#Emergence and #Selection of a Highly Pathogenic #Avian #Influenza #H7N3 Virus (J Virol., abstract)

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

J Virol  2020 Jan 22 [Online ahead of print]

Emergence and Selection of a Highly Pathogenic Avian Influenza H7N3 Virus

Nancy Beerens 1, Rene Heutink 2, Frank Harders 2, Alex Bossers 2, Guus Koch 2, Ben Peeters 2

Affiliations: 1 Wageningen Bioveterinary Research, Lelystad, The Netherlands. nancy.beerens@wur.nl. 2 Wageningen Bioveterinary Research, Lelystad, The Netherlands.

PMID: 31969434  DOI: 10.1128/JVI.01818-19



Low pathogenic avian influenza (LPAI) viruses of subtypes H5 and H7 have the ability to spontaneously mutate to highly pathogenic (HPAI) variants, causing high mortality in poultry. The highly pathogenic phenotype is caused by mutation of the hemagglutinin (HA) cleavage site, but additional mutations may play a role. Evidence from the field for the switch to high pathogenicity remains scarce. This study provides direct evidence for LPAI to HPAI mutation during H7N3 infection of a turkey farm in the Netherlands. No severe clinical symptoms were reported at the farm, but deep-sequencing revealed a minority of HPAI sequences (0.06%) in the virus population isolated from infected turkeys. The HPAI virus contained a 12-nucleotide insertion in the HA cleavage site, that was likely introduced by a single event, as no intermediates with shorter inserts were identified. This suggests non-homologous recombination as the mechanism of insertion. Analysis of different organs of the infected turkeys showed the highest amount of HPAI virus in the lung (4.4%). The HPAI virus was rapidly selected in experimentally infected chickens, after both intravenous and intranasal/intratracheal inoculation with the mixed virus preparation. Full-genome sequencing revealed that both pathotypes contained a deletion in the stalk region of the neuraminidase protein. We identified additional mutations in HA and polymerase basic protein 1 (PB1) in the HPAI virus, which were already present as minority variants in the LPAI virus population. Our findings provide more insight in the molecular changes and mechanisms involved in the emergence and selection of HPAI viruses.



Low pathogenic avian influenza (LPAI) viruses circulate in wild birds, and can be transmitted to poultry. LPAI viruses can mutate to become highly pathogenic avian influenza (HPAI) viruses causing severe disease and death in poultry. Little is known about this switch to high pathogenicity. We isolated a LPAI H7N3 virus from an infected turkey farm, and showed that this contains small amounts of HPAI virus. The HPAI virus rapidly outcompeted the LPAI virus in chickens that were experimentally infected with this mixture of viruses. We analysed the genome sequences of the LPAI and HPAI viruses, and identified several changes that may be important for a virus to become highly pathogenic. This knowledge may be used for timely identification of LPAI viruses that pose a risk of becoming highly pathogenic in the field.

Copyright © 2020 American Society for Microbiology.

Keywords: Avian Influenza; H7N3; Poultry; Netherlands.


#Molecular, #antigenic, and #pathogenic characterization of #H5N8 highly pathogenic #avian #influenza viruses isolated in the #DRC in 2017 (Arch Virol., abstract)

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

Arch Virol. 2020 Jan;165(1):87-96. doi: 10.1007/s00705-019-04456-x. Epub 2019 Nov 9.

Molecular, antigenic, and pathogenic characterization of H5N8 highly pathogenic avian influenza viruses isolated in the Democratic Republic of Congo in 2017.

Twabela AT1,2, Okamatsu M1, Tshilenge GM2, Mpiana S2, Masumu J2, Nguyen LT1, Matsuno K1,3, Monne I4, Zecchin B4, Sakoda Y5,6.

Author information: 1 Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan. 2 Central Veterinary Laboratory of Kinshasa, Kinshasa I, Gombe, Democratic Republic of Congo. 3 Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Hokkaido, Japan. 4 Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, PD, Italy. 5 Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan. sakoda@vetmed.hokudai.ac.jp. 6 Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Hokkaido, Japan. sakoda@vetmed.hokudai.ac.jp.



In May 2017, high mortality of chickens and Muscovy ducks due to the H5N8 highly pathogenic avian influenza virus (HPAIV) was reported in the Democratic Republic of Congo (DR Congo). In this study, we assessed the molecular, antigenic, and pathogenic features in poultry of the H5N8 HPAIV from the 2017 Congolese outbreaks. Phylogenetic analysis of the eight viral gene segments revealed that all 12 DR Congo isolates clustered in clade together with other H5N8 HPAIVs isolated in Africa and Eurasia, suggesting a possible common origin of these viruses. Antigenically, a slight difference was observed between the Congolese isolates and a representative virus from group C in the same clade. After intranasal inoculation with a representative DR Congo virus, high pathogenicity was observed in chickens and Muscovy ducks but not in Pekin ducks. Viral replication was higher in chickens than in Muscovy duck and Pekin duck organs; however, neurotropism was pronounced in Muscovy ducks. Our data confirmed the high pathogenicity of the DR Congo virus in chickens and Muscovy ducks, as observed in the field. National awareness and strengthening surveillance in the region are needed to better control HPAIVs.

PMID: 31707455 DOI: 10.1007/s00705-019-04456-x [Indexed for MEDLINE]

Keywords: Avian Influenza; H5N8; Poultry; DRC.


Quantifying within-host #diversity of #H5N1 #influenza viruses in #humans and #poultry in #Cambodia (PLOS Pathog., abstract)

[Source: PLOS Pathogens, full page: (LINK). Abstract, edited.]


Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia

Louise H. Moncla , Trevor Bedford, Philippe Dussart, Srey Viseth Horm, Sareth Rith, Philippe Buchy, Erik A. Karlsson, Lifeng Li, Yongmei Liu, Huachen Zhu, Yi Guan, Thomas C. Friedrich, Paul F. Horwood


Published: January 17, 2020 / DOI: https://doi.org/10.1371/journal.ppat.1008191 / This is an uncorrected proof.



Avian influenza viruses (AIVs) periodically cross species barriers and infect humans. The likelihood that an AIV will evolve mammalian transmissibility depends on acquiring and selecting mutations during spillover, but data from natural infection is limited. We analyze deep sequencing data from infected humans and domestic ducks in Cambodia to examine how H5N1 viruses evolve during spillover. Overall, viral populations in both species are predominated by low-frequency (<10%) variation shaped by purifying selection and genetic drift, and half of the variants detected within-host are never detected on the H5N1 virus phylogeny. However, we do detect a subset of mutations linked to human receptor binding and replication (PB2 E627K, HA A150V, and HA Q238L) that arose in multiple, independent humans. PB2 E627K and HA A150V were also enriched along phylogenetic branches leading to human infections, suggesting that they are likely human-adaptive. Our data show that H5N1 viruses generate putative human-adapting mutations during natural spillover infection, many of which are detected at >5% frequency within-host. However, short infection times, genetic drift, and purifying selection likely restrict their ability to evolve extensively during a single infection. Applying evolutionary methods to sequence data, we reveal a detailed view of H5N1 virus adaptive potential, and develop a foundation for studying host-adaptation in other zoonotic viruses.


Author summary

H5N1 avian influenza viruses can cross species barriers and cause severe disease in humans. H5N1 viruses currently cannot replicate and transmit efficiently among humans, but animal infection studies and modeling experiments have suggested that human adaptation may require only a few mutations. However, data from natural spillover infection has been limited, posing a challenge for risk assessment. Here, we analyze a unique dataset of deep sequence data from H5N1 virus-infected humans and domestic ducks in Cambodia. We find that well-known markers of human receptor binding and replication arise in multiple, independent humans. We also find that 3 mutations detected within-host are enriched along phylogenetic branches leading to human infections, suggesting that they are likely human-adapting. However, we also show that within-host evolution in both humans and ducks are shaped heavily by purifying selection and genetic drift, and that a large fraction of within-host variation is never detected on the H5N1 phylogeny. Taken together, our data show that H5N1 viruses do generate human-adapting mutations during natural infection. However, short infection times, purifying selection, and genetic drift may severely limit how much H5N1 viruses can evolve during the course of a single infection.


Citation: Moncla LH, Bedford T, Dussart P, Horm SV, Rith S, Buchy P, et al. (2020) Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia. PLoS Pathog 16(1): e1008191. https://doi.org/10.1371/journal.ppat.1008191

Editor: Wendy S. Barclay, Imperial College London, UNITED KINGDOM

Received: July 8, 2019; Accepted: November 4, 2019; Published: January 17, 2020

Copyright: © 2020 Moncla et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All raw sequence data are available in the SRA under accession number PRJNA547644 (https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA547644). All code used to analyze the data, as well as data files with within-host variant calls and phylogenetic trees are available at https://github.com/blab/h5n1-cambodia.

Funding: The study was funded by the US Agency for International Development (grant No. AID-442-G-14-00005). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: Dr. Philippe Buchy is a former Head of Virology at Institut Pasteur du Cambodge and is currently an employee of GSK Vaccines, Singapore. The other authors declare no conflict of interest.

Keywords: Avian Influenza, H5N1, Human, Poultry, Cambodia.


Detection and #Isolation of #H9N2 Subtype of #Avian #Influenza Virus in House #Sparrows (Passer domesticus) of Ahvaz, #Iran (Arch Razi Inst., abstract)

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

Arch Razi Inst. 2019 Dec;74(4):439-444. doi: 10.22092/ari.2019.122504.1223. Epub 2019 Dec 1.

Detection and Isolation of H9N2 Subtype of Avian Influenza Virus in House Sparrows (Passer domesticus) of Ahvaz, Iran.

Broomand Z1,1, Mayahi M1, Hosseini H2, Valadbeigi S1.

Author information: 1 Department of avian health and diseases, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran. 2 Department of Clinical Sciences, Faculty of Veterinary Medicine, Karaj Branch, Islamic Azad University, Alborz, Iran.



Avian influenza (AI) is an acute infectious disease with worldwide significance causing extensive economic losses in the poultry industry. Avian influenza viruses (AIVs) belong to the family Orthomyxoviridae and categorized in the genus influenza virus A. These viruses have been isolated from more than 100 species of free-living birds. Migratory birds are considered as reservoirs for AIVs and are the major agents responsible for global outbreaks. The Passeriformes are found in most parts of the world and cover a variety of habitats from rural to urban areas. House sparrows are members of the family Passeridae and due to their free flying, are strongly associated with seabirds, indigenous, and industrial poultry. The aim of this study was to determine the role of house sparrows in AIV (H9N2) circulation in the Ahvaz region. The intestinal and tracheal samples were taken from 200 sparrows around Ahvaz during 2017. Reverse transcriptase-polymerase chain reaction (RT-PCR) was performed using specific primers in order to detect M and H9 genes of AIVs. The positive specimens in the PCR for the M gene were inoculated into 9-11-day-old embryonated chicken eggs via the allantoic fluid. The results showed that 11 out of 200 samples were positive for the two genes of M and H9. According to the findings of the present study, house sparrows are infected with H9N2 and pose a threat to commercial poultry. These birds may play a significant role in the transmission of AIV between wildlife and domestic animals. Therefore, this issue is important to be considered in preventive measurements.

Copyright © 2019, Archives of Razi Institute. Published by Kowsar.

KEYWORDS: Ahvaz; Avian influenza; House sparrows; Iran; Molecular detection

PMID: 31939262 DOI: 10.22092/ari.2019.122504.1223

Keywords: Avian Influenza; H9N2; Wild Birds; Poultry; Iran.


#Avian #Influenza Virus Detection Rates in #Poultry and #Environment at Live Poultry #Markets, #Guangdong, #China (Emerg Infect Dis., abstract)

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

Volume 26, Number 3—March 2020 / Dispatch

Avian Influenza Virus Detection Rates in Poultry and Environment at Live Poultry Markets, Guangdong, China

Kit Ling Cheng1, Jie Wu1, Wei Ling Shen, Alvina Y.L. Wong, Qianfang Guo, Jianxiang Yu, Xue Zhuang, Wen Su, Tie Song, Malik Peiris, Hui-Ling Yen2  , and Eric H.Y. Lau2

Author affiliations: University of Hong Kong, Hong Kong, China (K.L. Cheng, A.Y.L. Wong, W. Su, M. Peiris, H.-L. Yen, E.H.Y. Lau); Guangdong Provincial Center for Disease Control and Prevention, Guangdong, China (J. Wu, W.L. Shen, Q. Guo, J. Yu, X. Zhuang, T. Song)



We report the use of environmental samples to assess avian influenza virus activity in chickens at live poultry markets in China. Results of environmental and chicken samples correlate moderately well. However, collection of multiple environmental samples from holding, processing, and selling areas is recommended to detect viruses expected to have low prevalence.

Keywords: Avian Influenza; Poultry; Live poultry Market; Guangdong; China.


#Evolution of highly pathogenic #H7N3 #avian #influenza viruses in #Mexico (Zoonoses Public Health, abstract)

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

Zoonoses Public Health. 2020 Jan 7. doi: 10.1111/zph.12673. [Epub ahead of print]

Evolution of highly pathogenic H7N3 avian influenza viruses in Mexico.

Trovão NS1, Talavera GA2, Nelson MI1, Perez de la Rosa JD3.

Author information: 1 Fogarty International Center, National Institutes of Health, Bethesda, Maryland. 2 Universidad Autónoma de Yucatán, Yucatán, Mexico. 3 Centro Nacional de Servicios de Constatación en Salud Animal (CENAPA), Morelos, Mexico.



Highly pathogenic H7N3 influenza A viruses have persisted in poultry in Mexico since 2012, diversifying into multiple lineages that have spread to three Mexican states, as of 2016. The H7N3 viruses segregate into three distinct clades that are geographically structured. All 2016 viruses are resistant to adamantane antiviral drugs and have an extended 24-nucleotide insertion at the HA cleavage site that was acquired from host 28S ribosomal RNA.

Published 2020. This article is a U.S. Government work and is in the public domain in the USA.

KEYWORDS: BEAST; H7N3; H7N3 subtype; avian influenza virus; evolutionary dynamics; influenza in birds; phylogenetics

PMID: 31912652 DOI: 10.1111/zph.12673

Keywords: Avian Influenza; H7N3; Poultry; Mexico; Antivirals; Drugs Resistance; Amantadine.


Evaluation of #potential #risk of #transmission of #avian #influenza A viruses at live #bird #markets in response to unusual #crow die-offs in #Bangladesh (Influenza Other Respir Viruses, abstract)

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

Influenza Other Respir Viruses. 2020 Jan 7. doi: 10.1111/irv.12716. [Epub ahead of print]

Evaluation of potential risk of transmission of avian influenza A viruses at live bird markets in response to unusual crow die-offs in Bangladesh.

Rahman M1,2, Mangtani P3, Uyeki TM4, Cardwell JM1, Torremorell M5, Islam A6, Samad MA7, Muraduzzaman AKM2, Giasuddin M7, Sarkar S2, Alamgir ASM2, Salimuzzaman M2, Flora MS2.

Author information: 1 Royal Veterinary College, Hatfield, UK. 2 Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh. 3 London School of Hygiene and Tropical Medicine, London, UK. 4 Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA. 5 University of Minnesota, Twin Cities, MN, USA. 6 EcoHealth Alliance, New York, NY, USA. 7 Bangladesh Livestock Research Institute (BLRI), Savar, Bangladesh.



In response to unusual crow die-offs from avian influenza A(H5N1) virus infection during January-February 2017 in Dhaka, Bangladesh, a One Health team assessed potential infection risks in live bird markets (LBMs). Evidence of aerosolized avian influenza A viruses was detected in LBMs and in the respiratory tracts of market workers, indicating exposure and potential for infection. This study highlighted the importance of surveillance platforms with a coordinated One Health strategy to investigate and mitigate zoonotic risk.

© 2020 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

KEYWORDS: Bangladesh; avian influenza; avian influenza A virus; influenza in birds; live bird market; pathogen transmission

PMID: 31912608 DOI: 10.1111/irv.12716

Keywords: Avian Influenza; H5N1; Poultry; Live poultry markets; Bangladesh.