A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)

Abstract Background The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome. Findings This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (complementary DNA) from brain, ileum, lung, ovary, spleen, and testis using Illumina short-read and Pacific Biosciences long-read sequencing platforms, which were used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies a mean of 7.9 isoforms per gene. We also identified 246 small RNA families. Conclusions This annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long-read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to avian influenza viruses.

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A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duck Aythya fuligula (Tufted Duck)

10.1101/2021.02.24.432697 ◽

2021 ◽

Author(s):

Ralf C Mueller ◽

Patrik Ellström ◽

Kerstin Howe ◽

Marcela Uliano-Silva ◽

Richard I Kuo ◽

...

Keyword(s):

Influenza Virus ◽

Avian Influenza ◽

Avian Influenza Virus ◽

Genome Assembly ◽

Host Response ◽

High Quality ◽

Pathogenic Avian Influenza ◽

Tufted Duck ◽

Long Read ◽

High Quality Genome

BackgroundThe tufted duck is a non-model organism that suffers high mortality in highly pathogenic avian influenza out-breaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome.ResultsThis study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (cDNA) from brain, ileum, lung, ovary, spleen and testis using Illumina short-read and PacBio long-read sequencing platforms, which was used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies an average of 7.9 isoforms per gene. We also identified 246 small RNA families.ConclusionsThis annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long-read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to the avian influenza virus.

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Domestic ducks play a major role in the maintenance and spread of H5N8 highly pathogenic avian influenza viruses in South Korea

Transboundary and Emerging Diseases ◽

10.1111/tbed.13406 ◽

2019 ◽

Vol 67 (2) ◽

pp. 844-851 ◽

Cited By ~ 5

Author(s):

Jung‐Hoon Kwon ◽

Justin Bahl ◽

David E. Swayne ◽

Yu‐Na Lee ◽

Youn‐Jeong Lee ◽

...

Keyword(s):

Avian Influenza ◽

South Korea ◽

Highly Pathogenic Avian Influenza ◽

Influenza Viruses ◽

Avian Influenza Viruses ◽

Domestic Ducks ◽

Highly Pathogenic ◽

Pathogenic Avian Influenza

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Detection of low pathogenic avian influenza viruses in wild birds in Castilla-La Mancha (south central Spain)

Veterinary Microbiology ◽

10.1016/j.vetmic.2010.05.008 ◽

2010 ◽

Vol 146 (3-4) ◽

pp. 200-208 ◽

Cited By ~ 29

Author(s):

Elisa Pérez-Ramírez ◽

Xeider Gerrikagoitia ◽

Marta Barral ◽

Ursula Höfle

Keyword(s):

Avian Influenza ◽

Wild Birds ◽

Influenza Viruses ◽

Avian Influenza Viruses ◽

Central Spain ◽

Pathogenic Avian Influenza ◽

South Central ◽

La Mancha ◽

Low Pathogenic Avian Influenza

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Detection of Low Pathogenic Avian Influenza Viruses in Wild Ducks from Canada: Comparison of Two Sampling Methods

Journal of Wildlife Diseases ◽

10.7589/0090-3558-47.2.466 ◽

2011 ◽

Vol 47 (2) ◽

pp. 466-470 ◽

Cited By ~ 8

Author(s):

E. Jane Parmley ◽

Catherine Soos ◽

André Breault ◽

Madeleine Fortin ◽

Emily Jenkins ◽

...

Keyword(s):

Avian Influenza ◽

Sampling Methods ◽

Influenza Viruses ◽

Avian Influenza Viruses ◽

Pathogenic Avian Influenza ◽

Low Pathogenic Avian Influenza

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Opposite outcomes of the within-host competition between highly and low pathogenic H5N8 avian influenza viruses in chickens compared to ducks

Journal of Virology ◽

10.1128/jvi.01366-21 ◽

2021 ◽

Author(s):

Pierre Bessière ◽

Thomas Figueroa ◽

Amelia Coggon ◽

Charlotte Foret-Lucas ◽

Alexandre Houffschmitt ◽

...

Keyword(s):

Avian Influenza ◽

Reverse Genetics ◽

Highly Pathogenic Avian Influenza ◽

Viral Evolution ◽

Influenza Viruses ◽

Poultry Production ◽

Avian Influenza Viruses ◽

Highly Pathogenic ◽

Pathogenic Avian Influenza ◽

Low Pathogenic Avian Influenza

Highly pathogenic avian influenza viruses (HPAIV) emerge from low pathogenic avian influenza viruses (LPAIV) through the introduction of basic amino acids at the hemagglutinin (HA) cleavage site. Following viral evolution, the newly formed HPAIV likely represents a minority variant within the index host, predominantly infected with the LPAIV precursor. Using reverse-genetics engineered H5N8 viruses differing solely at the HA cleavage, we tested the hypothesis that the interaction between the minority HPAIV and the majority LPAIV could modulate the risk of HPAIV emergence and that the nature of the interaction could depend on the host species. In chickens, we observed that the H5N8 LP increased H5N8 HP replication and pathogenesis. By contrast, the H5N8 LP antagonized H5N8 HP replication and pathogenesis in ducks. Ducks mounted a more potent antiviral innate immune response than chickens against the H5N8 LP , which correlated with H5N8 HP inhibition. These data provide experimental evidence that HPAIV may be more likely to emerge in chickens than in ducks and underscore the importance of within-host viral variants interactions in viral evolution. IMPORTANCE Highly pathogenic avian influenza viruses represent a threat to poultry production systems and to human health because of their impact on food security and because of their zoonotic potential. It is therefore crucial to better understand how these viruses emerge. Using a within-host competition model between highly and low pathogenic avian influenza viruses, we provide evidence that highly pathogenic avian influenza viruses could be more likely to emerge in chickens than in ducks. These results have important implications for highly pathogenic avian influenza virus emergence prevention and they underscore the importance of within-host viral variants interactions in virus evolution.

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Highly Pathogenic Avian Influenza Virus Infection of Mallards with Homo- and Heterosubtypic Immunity Induced by Low Pathogenic Avian Influenza Viruses

PLoS ONE ◽

10.1371/journal.pone.0006706 ◽

2009 ◽

Vol 4 (8) ◽

pp. e6706 ◽

Cited By ~ 76

Author(s):

Sasan R. Fereidouni ◽

Elke Starick ◽

Martin Beer ◽

Hendrik Wilking ◽

Donata Kalthoff ◽

...

Keyword(s):

Influenza Virus ◽

Avian Influenza ◽

Highly Pathogenic Avian Influenza ◽

Influenza Virus Infection ◽

Influenza Viruses ◽

Avian Influenza Viruses ◽

Highly Pathogenic ◽

Pathogenic Avian Influenza ◽

Heterosubtypic Immunity ◽

Pathogenic Avian Influenza Virus

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Genetic Characterization and Pathogenicity of H7N7 and H7N9 Avian Influenza Viruses Isolated from South Korea

Viruses ◽

10.3390/v13102057 ◽

2021 ◽

Vol 13 (10) ◽

pp. 2057

Author(s):

Eun-Jee Na ◽

Young-Sik Kim ◽

Yoon-Ji Kim ◽

Jun-Soo Park ◽

Jae-Ku Oem

Keyword(s):

Influenza Virus ◽

Avian Influenza ◽

South Korea ◽

Influenza Viruses ◽

The Body ◽

Avian Influenza Viruses ◽

Receptor Binding Site ◽

Phylogenetic Tree Analysis ◽

Pathogenic Avian Influenza ◽

Ha Gene

H7 low pathogenic avian influenza viruses (LPAIVs) can mutate into highly pathogenic avian influenza viruses (HPAIVs). In addition to avian species, H7 avian influenza viruses (AIVs) also infect humans. In this study, two AIVs, H7N9 (20X-20) and H7N7 (34X-2), isolated from the feces of wild birds in South Korea in 2021, were genetically analyzed. The HA cleavage site of the two H7 Korean viruses was confirmed to be ELPKGR/GLF, indicating they are LPAIVs. There were no amino acid substitutions at the receptor-binding site of the HA gene of two H7 Korean viruses compared to that of A/Anhui/1/2013 (H7N9), which prefer human receptors. In the phylogenetic tree analysis, the HA gene of the two H7 Korean viruses shared the highest nucleotide similarity with the Korean H7 subtype AIVs. In addition, the HA gene of the two H7 Korean viruses showed high nucleotide similarity to that of the A/Jiangsu/1/2018(H7N4) virus, which is a human influenza virus originating from avian influenza virus. Most internal genes (PB2, PB1, PA, NP, NA, M, and NS) of the two H7 Korean viruses belonged to the Eurasian lineage, except for the M gene of 34X-2. This result suggests that active reassortment occurred among AIVs. In pathogenicity studies of mice, the two H7 Korean viruses replicated in the lungs of mice. In addition, the body weight of mice infected with 34X-2 decreased 7 days post-infection (dpi) and inflammation was observed in the peribronchiolar and perivascular regions of the lungs of mice. These results suggest that mammals can be infected with the two H7 Korean AIVs. Our data showed that even low pathogenic H7 AIVs may infect mammals, including humans, as confirmed by the A/Jiangsu/1/2018(H7N4) virus. Therefore, continuous monitoring and pathogenicity assessment of AIVs, even of LPAIVs, are required.

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