Novel avian coronavirus and fulminating disease in guinea fowl, France.

For decades, French guinea fowl have been affected by fulminating enteritis of unclear origin. By using metagenomics, we identified a novel avian gammacoronavirus associated with this disease that is distantly related to turkey coronaviruses. Fatal respiratory diseases in humans have recently been caused by coronaviruses of animal origin.

Goose Hemorrhagic polyomavirus detection in geese using real-time PCR assay.

Goose hemorrhagic polyomavirus (GHPV) is the viral agent of hemorrhagic nephritis enteritis of geese (HNEG), a lethal disease of goslings. Although death is the most common outcome, geese that recover from HNEG are persistently infected. Here, we present the development of real-time SYBR Green real-time PCR targeted to GHPV and its use to assess the prevalence of GHPV infection in French geese flocks. When compared with classical end-point PCR, real-time PCR revealed a much better sensitivity and equivalent specificity. Real-time PCR could, therefore, be considered a gold standard for the detection of GHPV. Results of field investigations evidenced a very high prevalence of GHPV infections in French geese, largely associated with healthy carriage.

A low-pathogenic avian influenza H6N1 outbreak in a turkey flock in France: a comprehensive case report.

Based on a case observed and investigated on a commercial turkey farm in western France in 81-day-old birds, we report the pattern of H6N1 low-pathogenic avian influenza in this species. Diseased birds displayed an acute severe dyspnoea, leading to death by asphyxia of more than 5% of the flock. The most specific pathological feature was a constant diffuse infraorbital sinusitis, along with a focal necrotic exudate inside the lumen of the upper respiratory tract, characterized microscopically as a mixed fibrinous and leucocytic material. Influenza A immunohistochemistry revealed an intense staining of epithelial cells in tracheas, bronchi, air sacs and their luminal necrotic material. While no primary bacterial infection could be detected from diseased turkeys, influenza H6 reverse transcription-polymerase chain reaction analysis performed on tracheal swabs tested positive. Direct sequencing and phylogenetic analysis of the eight segments showed that this H6N1 virus clustered closely within West European mallards' (group 3) H6 genotypes. A thorough analysis of genetic databases suggests that a regional waterfowl reservoir is likely to play a central role in H6 introductions in poultry farms, whose pathways remain to be elucidated.

Pathological and epidemiological significance of goose haemorrhagic polyomavirus infection in ducks.

Goose haemorrhagic polyomavirus (GHPV) is the viral agent of haemorrhagic nephritis enteritis of geese, a lethal disease of goslings. It was recently shown that GHPV can also be detected in Muscovy and mule ducks. The goal of the present study was to investigate the pathobiology of GHPV in ducks. In the first experiment, field isolates of GHPV from Muscovy or mule ducks were fully sequenced and compared with goose GHPV. These duck isolates were then used to inoculate 1-day-old goslings. Typical clinical signs and lesions of haemorrhagic nephritis enteritis of geese were reproduced, indicating that "duck-GHPV" isolates are virulent in geese. In the second experiment, 1-day-old and 21-day-old Muscovy ducklings were infected by a reference GHPV strain. In both cases, neither clinical signs nor histopathological lesions were observed. However, the virus was detected in cloacal bursae and sera, and serological responses were detected at 12 days post infection. These findings suggest firstly that one common genotype of GHPV circulates among ducks and geese, and secondly that ducks may be infected by GHPV but show no pathologic evidence of infection, whereas geese express clinical signs. GHPV infection should therefore be considered as being carried in ducks and of epidemiological relevance in cases of contact with goose flocks.

Detection and Typing of a Fowl Adenovirus Type 1 Agent of Pancreatitis in Guinea Fowl.

Adenoviral pancreatitis has been amply described for decades in guinea fowl. Although its pathologic picture has been characterized fairly well, its etiology still remains only partially clarified. Based on several outbreaks diagnosed on commercial guinea flocks raised in France since 2017, we performed direct whole-genome sequencing from pancreatic lesional tissue by using the Oxford Nanopore Technologies (ONT) sequencing method. We generated 4781 viral reads and assembled a whole genome of 43,509 bp, clustering within fowl adenovirus type 1 (FAdV-1). A phylogenetic analysis based on a partial sequence of the hexon and short fiber genes on viruses collected in France showed 98.7% and 99.8% nucleotide identity, respectively. Altogether, these results confirm that an FAdV-1 closely related to chicken and other avian strains is the agent of pancreatitis in guinea fowl. This study illustrates the potential of ONT sequencing method to achieve rapid whole-genome sequencing directly from pathologic material.

Detección y tipificación de un adenovirus aviar tipo 1 (FAdV-1), agente de pancreatitis en gallinas de Guinea. La pancreatitis adenoviral se ha descrito ampliamente durante décadas en gallinas de Guinea. Aunque su cuadro patológico se ha caracterizado bastante bien, su etiología todavía permanece sólo parcialmente aclarada. Sobre la base de varios brotes diagnosticados en parvadas comerciales de guineas criadas en Francia desde el año 2017, se realizó una secuenciación directa del genoma completo a partir del tejido de la lesión pancreática mediante el método de secuenciación desarrollado por Oxford Nanopore Technologies. Se generaron 4781 lecturas virales y se ensambló un genoma completo de 43,509 pb, que se agrupó dentro del adenovirus aviar tipo 1 (FAdV-1). Un análisis filogenético basado en una secuencia parcial de los genes hexón y de fibra corta de virus recolectados en Francia mostró identidades de nucleótidos de 98.7% y 99.8%, respectivamente. En conjunto, estos resultados confirman que un adenovirus aviar tipo 1 estrechamente relacionado con el pollo y otras cepas aviares es el agente de la pancreatitis en la gallina de Guinea. Este estudio ilustra el potencial de las tecnologías desarrolladas por Oxford Nanopore Thechnologies para lograr una secuenciación rápida de todo el genoma directamente a partir de material patológico.