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

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

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.

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--).

Attention has been paid to H5N6 highly pathogenic avian influenza virus (HPAIV) because of its heavy burden on the poultry industry and human mortality. Since an influenza A virus carrying N6 neuraminidase (NA) has never spread in humans, the potential for H5N6 HPAIV to cause disease in humans and the efficacy of antiviral drugs against the virus need to be urgently assessed. We used non-human primates to elucidate the pathogenesis of H5N6 HPAIV as well as to determine the efficacy of antiviral drugs against the virus. H5N6 HPAIV infection led to high fever in cynomolgus macaques. The lung injury caused by the virus was severe with diffuse alveolar damage and neutrophil infiltration. In addition, an increase in IFN-α showed an inverse correlation with virus titers during the infection process. Oseltamivir was effective for reducing H5N6 HPAIV propagation, and continuous treatment with peramivir reduced virus propagation and severity of symptoms in the early stage. This study also showed the pathologically severe lung injury states in the cynomolgus macaques infected with H5N6 HPAIV, even in those that received early antiviral drug treatments, indicating the need for close monitoring and the need for further studies on the virus pathogenicity and new antiviral therapies.

DOVER – Delaware authorities are urging poultry and bird owners to be vigilant in the wake of avian influenza cases reported in Oregon and Washington state. “Though it’s far away at the moment, we know that avian influenza can spread rapidly,” said Delaware State Veterinarian Dr. Heather Hirst, who heads the Delaware Department of Agriculture’s […]

To protect against the spread of avian influenza, the Delaware Department of Agriculture is prohibiting waterfowl entries in the poultry competitions at the Delaware State Fair next month. "This action is being taken out of an abundance of caution to guard against the spread of avian influenza," said Delaware State Veterinarian Dr. Heather Hirst. There have been no East Coast cases of the disease. There are no immediate public health concerns, and poultry and eggs which are properly prepared and cooked are still safe to eat.

Accurate detection of influenza A virus (IAV) is crucial for patient management, infection control, and epidemiological surveillance. The World Health Organization and the Centers for Disease Control and Prevention have recommended using the M gene as the diagnostic gene target for reverse-transcription-PCR (RT-PCR). However, M gene RT-PCR has reduced sensitivity for recent IAV due to novel gene mutations. Here, we sought to identify novel diagnostic targets for the molecular detection of IAV using long-read third-generation sequencing. Direct nanopore sequencing from 18 nasopharyngeal specimens and one saliva specimen showed that the 5' and 3' ends of the PB2 gene and the entire NS gene were highly abundant. Primers selected for PB2 and NS genes were well matched with seasonal or avian IAV gene sequences. Our novel PB2 and NS gene real-time RT-PCR assays showed limits of detection similar to or lower than that of M gene RT-PCR and achieved 100% sensitivity and specificity in the detection of A(H1N1), A(H3N2), and A(H7N9) in nasopharyngeal and saliva specimens. For 10 patients with IAV detected by M gene RT-PCR conversion in sequentially collected specimens, NS and/or PB2 gene RT-PCR was positive in 2 (20%) of the initial specimens that were missed by M gene RT-PCR. In conclusion, we have shown that PB2 or NS gene RT-PCRs are suitable alternatives to the recommended M gene RT-PCR for diagnosis of IAV. Long-read nanopore sequencing facilitates the identification of novel diagnostic targets.

Malo Bulu, Petrus, author