#Molecular characterisation of an #avian #influenza (#H5N8) #outbreak in backyard #flocks in Al Ahsa, Eastern #Saudi Arabia, 2017-2018 (Vet Res Open., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Vet Rec Open. 2019 Dec 1;6(1):e000362. doi: 10.1136/vetreco-2019-000362. eCollection 2019.

Molecular characterisation of an avian influenza (H5N8) outbreak in backyard flocks in Al Ahsa, Eastern Saudi Arabia, 2017-2018.

Hemida MG1,2, Chu D3, Abdelaziz A4, Alnaeem A5, Chan SMS3, Peiris M3.

Author information: 1 Department of Microbiology and Parasitology, College of Veterinary Medicine, King Faisal University, Al-Hufuf, Saudi Arabia. 2 Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr el-Sheikh, Egypt. 3 School of Public Health, The University of Hong Kong, Hong Kong. 4 Veterinary Education Hospital, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt. 5 College of Veterinary Medicine, King Faisal University, Al-Hasa, Saudi Arabia.




Avian influenza viruses are still causing major concern not only to the poultry industry but also to human health across the globe. The live poultry markets and the small-scale local breeding of various species of birds in backyards are still playing important roles in the sustainability of most virulent influenza viruses, especially H5N8.


The authors investigated an outbreak of highly pathogenic avian influenza H5N8 in backyard flocks in Al Ahsa, Eastern Saudi Arabia that occurred in 2017-2018.


A range of poultry including chickens, ostriches, ducks, pigeons and turkeys were clinically affected. Phylogenetic analysis suggested that this was a common source outbreak caused by a virus closely related to H5N8 viruses causing outbreaks elsewhere in Saudi Arabia in early 2018.


Small backyard flocks are still contributing to the epidemiology and transmission of H5N8.

© British Veterinary Association 2019. Re-use permitted under CC BY-NC. No commercial re-use. Published by BMJ.

KEYWORDS: H5N8; Saudi Arabia; backyards; eastern region; highly pathogenic avian influenza; influenza; outbreak; phylogenetic analysis

PMID: 31897300 PMCID: PMC6924712 DOI: 10.1136/vetreco-2019-000362

Keywords: Avian Influenza; H5N8; Poultry; Saudi Arabia.


#Outbreaks of Clade #H5N8 highly pathogenic #avian #influenza in 2018 in the northern regions of South Africa [#ZA] were unrelated to those of 2017 (Transbound Emerg Dis., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Transbound Emerg Dis. 2019 Dec 13. doi: 10.1111/tbed.13448. [Epub ahead of print]

Outbreaks of Clade H5N8 highly pathogenic avian influenza in 2018 in the northern regions of South Africa were unrelated to those of 2017.

Abolnik C1.

Author information: 1 Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Old Soutpan Road, Onderstepoort, 0110, South Africa.



Asian-origin H5N8 highly pathogenic avian influenza (HPAI) viruses of the H5 Goose/Guangdong/96 lineage, clade group B reached South Africa by June 2017. By the end of that year, 5.4 million layers and broiler chickens died or were culled, with total losses in the poultry industry estimated at US$ 140 million, and thousands of exotic birds in zoological collections, endangered endemic species and backyard poultry and pet birds also perished. The 2017 H5N8 HPAI outbreaks were characterised by two distinct spatial clusters, each associated with specific reassortant viral genotypes. Genotypes 1, 2, 3 and 5 were restricted to the northern regions, spanning the provinces of Limpopo, Gauteng, North West, Mpumalanga, KwaZulu-Natal and Free State. The second, much larger cluster of outbreaks was in the south, in the Western and Eastern Cape provinces, where in 2017 and 2018 outbreaks were caused solely by genotype 4. The last confirmed case of H5N8 HPAI in the northern region in 2017 was in early October, and the viruses seemed to disappear over the summer. However, starting in mid-February 2018, H5N8 HPAI outbreaks resurged in the north. Viruses from two of the eight outbreaks were sequenced, one from an outbreak in quails (Coturnix japonica) in the North West Province, and another from commercial pullets in the Gauteng province. Phylogenetic analysis identified the viruses as a distinct sixth genotype that was most likely a new introduction to South Africa in early 2018.

© 2019 Blackwell Verlag GmbH.

KEYWORDS: H5N8; Highly pathogenic avian influenza; poultry; quail; wild birds

PMID: 31833671 DOI: 10.1111/tbed.13448

Keywords: Avian Influenza; H5N8; Reassortant strain; Poultry; Wild Birds; South Africa.


Spatiotemporal reconstruction and #transmission #dynamics during the 2016-17 #H5N8 highly pathogenic #avian #influenza #epidemic in #Italy (Transbound Emerg Dis., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Transbound Emerg Dis. 2019 Dec 1. doi: 10.1111/tbed.13420. [Epub ahead of print]

Spatiotemporal reconstruction and transmission dynamics during the 2016-17 H5N8 highly pathogenic avian influenza epidemic in Italy.

Harvey WT1, Mulatti P2, Fusaro A2, Scolamacchia F2, Zecchin B2, Monne I2, Marangon S2.

Author information: 1 Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK. 2 Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (Padua), Italy.



Effective control of avian diseases in domestic populations requires understanding of the transmission dynamics facilitating viral emergence and spread. In 2016-17, Italy experienced a significant avian influenza epidemic caused by a highly pathogenic A(H5N8) virus, which affected domestic premises housing around 2.7 million birds, primarily in the north-eastern regions with the highest density of poultry farms (Lombardy, Emilia-Romagna and Veneto). We perform integrated analyses of genetic, spatiotemporal and host data within a Bayesian phylogenetic framework. Using continuous and discrete phylogeography, we estimate the locations of movements responsible for the spread and persistence of the epidemic. The information derived from these analyses on rates of transmission between regions through time can be used to assess the success of control measures. Using an approach based on phylogenetic-temporal distances between domestic cases, we infer the presence of cryptic wild bird-mediated transmission, information that can be used to complement existing epidemiological methods for distinguishing transmission within the domestic population from incursions across the wildlife-domestic interface, a common challenge in veterinary epidemiology. Spatiotemporal reconstruction of the epidemic reveals a highly skewed distribution of virus movements with a high proportion of shorter distance local movements interspersed with occasional long-distance dispersal events associated with wild birds. We also show how such inference be used to identify possible instances of human-mediated movements where distances between phylogenetically linked domestic cases are unusually high.

© 2019 The Authors. Transboundary and Emerging Diseases published by Blackwell Verlag GmbH.

KEYWORDS: H5N8 subtype; avian influenza; infectious disease outbreaks; infectious disease reservoirs; phylogeny; phylogeography

PMID: 31788978 DOI: 10.1111/tbed.13420

Keywords: Avian Influenza; H5N8; Poultry; Wild Birds; Italy.


Novel #Reassortant Highly Pathogenic #Avian #Influenza A(#H5N2) Virus in Broiler #Chickens, #Egypt (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 26, Number 1—January 2020 / Dispatch

Novel Reassortant Highly Pathogenic Avian Influenza A(H5N2) Virus in Broiler Chickens, Egypt

Kareem E. Hassan, Jacqueline King, Magdy El-Kady, Manal Afifi, Hassanein H. Abozeid, Anne Pohlmann, Martin Beer, and Timm Harder

Author affiliations: Friedrich-Loeffler-Institut, Greifswald-Riems, Germany (K.E. Hassan, J. King, A. Pohlmann, M. Beer, T. Harder); Beni Suef University, Beni Suef, Egypt (K.E. Hassan, M. El-Kady); Cairo University, Cairo, Egypt (M. Afifi, H.H. Abozeid)



We detected a novel reassortant highly pathogenic avian influenza A(H5N2) virus in 3 poultry farms in Egypt. The virus carried genome segments of a pigeon H9N2 influenza virus detected in 2014, a nucleoprotein segment of contemporary chicken H9N2 viruses from Egypt, and hemagglutinin derived from the H5N8 virus clade.

Keywords: Avian Influenza; H5N2; H9N2; H5N8; Reassortant strain; Poultry; Egypt.


A study of the relationship between #human #infection with #avian #influenza A #H5N6 and environmental avian influenza viruses in #Fujian, #China (BMC Infect Dis., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

BMC Infect Dis. 2019 Sep 2;19(1):762. doi: 10.1186/s12879-019-4145-6.

A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China.

Chen P1, Xie JF1,2, Lin Q2, Zhao L2, Zhang YH2, Chen HB2, Weng YW1,2, Huang Z2, Zheng KC3,4.

Author information: 1 College of Public Health, Fujian Medical University, No. 88, Jiaotong Road, Taijiang District, Fuzhou, 350000, China. 2 Fujian Center for Disease Control and Prevention, Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou, 350001, China. 3 College of Public Health, Fujian Medical University, No. 88, Jiaotong Road, Taijiang District, Fuzhou, 350000, China. kingdadi9909@126.com. 4 Fujian Center for Disease Control and Prevention, Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou, 350001, China. kingdadi9909@126.com.




Avian influenza A (H5N6) virus poses a great threat to the human health since it is capable to cross the species barrier and infect humans. Although human infections are believed to largely originate from poultry contaminations, the transmissibility is unclear and only limited information was available on poultry environment contaminations, especially in Fujian Province.


A total of 4901 environmental samples were collected and tested for Avian Influenza Virus (AIV) from six cities in Fujian Province through the Fujian Influenza Surveillance System from 2013 to 2017. Two patient-related samples were taken from Fujian’s first confirmed H5N6 human case and his backyard chicken feces in 2017. Chi-square test or Fisher’s exact probability test was used to compare the AIV and the viral subtype positive rates among samples from different Surveillance cities, surveillance sites, sample types, and seasons. Phylogenetic tree analysis and molecular analysis were conducted to track the viral transmission route of the human infection and to map out the evolutions of H5N6 in Fujian.


The overall positive rate of the H5 subtype AIVs was 4.24% (208/4903). There were distinctive differences (p < 0.05) in the positive rates in samples from different cities, sample sites, sample types and seasons. The viruses from the patient and his backyard chicken feces shared high homologies (99.9-100%) in all the eight gene segments. Phylogenetic trees also showed that these two H5N6 viruses were closely related to each other, and were classified into the same genetic clade with another six H5N6 isolates from the environmental samples. The patient’s H5N6 virus carried genes from H6N6, H5N8 and H5N6 viruses originated from different areas. The R294K or N294S substitution was not detected in the neuraminidase (NA). The S31 N substitution in the matrix2 (M2) gene was detected but only in one strain from the environmental samples.


The H5 subtype of AIVs has started circulating in the poultry environments in Fujian Province. The patient’s viral strain originated from the chicken feces in his backyard. Genetic reassortment in H5N6 viruses in Fujian Province was indicated. The H5N6 viruses currently circulating in Fujian Province were still commonly sensitive to Oseltamivir and Zanamivir, but the resistance against Amantadine has emerged.

KEYWORDS: Avian influenza a (H5N6) virus; Environmental contamination; Phylogenetic analysis

PMID: 31477028 PMCID: PMC6719373 DOI: 10.1186/s12879-019-4145-6 [Indexed for MEDLINE] Free PMC Article

Keywords: Avian Influenza; H5N6; H5N8; H6N6; Reassortant strain; Human; Poultry; Fujian; China.


Comparative Virological and Pathogenic Characteristics of #Avian #Influenza #H5N8 Viruses Detected in #WildBirds and Domestic #Poultry in #Egypt during the Winter of 2016/2017 (Viruses, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Viruses. 2019 Oct 27;11(11). pii: E990. doi: 10.3390/v11110990.

Comparative Virological and Pathogenic Characteristics of Avian Influenza H5N8 Viruses Detected in Wild Birds and Domestic Poultry in Egypt during the Winter of 2016/2017.

Moatasim Y1, Kandeil A1, Aboulhoda BE2, El-Shesheny R1,3, Alkhazindar M4, AbdElSalam ET4, Kutkat O1, Kamel MN1, El Taweel AN1, Mostafa A1, Hicks JT5, Abd Elghaffar SK6, Kayali G7,8, Ali MA1.

Author information: 1 Center of Scientific Excellence for Influenza Virus, Environmental Research Division, National Research Centre, Giza 12622, Egypt. 2 Department of Anatomy and Embryology, Faculty of Medicine, Cairo University, Cairo 11562, Egypt. 3 St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA. 4 Department of Botany and Microbiology, Faculty of Science, Cairo University, Gamaa Street, Giza 12613, Egypt. 5 Center for Ecology of Infectious Disease, University of Georgia, Athens, GA 30602, USA. 6 Pathology and Clinical Pathology Department, Faculty of Veterinary Medicine, Assuit University, Assuit 71526, Egypt. 7 Human Link, Hazmieh 1109, Lebanon. 8 Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas, Houston, TX 77030, USA.



The surveillance and virological characterization of H5N8 avian influenza viruses are important in order to assess their zoonotic potential. The genetic analyses of the Egyptian H5N8 viruses isolated through active surveillance in wild birds and domestic poultry in the winter of 2016/2017 showed multiple introductions of reassortant viruses. In this study, we investigated and compared the growth kinetics, infectivity, and pathogenicity of the three reassortant forms of H5N8 viruses detected in wild birds and domestic poultry in Egypt during the first introduction wave in the winter of 2016/2017. Three representative H5N8 viruses (abbreviated as 813, 871, and 13666) were selected. The 871/H5N8 virus showed enhanced growth properties in vitro in Madin Darby canine kidney (MDCK) and A549 cells. Interestingly, all viruses replicated well in mice without prior adaptation. Infected C57BL/6 mice showed 20% mortality for 813/H5N8 and 60% mortality for 871/H5N8 and 13666/H5N8, which could be attributed to the genetic differences among the viruses. Studies on the pathogenicity in experimentally infected ducks revealed a range of pathogenic effects, with mortality rate ranging from 0% for 813/H5N8 and 13666/H5N8 to 28% for 871/H5N8. No significant differences were observed among the three compared viruses in infected chickens. Overall, different H5N8 viruses had variable biological characteristics, indicating a continuous need for surveillance and virus characterization efforts.

KEYWORDS: Egypt; H5N8; avian influenza virus; pathogenicity

PMID: 31717865 DOI: 10.3390/v11110990

Keywords: Avian Influenza; H5N8; Reassortant strain; Wild Birds; Poultry; Egypt.


Highly Pathogenic and Low Pathogenic #Avian #Influenza #H5 Subtype Viruses in #WildBirds in #Ukraine (Avian Dis., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Avian Dis. 2019 Mar 1;63(sp1):235-245. doi: 10.1637/11880-042718.1.

Highly Pathogenic and Low Pathogenic Avian Influenza H5 Subtype Viruses in Wild Birds in Ukraine.

Muzyka D1, Rula O2, Tkachenko S2, Muzyka N3, Köthe S4, Pishchanskyi O2, Stegniy B2, Pantin-Jackwood M5, Beer M4.

Author information: 1 National Scientific Center “Institute of Experimental and Clinical Veterinary Medicine”, Kharkiv, 61023, Ukraine, dmuzyka77@gmail.com. 2 National Scientific Center “Institute of Experimental and Clinical Veterinary Medicine”, Kharkiv, 61023, Ukraine. 3 State Poultry Research Station, v. Birky, Kharkiv Region, 63422, Ukraine. 4 Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany. 5 Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30677.


Abstract in English, Spanish

There have been three waves of highly pathogenic avian influenza (HPAI) outbreaks in commercial, backyard poultry, and wild birds in Ukraine. The first (2005-2006) and second (2008) waves were caused by H5N1 HPAI virus, with 45 outbreaks among commercial poultry (chickens) and backyard fowl (chickens, ducks, and geese) in four regions of Ukraine (AR Crimea, Kherson, Odesa, and Sumy Oblast). H5N1 HPAI viruses were isolated from dead wild birds: cormorants (Phalacrocorax carbo) and great crested grebes (Podiceps cristatus) in 2006 and 2008. The third HPAI wave consisted of nine outbreaks of H5N8 HPAI in wild and domestic birds, beginning in November 2016 in the central and south regions (Kherson, Odesa, Chernivtsi, Ternopil, and Mykolaiv Oblast). H5N8 HPAI virus was detected in dead mute swans (Cygnus olor), peacocks (Pavo cristatus) (in zoo), ruddy shelducks (Tadorna ferruginea), white-fronted geese (Anser albifrons), and from environmental samples in 2016 and 2017. Wide wild bird surveillance for avian influenza (AI) virus was conducted from 2006 to 2016 in Ukraine regions suspected of being intercontinental (north-south and east-west) flyways. A total of 21 511 samples were collected from 105 species of wild birds representing 27 families and 11 orders. Ninety-five avian influenza (AI) viruses were isolated (including one H5N2 LPAI virus in 2010) from wild birds with a total of 26 antigenic hemagglutinin (HA) and neuraminidase (NA) combinations. Fifteen of 16 known avian HA subtypes were isolated. Two H5N8 HPAI viruses (2016-2017) and two H5N2 LPAI viruses (2016) were isolated from wild birds and environmental samples (fresh bird feces) during surveillance before the outbreak in poultry in 2016-2017. The Ukrainian H5N1, H5N8 HPAI, and H5N2 LPAI viruses belong to different H5 phylogenetic groups. Our results demonstrate the great diversity of AI viruses in wild birds in Ukraine, as well as the importance of this region for studying the ecology of avian influenza.

KEYWORDS: Azov–Black Sea region of Ukraine; highly pathogenic and low pathogenic avian influenza virus subtype H5; surveillance; wild birds

PMID: 31713401 DOI: 10.1637/11880-042718.1

Keywords: Avian Influenza; H5N1; H5N2; H5N8; Wild Birds; Ukraine.