Variation in viral shedding patterns between domestic and wild terrestrial birds infected experimentally with reassortant avian influenza virus (H9N2)

Authors: Umar, Sajid; Rehman, Abdul; Asif, Sajjad; Usman, Muhammad; Atif, Muhammad; Ali, Shahzad; Munir, Muhammad Tanveer; Ali, Asif; Shahzad, Muhammad; Shah, Muhammad Ali Abdullah
Source: Avian Biology Research, Volume 9, Number 3, September 2016, pp. 200-206(7)

Avian influenza (H9N2) virus infection is an emerging respiratory problem and its prevalence varies significantly among different species of birds. The current knowledge about virus shedding parameters in terrestrial birds is limited. With this in mind, the present study was conducted in different domestic and wild terrestrial birds to investigate species-related differences in infectivity and pattern of viral shedding associated with H9N2 AI virus. Groups of terrestrial birds (domestic Guinea Fowl Numida meleagridis, Japanese Quail Coturnix coturnix japonica, House Sparrows Passer domesticus, House Crows Corvus splendens and Bank Myna Acridotheres ginginianus) were inoculated intra-nasally with A/chicken/Pakistan/10RS3039-284-48/2010 (H9N2) AI virus (106 EID50) and then examined for infectivity and virus shedding patterns. With the exception of House Crows, all infected birds showed clinical signs of different severity, showing the most prominent disease signs in Japanese Quail. All infected birds showed positive results for virus shedding, however, the pattern of virus shedding was different among wild terrestrial birds. Japanese Quail showed the highest levels of virus shedding while samples collected from House Crows revealed only very low levels. Interestingly, virus shedding was observed predominantly via the gastrointestinal tract in House Sparrows and Bank Myna and via the buccal cavity route in Guinea Fowl and Japanese Quail. Here we investigated that the novel genotype of H9N2 AI virus circulating in Pakistan causes clinical disease signs in domestic and wild terrestrial birds. The results of this study suggest that virus shedding varies between different related avian species and highlights the potential role of Guinea Fowl, Japanese Quail, House Sparrows and Bank Myna as mixing bowls for the transmission and maintenance of H9N2 AI viruses between premises.
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CIDRAP — H7N8 detections at more Indiana farms suggest mutation

Lisa Schnirring | News Editor | CIDRAP News | Jan 19, 2016

Testing at nearby farms in the wake of a highly pathogenic H7N8 avian flu outbreak that struck a turkey facility in southern Indiana last week turned up a low-pathogenic version of the virus eight more farms, hinting that the virus mutated to a more lethal strain as it spread.

In a related development, the US Centers for Disease Control and Prevention (CDC) warned that, because H7 viruses have infected people before, so human infections from the new strain could occur, though the risk to the general public is low.

Although many questions remain about the newly detected strain, tests show that Indiana’s H7N8 strain is a North American lineage virus, according to a Jan 15 report to the World Organization for Animal Health (OIE). Deaths at the Dubois County turkey producer prompted testing, and results were confirmed and announced on Jan 15

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For the complete CIDRAP article, please see:

CIDRAP — High-path H7N8 outbreak reported at Indiana turkey farm

Lisa Schnirring | News Editor | CIDRAP News | Jan 15, 2016

A highly pathogenic H7N8 avian influenza strain that hasn’t been seen in the United States before has struck a commercial turkey farm in southern Indiana, prompting the culling of about 60,000 birds, federal and state officials announced today.

The strain is different than the one that caused more than 200 outbreaks in US poultry last year and hasn’t caused any known human infections, according to a statement from the US Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS).

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For the complete CIDRAP article, see:

RE: A simple explanation for the evolution of complex song syntax in Bengalese finches by Anthony Olszewski

RE: A simple explanation for the evolution of complex song syntax in Bengalese finches
by Anthony Olszewski

The comments below concern
A simple explanation for the evolution of complex song syntax in Bengalese finches
Kentaro Katahira, Kenta Suzuki, Hiroko Kagawa, Kazuo Okanoya
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Sound Analysis Tools for Matlab & Bird-Puffer system

Ofer Tchernichovski
to birdsong-L

Dear friends,

We would like to share with you two methods and software tools we developed: Sound Analysis Tools for Matlab, and a system, which we call ‘Bird-puffer’, for rapid auditory discrimination training of zebra finches using social reinforcement.

Sound Analysis Tools for Matlab (SAT) is similar to Sound Analysis Pro, but is modular and easy to manipulate and combine with your own code. It should be useful even without any coding: the user interface is similar to that of SAP, and it can be used for exploring sounds, extracting features, and calculating similarity. Through Matlab, these tools are now available for both Mac and PC users.

Click here for download and more information (including user manual).      I am happy to answer questions.

Bird-puffer is a combined software/hardware solution to rapidly train zebra finches to discriminate between songs. It can be used to train naïve birds within 3 hourly sessions, while experienced birds can lean to discriminate between songs within several minutes. Zebra finches love to socialize and they never seem to get enough of it. The system includes two cages with a little window for socializing. By choosing to socialize next to the window, the bird will voluntarily risk receiving an air-puff (harmless but unpleasant), which our software associates with specific sounds. Birds quickly learn to escape the air puff by flying away after hearing those sounds. Click here for downloading the software (for Windows only) and for hardware installation instructions. Kirill Tokarev (who co-developed this system) and I will be happy to answer questions.

We hope you will find these useful,

Happy New Year!

Kirill & Ofer

Avian Influenza of high pathogenicity (H5N1, H5N2, and H5N9) in poultry in France

Department for Environment, Food and Rural Affairs
Animal & Plant Health Agency
Veterinary & Science Policy Advice Team – International Disease Monitoring
Updated Outbreak Assessment
Avian Influenza of high pathogenicity (H5N1, H5N2,and H5N9) in poultry in France 23 December 2015 Ref: VITT/1200 HPAI in France
Disease ReportSince the last update on the 16th December, more outbreaks in poultry have been reported as a result of increased surveillance in South West France (Ministère de l’Agriculture,
France, 2015; see map – not all outbreaks visible at this scale). To date there are 61 outbreaks of HPAI H5 (N1, N2 and N9), 54 of which have been reported to the EU Animal Disease Notification System. Six regions are affected –Dordogne (12 outbreaks); Landes (27 outbreaks); HauteVienne (1); Gers (9); Pyrenees Atlantique (10) and; Haute Pyrenees (2). The situation continues to evolve and the French Authorities have increased the size of restriction zones to cover more regions (hatched / grey area in map) and this has been adopted by the European Commission under special written procedure (SANTE/7135/2015). Movements of live birds from any control zone are subject to pre-movement testing, which has led to the detection of more infected flocks, but does provide some additional assurance

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For the complete report, click on

OiE declares US Avian Influenza outbreak ended

All HPAI H5N2 outbreaks in all affected States (Arkansas, California, Idaho, Indiana, Iowa, Kansas, Minnesota, Missouri, Montana, Nebraska, North Dakota, Oregon, South Dakota, Washington, and Wisconsin) are now final, closed, and resolved. The last positive detection of HPAI H5N2 in poultry was made on June 18, 2015. In addition to having no further HPAI detections, all States affected with HPAI (listed above) have met the following: – Mandatory surveillance in the State and control areas has been completed with negative results for HPAI. As a precaution, additional enhanced surveillance and procedures may continue in the State and area. – Depopulation of all infected premises has been completed and appropriate disposal was completed. – Cleaning and disinfection of the infected premises (including, but not limited to, outside areas, equipment, trucks, and other fomites). – No HPAI detections through wild bird surveillance have been made within the past 3 months. The USDA Animal and Plant Health Inspection Service (APHIS), in conjunction with State Departments of Agriculture and Wildlife, and industry, continue to conduct thorough surveillance nationally for avian influenza virus through the National Poultry Improvement Plan (NPIP), Live Bird Market System, and wild bird surveillance programs, as well as completely investigate any suspected avian influenza virus event. No HPAI has been detected in poultry over 5 months. Each outbreak has been closed after the requested three-month period of stamping out, disinfection and surveillance. The HPAI event in the United States is considered CLOSED. In accordance with the World Organisation for Animal Health (OIE) Terrestrial Animal Health Code Chapter 10.4 (Articles 10.4.3 and 10.4.4), the United States has completely fulfilled the necessary actions and surveillance requirements to again self-declare itself free from HPAI.

For the complete OiE report, please click on the Link below:

OiE — Highly pathogenic avian influenza, France

Report type Immediate notification
Date of start of the event 27/11/2015
Date of confirmation of the event 30/11/2015
Report date 02/12/2015
Date submitted to OIE 02/12/2015
Reason for notification New strain of a listed disease
Manifestation of disease Clinical disease
Causal agent Highly pathogenic avian influenza virus
Serotype H5N2
Nature of diagnosis Clinical, Laboratory (advanced)
This event pertains to the whole country

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For the complete report, please see:

The vocal repertoire of the domesticated zebra finch: a data-driven approach to decipher the information-bearing acoustic features of communication signals

Although a universal code for the acoustic features of animal vocal communication calls may not exist, the thorough analysis of the distinctive acoustical features of vocalization categories is important not only to decipher the acoustical code for a specific species but also to understand the evolution of communication signals and the mechanisms used to produce and understand them.

Here, we recorded more than 8,000 examples of almost all the vocalizations of the domesticated Zebra finch, Taeniopygia guttata: vocalizations produced to establish contact, to form and maintain pair bonds, to sound an alarm, to communicate distress or to advertise hunger or aggressive intents. We characterized each vocalization type using complete representations that avoided any a priori assumptions on the acoustic code, as well as classical bioacoustics measures that could provide more intuitive interpretations. We then used these acoustical features to rigorously determine the potential information-bearing acoustical features for each vocalization type using both a novel regularized classifier and an unsupervised clustering algorithm. Vocalization categories are discriminated by the shape of their frequency spectrum and by their pitch saliency (noisy to tonal vocalizations) but not particularly by their fundamental frequency. Notably, the spectral shape of zebra finch vocalizations contains peaks or formants that vary systematically across categories and that would be generated by active control of both the vocal organ (source) and the upper vocal tract (filter).

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Click on the Link below to access the complete paper:

Universal mechanisms of sound production and control in birds and mammals

Universal mechanisms of sound production and control in birds and mammals

C.P.H Elemans, J.H. Rasmussen, C.T. Herbst, D.N. Düring, S.A. Zollinger, H. Brumm, K. Srivastava, N. Svane, M. Ding, O.N. Larsen, S.J. Sober & J.G. Švec

Nature Communications 6, Article number: 8978 doi:10.1038/ncomms9978
Received 24 March 2015 Accepted 22 October 2015 Published 27 November 2015

As animals vocalize, their vocal organ transforms motor commands into vocalizations for social communication. In birds, the physical mechanisms by which vocalizations are produced and controlled remain unresolved because of the extreme difficulty in obtaining in vivo measurements. Here, we introduce an ex vivo preparation of the avian vocal organ that allows simultaneous high-speed imaging, muscle stimulation and kinematic and acoustic analyses to reveal the mechanisms of vocal production in birds across a wide range of taxa. Remarkably, we show that all species tested employ the myoelastic-aerodynamic (MEAD) mechanism, the same mechanism used to produce human speech. Furthermore, we show substantial redundancy in the control of key vocal parameters ex vivo, suggesting that in vivo vocalizations may also not be specified by unique motor commands. We propose that such motor redundancy can aid vocal learning and is common to MEAD sound production across birds and mammals, including humans.

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Access the paper here: