animals were intended for the commercial food supply.
Pork continues to be safe for consumption.
There is no concern about the safety of the nation's pork supply as a result of this finding.
The other aspect of this detection is that none of the pigs that were housed on the operation, including the one that was found to be infected, had any clinical signs.
They were completely healthy so this could indicate a low pathogenicity in pigs.
We're still learning about that.
Only a single pig has been shown to be infected so there's a lot to learn about the potential risk to the swine industry.

Dr. Niederwerder encourages pork producers to review their biosecurity procedures focussing on areas where workers or equipment may be exposed to both dairy farms and pig farms or poultry farms and pig farms.
To keep up to date on the situation visit swinehealth.org.
For more visit Farmscape.Ca.
Bruce Cochrane.

       *Farmscape is produced on behalf of North America’s pork producers

CDC: Influenza fatality rates vary widely

The National Academy of Medicine (NAM) has established an international committee (IC) in coordination with the U.S. Department of Health and Human Services’ Office of Global Affairs (OGA) to inform and facilitate efforts to advance global influenza pandemic preparedness.

Seasonal influenza and the next influenza pandemic could emerge at any time. Four new reports examine lessons learned from COVID-19 that can improve preparedness for an influenza pandemic, including vaccine R&D, supply chain resilience, and non-vaccine public health measures.

The aftermath of the avian influenza outbreak reveals multiple ingredient options for bakers.

Influenza A virus (IAV) mutates rapidly, resulting in antigenic drift and poor year-to-year vaccine effectiveness. One challenge in designing effective vaccines is that genetic mutations frequently cause amino acid variations in IAV envelope protein hemagglutinin (HA) that create new N-glycosylation sequons; resulting N-glycans cause antigenic shielding, allowing viral escape from adaptive immune responses. Vaccine candidate strain selection currently involves correlating antigenicity with HA protein sequence among circulating strains, but quantitative comparison of site-specific glycosylation information may likely improve the ability to design vaccines with broader effectiveness against evolving strains. However, there is poor understanding of the influence of glycosylation on immunodominance, antigenicity, and immunogenicity of HA, and there are no well-tested methods for comparing glycosylation similarity among virus samples. Here, we present a method for statistically rigorous quantification of similarity between two related virus strains that considers the presence and abundance of glycopeptide glycoforms. We demonstrate the strength of our approach by determining that there was a quantifiable difference in glycosylation at the protein level between WT IAV HA from A/Switzerland/9715293/2013 (SWZ13) and a mutant strain of SWZ13, even though no N-glycosylation sequons were changed. We determined site-specifically that WT and mutant HA have varying similarity at the glycosylation sites of the head domain, reflecting competing pressures to evade host immune response while retaining viral fitness. To our knowledge, our results are the first to quantify changes in glycosylation state that occur in related proteins of considerable glycan heterogeneity. Our results provide a method for understanding how changes in glycosylation state are correlated with variations in protein sequence, which is necessary for improving IAV vaccine strain selection. Understanding glycosylation will be especially important as we find new expression vectors for vaccine production, as glycosylation state depends greatly on the host species.

DOVER, Del. (February 23, 2022) – Testing has confirmed a case of avian influenza on a Delaware poultry farm that showed increased mortality over the past few days. Following an investigation by the Delaware Department of Agriculture, the U.S. Department of Agriculture’s National Veterinary Services Laboratory has confirmed poultry from this farm have tested positive […]

Federal laboratory testing has confirmed two cases of highly pathogenic H5N1 avian influenza (HPAI)—one in New Castle County, Delaware, and one in Queen Anne’s County, Maryland. These avian influenza findings follow previously announced cases on farms in New Castle County, Delaware, and Cecil County, Maryland.

Federal laboratory testing has confirmed a highly pathogenic H5N1 avian influenza (HPAI) case in a commercial broiler farm in Kent County, Delaware. Following an investigation by the Delaware Department of Agriculture and the U.S. Department of Agriculture’s (USDA) National Veterinary Services Laboratory confirmed poultry from this farm tested positive for highly pathogenic H5N1 avian influenza (HPAI).

Federal laboratory testing confirmed cases of highly pathogenic H5N1 avian influenza (HPAI) in samples taken from black vultures initially found sick and dead on April 22 in Harford County, Maryland. Considering the ongoing detections in the black vulture population, all poultry owners need to continue with increased vigilance in protecting their flocks from contracting avian influenza.

DOVER, DE (16 de Diciembre de 2022) – La División de Salud Pública de Delaware (DPH) anunció hoy la primera muerte sospechada a estar relacionada con la influenza en el estado para la temporada de influenza 2022-2023. El paciente era residente del condado de Kent y tenía entre 55 y 64 años y no se […]

Influenza A virus (IAV) is one of the leading causes of respiratory infections. The lack of efficient anti-influenza therapeutics requires a better understanding of how IAV interacts with host cells. Alveolar macrophages are tissue-specific macrophages that play a critical role in lung innate immunity and homeostasis, yet their role during influenza infection remains unclear. First, our review highlights an active IAV replication within alveolar macrophages, despite an abortive viral cycle. Such infection leads to persistent alveolar macrophage inflammation and diminished phagocytic function, alongside direct mitochondrial damage and indirect metabolic shifts in the alveolar micro-environment. We also discuss the "macrophage disappearance reaction", which is a drastic reduction of the alveolar macrophage population observed after influenza infection in mice but debated in humans, with unclear underlying mechanisms. Furthermore, we explore the dual nature of alveolar macrophage responses to IAV infection, questioning whether they are deleterious or protective for the host. While IAV may exploit immuno-evasion strategies and induce alveolar macrophage alteration or depletion, this could potentially reduce excessive inflammation and allow for the replacement of more effective cells. Despite these insights, the pathophysiological role of alveolar macrophages during IAV infection in humans remains understudied, urging further exploration to unravel their precise contributions to disease progression and resolution.

In China's Jiangsu province, a human infection with the H10N3 strain of avian influenza has been detected, said the National Health Commission (NHC).

In the South West of England, a person has contracted avian influenza. Avian influenza, also known as bird flu, is a type of influenza that spreads among birds.

First mortality case linked to medlinkavian influenza/medlink A (H3N8) virus has been reported by China, revealed the World Health Organisation. China,

Experts from Australia's national science agency warn that the country is facing an unprecedented threat from three distinct strains of medlinkavian influenza/medlink (!--ref1--).

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Influenza activity in the U.S. remained relatively low from October through January — so low, in fact, that the current flu season is considered not to have o

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The lower vaccination rate in this age group may be one reason for the unusually high number of hospitalizations and deaths, the CDC says.

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Margaret Parker, MD, FCCM, speaks with Carl O. Eriksson, MD, MPH, lead author on an article published in the November Pediatric Critical Care Medicine

An influenza expert says getting vaccinated against the infectious disease is more likely to save your life than going without the flu shot, yet only around 30-40 per cent of people are getting their jab.

The Health Department confirms a massive spike in the number of influenza cases in Western Australia this year, with 3,000 extra notifications and 14 deaths in the past week alone.

James Day died from complications caused by influenza eight days after he was admitted to hospital in eastern Victoria. He is one of 37 people killed so far this year.

Stuttgart : F. Enke, 1892.

Munchen : J.F. Lehmann, 1892.

Paul J. Birrell, Lorenz Wernisch, Brian D. M. Tom, Leonhard Held, Gareth O. Roberts, Richard G. Pebody, Daniela De Angelis.

Source: The Annals of Applied Statistics, Volume 14, Number 1, 74--93.

Abstract:
A prompt public health response to a new epidemic relies on the ability to monitor and predict its evolution in real time as data accumulate. The 2009 A/H1N1 outbreak in the UK revealed pandemic data as noisy, contaminated, potentially biased and originating from multiple sources. This seriously challenges the capacity for real-time monitoring. Here, we assess the feasibility of real-time inference based on such data by constructing an analytic tool combining an age-stratified SEIR transmission model with various observation models describing the data generation mechanisms. As batches of data become available, a sequential Monte Carlo (SMC) algorithm is developed to synthesise multiple imperfect data streams, iterate epidemic inferences and assess model adequacy amidst a rapidly evolving epidemic environment, substantially reducing computation time in comparison to standard MCMC, to ensure timely delivery of real-time epidemic assessments. In application to simulated data designed to mimic the 2009 A/H1N1 epidemic, SMC is shown to have additional benefits in terms of assessing predictive performance and coping with parameter nonidentifiability.

In the days before his death, the New York man spoke often of his lost twin and the lessons humanity seemed not to have learned

As Babe Ruth was emerging as baseball's great slugger in 1918, he fell sick with the flu

A previously healthy 9-year-old immigrant girl from Mexico was evaluated in the emergency department (ED) with one week of fatigue, fevers, rhinorrhea, and cough. She initially presented to her primary pediatrician, where a complete blood count revealed neutropenia, prompting referral to the ED. In the ED, she was found to be influenza A–positive. Because of dehydration, she received intravenous fluids and was admitted to the pediatric hospital medicine service. After 2 days, influenza symptoms improved, and oral intake increased. However, she was noted to have decreased bilateral lower-extremity strength, absent Achilles reflexes, decreased lower-extremity sensation and proprioception, a positive result on the Romberg sign, and abnormal heel-to-shin testing results. These findings prompted an urgent neurology consultation. After extensive imaging, laboratory evaluation, and further consultations, a diagnosis was established.

Children with sickle cell disease are at high risk of complications from influenza infection and have been recommended to receive annual influenza vaccine since the 1970s. Few safety studies, however, have examined the safety of influenza vaccine in this population.

This large cohort study did not find an association between influenza vaccination and hospitalization for sickle cell crises in children with sickle cell anemia. (Read the full article)

Despite recommendations and a universal immunization program, a recent survey reported suboptimal influenza vaccination coverage in children aged 6 to 23 months in Ontario. Little is known about predictors of coverage in young children to target immunization strategies.

Full influenza vaccination coverage in young children in Ontario is <10% and declining since the 2006–2007 season. Medically high-risk children including low birth weight infants are more likely to be immunized, but maternal and health services characteristics remain important. (Read the full article)

A single inhalation of laninamivir octanoate has previously been shown to be as effective as repeated doses of zanamivir in vitro and in vivo, but it is not known whether this is also the case for children.

Median time to fever resolution was not significantly different between laninamivir octanoate and zanamivir for pediatric patients with influenza. The severity of influenza symptoms and the frequency of complications were similar in the 2 groups. (Read the full article)

Since the introduction of effective vaccines in the United States, the incidence of invasive Haemophilus influenzae type b (Hib) disease in children aged <5 years has decreased by 99%. In 2007, in response to limited vaccine supply, Hib booster doses were deferred for 18 months.

This review found no significant change in the incidence of invasive Hib disease in the United States during the booster dose deferral period, suggesting that booster dose deferral is a reasonable approach to Hib vaccine shortages in the short-term. (Read the full article)

The 2009 influenza A (H1N1) pandemic caused illness in all age groups, but children were disproportionately affected. Children with underlying neurologic disorders were at high risk of influenza-related complications, including death.

This study provides the first detailed description of underlying neurologic disorders among children who died of influenza A (H1N1)pdm09 virus infection. (Read the full article)

Although several studies have demonstrated increased morbidity and mortality with pH1N1 in children, others have found its clinical course to be similar to seasonal influenza. Moreover, most studies were conducted at single centers, thus raising concerns about generalizability of findings.

This analysis provides national-level active hospital-based surveillance data comparing pH1N1 with 5 previous years of seasonal influenza A and demonstrates differences in risk factors and clinical presentation but not in ICU admission or mortality. (Read the full article)