#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

 

Abstract

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.

 

IMPORTANCE

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.

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Keywords: Avian Influenza; H7N3; Poultry; Netherlands.

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Specificity, #Kinetics and Longevity of #Antibody #Responses to #Avian #Influenza A(#H7N9) Virus #Infection in #Humans (J Infect., abstract)

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

J Infect. 2020 Jan 16. pii: S0163-4453(20)30025-6. doi: 10.1016/j.jinf.2019.11.024. [Epub ahead of print]

Specificity, Kinetics and Longevity of Antibody Responses to Avian Influenza A(H7N9) Virus Infection in Humans.

Chen J1, Zhu H2, Horby PW3, Wang Q1, Zhou J1, Jiang H4, Liu L5, Zhang T6, Zhang Y7, Chen X1, Deng X1, Nikolay B8, Wang W1, Cauchemez S8, Guan Y2, Uyeki TM9, Yu H10.

Author information: 1 School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China. 2 Joint Institute of Virology (STU-HKU), Shantou University, Shantou, 515041, China; State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China. 3 Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK. 4 Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China; Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China. 5 Joint Institute of Virology (STU-HKU), Shantou University, Shantou, 515041, China. 6 Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, 330000, China. 7 Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China. 8 Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, 75015 Paris, France. 9 Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA. 10 School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China. Electronic address: yhj@fudan.edu.cn.

 

Abstract

OBJECTIVES:

The long-term dynamics of antibody responses in patients with influenza A(H7N9) virus infection are not well understood.

METHODS:

We conducted a longitudinal serological follow-up study in patients who were hospitalized with A(H7N9) virus infection, during 2013-2018. A(H7N9) virus-specific antibody responses were assessed by hemagglutination inhibition (HAI) and neutralization (NT) assays. A random intercept model was used to fit a curve to HAI antibody responses over time. HAI antibody responses were compared by clinical severity.

RESULTS:

Of 67 patients with A(H7N9) virus infection, HAI antibody titers reached 40 on average 11 days after illness onset and peaked at a titer of 290 after three months, and average titers of ≥80 and ≥40 were present until 11 months and 22 months respectively. HAI antibody responses were significantly higher in patients who experienced severe disease, including respiratory failure and acute respiratory distress syndrome, compared with patients who experienced less severe illness.

CONCLUSIONS:

Patients with A(H7N9) virus infection who survived severe disease mounted higher antibody responses that persisted for longer periods compared with those that experienced moderate disease. Studies of convalescent plasma treatment for A(H7N9) patients should consider collection of donor plasma from survivors of severe disease between 1-11 months after illness onset.

Copyright © 2020 Elsevier Ltd. All rights reserved.

KEYWORDS: Antibody response; Clinical severity; Follow-up; Influenza A(H7N9)

PMID: 31954742 DOI: 10.1016/j.jinf.2019.11.024

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Keywords: Avian Influenza; H7N9; Serotherapy; Human.

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#H7N9 #Influenza Virus Containing a #Polybasic HA Cleavage Site Requires Minimal Host #Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice (Viruses, abstract)

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

Viruses. 2020 Jan 5;12(1). pii: E65. doi: 10.3390/v12010065.

H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice.

Chan M1, Leung A1, Hisanaga T2, Pickering B2,3, Griffin BD1,3, Vendramelli R1, Tailor N1, Wong G4,5, Bi Y6, Babiuk S2, Berhane Y2, Kobasa D1,3.

Author information: 1 Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada. 2 National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada. 3 Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB R3E 0J9, Canada. 4 Institut Pasteur of Shanghai, Chinese Academy of Sciences, Life Science Research Building 320 Yueyang Road, Xuhui District, Shanghai 200031, China. 5 Département de microbiologie-infectiologie et d’immunologie, Université Laval, 1050 avenue de la Médecine, QC G1V 0A6, Canada. 6 CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China.

 

Abstract

Low pathogenic avian influenza (LPAI) H7N9 viruses have recently evolved to gain a polybasic cleavage site in the hemagglutinin (HA) protein, resulting in variants with increased lethality in poultry that meet the criteria for highly pathogenic avian influenza (HPAI) viruses. Both LPAI and HPAI variants can cause severe disease in humans (case fatality rate of ~40%). Here, we investigated the virulence of HPAI H7N9 viruses containing a polybasic HA cleavage site (H7N9-PBC) in mice. Inoculation of mice with H7N9-PBC did not result in observable disease; however, mice inoculated with a mouse-adapted version of this virus, generated by a single passage in mice, caused uniformly lethal disease. In addition to the PBC site, we identified three other mutations that are important for host-adaptation and virulence in mice: HA (A452T), PA (D347G), and PB2 (M483K). Using reverse genetics, we confirmed that the HA mutation was the most critical for increased virulence in mice. Our study identifies additional disease determinants in a mammalian model for HPAI H7N9 virus. Furthermore, the ease displayed by the virus to adapt to a new host highlights the potential for H7N9-PBC viruses to rapidly acquire mutations that may enhance their risk to humans or other animal species.

KEYWORDS: H7N9; HPAI; influenza virus; mammalian adaptation; mice; polybasic HA

PMID: 31948040 DOI: 10.3390/v12010065

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Keywords: Avian Influenza; H7N9; Viral pathogenesis; Animal models.

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#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.

 

Abstract

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 2.3.4.4B 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]

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Keywords: Avian Influenza; H5N8; Poultry; DRC.

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#Reassortment and #adaptive #mutations of an emerging #avian #influenza virus #H7N4 subtype in #China (PLOS One, abstract)

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

OPEN ACCESS /  PEER-REVIEWED / RESEARCH ARTICLE

Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China

Bingqian Qu , Xue Li , Carol J. Cardona, Zheng Xing

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Published: January 17, 2020 / DOI: https://doi.org/10.1371/journal.pone.0227597

 

Abstract

Human infections with avian influenza viruses including H5, H7 and H9 hemagglutinin subtypes occur at a low rate. Among human infections with H7 viruses, regional outbreaks with H7N2, H7N3, H7N7 and H7N9 have been documented. Early in 2018, a human infection with a novel H7N4 avian influenza virus was reported in Jiangsu, China. This study is aimed at understanding the probable origin and molecular features of this emerging H7N4 virus. Genomic segments encoding hemagglutinin (HA) and neuraminidase (NA) of H7Nx and HxN4 viruses were compared with this H7N4 strain by alignment and phylogenetic tree analysis. Phylogenetic analysis indicated that the human H7N4 virus probably originated from multiple reassortments of avian H7N7 and H8N4 viruses for its HA and NA, respectively, and likely a regional uncharacterized virus for its internal segments. Our data excluded that circulating avian H9N2 viruses were the origin of the H7N4 internal segments, unlike the human H5N1 and H7N9 viruses that both had H9N2 backbones. This index case provided a unique opportunity to examine viral mutations by directly comparing the human isolate with its closest viral relatives isolated from avian species from the patient’s farm, which may suggest critical mutations required for viral adaptation in humans. Whole-genome scanning was performed and the sequences of the human and related avian H7N4 isolates were compared. Mutations in PB2 (E627K), PB2 (K683T), PB1-F2 (N47S), HA (N283D), HA(K321E), NA(A137V), NA(K296R) and M2 (C19Y) were identified in the human isolate while no mutations were found in PB1, NP, NS1, and NS2 of the human H7N4 compared to the avian H7N4 viruses. Our data in this report provide further evidence for the genesis of this novel H7N4 virus with a multi-reassortment model and show molecular changes that might be responsible for the transmission of this virus from chickens or ducks to and subsequent replication in humans.

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Citation: Qu B, Li X, Cardona CJ, Xing Z (2020) Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China. PLoS ONE 15(1): e0227597. https://doi.org/10.1371/journal.pone.0227597

Editor: Florian Krammer, Icahn School of Medicine at Mount Sinai, UNITED STATES

Received: August 26, 2019; Accepted: December 23, 2019; Published: January 17, 2020

Copyright: © 2020 Qu 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 relevant data are within the manuscript

Funding: ZX; National Natural Science Foundation of China; Grant No. 81571993; www.nsfc.gov.cn/; The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

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Keywords: Avian Influenza; H7N4; H7N7; H8N4; Reassortant strain; Human; China.

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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.]

OPEN ACCESS /  PEER-REVIEWED / RESEARCH ARTICLE

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

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

 

Abstract

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.

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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.

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

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Detection of a #Reassortant #H9N2 #Avian #Influenza Virus with #Intercontinental Gene Segments in a Resident #Australian Chestnut #Teal (Viruses, abstract)

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

Viruses. 2020 Jan 13;12(1). pii: E88. doi: 10.3390/v12010088.

Detection of a Reassortant H9N2 Avian Influenza Virus with Intercontinental Gene Segments in a Resident Australian Chestnut Teal.

Bhatta TR1,2, Chamings A1,2, Vibin J1,2, Klaassen M1,3, Alexandersen S1,2,4.

Author information: 1 Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia. 2 School of Medicine, Deakin University, Geelong, Victoria 3220, Australia. 3 Centre for Integrative Ecology, Deakin University, Victoria 3220, Australia. 4 Barwon Health, University Hospital Geelong, Geelong, Victoria 3220, Australia.

 

Abstract

The present study reports the genetic characterization of a low-pathogenicity H9N2 avian influenza virus, initially from a pool and subsequently from individual faecal samples collected from Chestnut teals (Anas castanea) in southeastern Australia. Phylogenetic analyses of six full gene segments and two partial gene segments obtained from next-generation sequencing showed that this avian influenza virus, A/Chestnut teal/Australia/CT08.18/12952/2018 (H9N2), was a typical, low-pathogenicity, Eurasian aquatic bird lineage H9N2 virus, albeit containing the North American lineage nucleoprotein (NP) gene segment detected previously in Australian wild birds. This is the first report of a H9N2 avian influenza virus in resident wild birds in Australia, and although not in itself a cause of concern, is a clear indication of spillover and likely reassortment of influenza viruses between migratory and resident birds, and an indication that any lineage could potentially be introduced in this way.

KEYWORDS: Chestnut teal; Eurasian lineage; H9N2; avian influenza virus; low pathogenicity; phylogenetic analysis; reassortant

PMID: 31940999 DOI: 10.3390/v12010088

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Keywords: Avian Influenza; H9N2; Wild Birds; Reassortant strain; Australia.

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