Characterization, Whole-Genome Sequencing and Phylogenetic Analysis of Three H3N2 Avian Influenza Viruses Isolated From Domestic Ducks at Live Poultry Markets of Iran, 2017: First Report

Abstract Avian influenza type A viruses (AIV) can infect a broad range of hosts including human and birds, making them an important viral pathogen with zoonotic potential. Among birds, ducks are a known reservoir for many avian viruses including the AIV. During migration seasons in Iran, this bird species is generally at a high risk of being infected by free-living aquatic birds. In this study, 962 cloacal swabs were collected from domestic ducks at several live poultry markets (LPMs) of Gilan, Mazandaran and Golestan provinces of Iran in the year 2017. Preliminary assays such as HI, NI, MDT, ICPI and RT-qPCR suggested that 0.5% of the birds were infected by H3 low pathogenic influenza viruses (LPAI). Three isolates were selected for whole genome sequencing. The cleavage site of the HA genes showed a PEKQTR/GLF motif, an indicator of LPAI. Furthermore, BLAST and phylogenetic analyses of the HA gene showed high homology to the Eurasian lineage of H3N8 AIV (95.5–97.1% to several European and East Asian isolates). However, the NA genes showed high homology (at most 96.5–96.9%) to those belonging to AIV N2 subtype. Furthermore, internal genes showed high homology (96–98%) to a variety of duck-origin subtypes and glycoprotein combinations, which were different for each segment. This showed a complex reassortment between different subtypes. Our report is the first whole genome sequencing and complete characterization of H3N2 AIV from Iran. Such surveillance should continue to study the evolution and possible emergence of viruses with pandemic potential.

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Field Monitoring of Avian Influenza Viruses: Whole-Genome Sequencing and Tracking of Neuraminidase Evolution Using 454 Pyrosequencing

Journal of Clinical Microbiology ◽

10.1128/jcm.01142-12 ◽

2012 ◽

Vol 50 (9) ◽

pp. 2881-2887 ◽

Cited By ~ 19

Author(s):

G. Croville ◽

S. M. Soubies ◽

J. Barbieri ◽

C. Klopp ◽

J. Mariette ◽

...

Keyword(s):

Avian Influenza ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

454 Pyrosequencing ◽

Field Monitoring ◽

Influenza Viruses ◽

Whole Genome ◽

Avian Influenza Viruses

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Ecology of H3 avian influenza viruses in Korea and assessment of their pathogenic potentials

Journal of General Virology ◽

10.1099/vir.0.83462-0 ◽

2008 ◽

Vol 89 (4) ◽

pp. 949-957 ◽

Cited By ~ 34

Author(s):

Min-Suk Song ◽

Taek-Kyu Oh ◽

Ho Jin Moon ◽

Dai-Woon Yoo ◽

Eun Ho Lee ◽

...

Keyword(s):

Avian Influenza ◽

Wild Bird ◽

Migratory Birds ◽

Influenza Viruses ◽

Interspecies Transmission ◽

Avian Influenza Viruses ◽

Backyard Poultry ◽

Live Poultry ◽

Live Poultry Markets

To determine the genetic origins of novel H3 avian influenza viruses of chickens and ducks in Korea, genetic characterization of H3 avian influenza viruses isolated from live poultry markets and migratory aquatic birds in South Korea during 2004–2006 was conducted. Phylogenetic analysis revealed that at least four novel genotypes of H3N2 and two genotypes of H3N6 avian influenza viruses were co-circulating in backyard poultry of Korea. The viruses were reassortants between H9N2 viruses of Korean chickens and unknown influenza viruses of migratory birds. Genetic comparison of H3 viruses from live bird markets with those from wild bird isolates revealed that certain gene segments of wild bird isolates are related closely to those of Korean group H9N2 viruses isolated from live poultry markets in 2003. Furthermore, animal-challenge studies demonstrated that the pathogenicity of certain avian H3 influenza viruses was altered due to reassortment, leading to H3 avian influenza viruses in Korea that can potentially expand their host range to include mammals. These studies emphasize the continuing need to monitor backyard poultry at live poultry markets to better understand interspecies transmission and the emergence of novel influenza viruses that have the potential to infect humans.

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Whole Genome Sequencing of A(H3N2) Influenza Viruses Reveals Variants Associated with Severity during the 2016–2017 Season

Viruses ◽

10.3390/v11020108 ◽

2019 ◽

Vol 11 (2) ◽

pp. 108 ◽

Cited By ~ 10

Author(s):

Bruno Simon ◽

Maxime Pichon ◽

Martine Valette ◽

Gwendolyne Burfin ◽

Mathilde Richard ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Influenza Viruses ◽

Influenza Surveillance ◽

Whole Genome ◽

University Hospitals ◽

Surveillance Network ◽

Genetic Traits ◽

H3n2 Influenza ◽

The Impact

Influenza viruses cause a remarkable disease burden and significant morbidity and mortality worldwide, and these impacts vary between seasons. To understand the mechanisms associated with these differences, a comprehensive approach is needed to characterize the impact of influenza genomic traits on the burden of disease. During 2016–2017, a year with severe A(H3N2), we sequenced 176 A(H3N2) influenza genomes using next generation sequencing (NGS) for routine surveillance of circulating influenza viruses collected via the French national influenza community-based surveillance network or from patients hospitalized in the intensive care units of the University Hospitals of Lyon, France. Taking into account confounding factors, sequencing and clinical data were used to identify genomic variants and quasispecies associated with influenza severity or vaccine failure. Several amino acid substitutions significantly associated with clinical traits were found, including NA V263I and NS1 K196E which were associated with severity and co-occurred only in viruses from the 3c.2a1 clade. Additionally, we observed that intra-host diversity as a whole and on a specific set of gene segments increased with severity. These results support the use of whole genome sequencing as a tool for the identification of genetic traits associated with severe influenza in the context of influenza surveillance.

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Characterizations of H4 avian influenza viruses isolated from ducks in live poultry markets and farm in Shanghai

Scientific Reports ◽

10.1038/srep37843 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 9

Author(s):

Ying Shi ◽

Hongrui Cui ◽

Junheng Wang ◽

Qiuyan Chi ◽

Xuesong Li ◽

...

Keyword(s):

Avian Influenza ◽

Influenza Viruses ◽

Avian Influenza Viruses ◽

Live Poultry ◽

Live Poultry Markets

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Genomic Dissection of an Icelandic Epidemic of Respiratory Disease in Horses and Associated Zoonotic Cases

mBio ◽

10.1128/mbio.00826-17 ◽

2017 ◽

Vol 8 (4) ◽

Cited By ~ 9

Author(s):

Sigríður Björnsdóttir ◽

Simon R. Harris ◽

Vilhjálmur Svansson ◽

Eggert Gunnarsson ◽

Ólöf G. Sigurðardóttir ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Respiratory Disease ◽

Genome Sequencing ◽

Causative Agent ◽

Opportunistic Pathogen ◽

Whole Genome ◽

National Scale ◽

Horse Population ◽

Viral Pathogen ◽

First Time

ABSTRACT Iceland is free of the major infectious diseases of horses. However, in 2010 an epidemic of respiratory disease of unknown cause spread through the country’s native horse population of 77,000. Microbiological investigations ruled out known viral agents but identified the opportunistic pathogen Streptococcus equi subsp. zooepidemicus (S. zooepidemicus) in diseased animals. We sequenced the genomes of 257 isolates of S. zooepidemicus to differentiate epidemic from endemic strains. We found that although multiple endemic clones of S. zooepidemicus were present, one particular clone, sequence type 209 (ST209), was likely to have been responsible for the epidemic. Concurrent with the epidemic, ST209 was also recovered from a human case of septicemia, highlighting the pathogenic potential of this strain. Epidemiological investigation revealed that the incursion of this strain into one training yard during February 2010 provided a nidus for the infection of multiple horses that then transmitted the strain to farms throughout Iceland. This study represents the first time that whole-genome sequencing has been used to investigate an epidemic on a national scale to identify the likely causative agent and the link to an associated zoonotic infection. Our data highlight the importance of national biosecurity to protect vulnerable populations of animals and also demonstrate the potential impact of S. zooepidemicus transmission to other animals, including humans. IMPORTANCE An epidemic of respiratory disease affected almost the entire native Icelandic horse population of 77,000 animals in 2010, resulting in a self-imposed ban on the export of horses and significant economic costs to associated industries. Although the speed of transmission suggested that a viral pathogen was responsible, only the presence of the opportunistic pathogen Streptococcus zooepidemicus was consistent with the observed clinical signs. We applied genomic sequencing to differentiate epidemic from endemic strains and to shed light on the rapid transmission of the epidemic strain throughout Iceland. We further highlight the ability of epidemic and endemic strains of S. zooepidemicus to infect other animals, including humans. This study represents the first time that whole-genome sequencing has been used to elucidate an outbreak on a national scale and identify the likely causative agent. An epidemic of respiratory disease affected almost the entire native Icelandic horse population of 77,000 animals in 2010, resulting in a self-imposed ban on the export of horses and significant economic costs to associated industries. Although the speed of transmission suggested that a viral pathogen was responsible, only the presence of the opportunistic pathogen Streptococcus zooepidemicus was consistent with the observed clinical signs. We applied genomic sequencing to differentiate epidemic from endemic strains and to shed light on the rapid transmission of the epidemic strain throughout Iceland. We further highlight the ability of epidemic and endemic strains of S. zooepidemicus to infect other animals, including humans. This study represents the first time that whole-genome sequencing has been used to elucidate an outbreak on a national scale and identify the likely causative agent.

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Diversity and evolution of avian influenza viruses in live poultry markets, free-range poultry and wild wetland birds in China

Journal of General Virology ◽

10.1099/jgv.0.000399 ◽

2016 ◽

Vol 97 (4) ◽

pp. 844-854 ◽

Cited By ~ 28

Author(s):

Liang-Jun Chen ◽

Xian-Dan Lin ◽

Wen-Ping Guo ◽

Jun-Hua Tian ◽

Wen Wang ◽

...

Keyword(s):

Avian Influenza ◽

Influenza Viruses ◽

Avian Influenza Viruses ◽

Wetland Birds ◽

Free Range ◽

Live Poultry ◽

Live Poultry Markets

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Efficient whole genome sequencing of influenza A viruses

10.1101/749234 ◽

2019 ◽

Author(s):

Marina Escalera-Zamudio ◽

Ana Georgina Cobián-Güemes ◽

Blanca Taboada ◽

Irma López-Martínez ◽

Joel Armando Vázquez-Pérez ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Influenza A Virus ◽

Genome Sequencing ◽

Influenza A ◽

Genetic Material ◽

Influenza Viruses ◽

Epidemiological Surveillance ◽

Clinical Samples ◽

Whole Genome ◽

Influenza A Viruses

ABSTRACTThe constant threat of emergence for novel pathogenic influenza A viruses with pandemic potential, makes full-genome characterization of circulating influenza viral strains a high priority, allowing detection of novel and re-assorting variants. Sequencing the full-length genome of influenza A virus traditionally required multiple amplification rounds, followed by the subsequent sequencing of individual PCR products. The introduction of high-throughput sequencing technologies has made whole genome sequencing easier and faster. We present a simple protocol to obtain whole genome sequences of hypothetically any influenza A virus, even with low quantities of starting genetic material. The complete genomes of influenza A viruses of different subtypes and from distinct sources (clinical samples of pdmH1N1, tissue culture-adapted H3N2 viruses, or avian influenza viruses from cloacal swabs) were amplified with a single multisegment reverse transcription-PCR reaction and sequenced using Illumina sequencing platform. Samples with low quantity of genetic material after initial PCR amplification were re-amplified by an additional PCR using random primers. Whole genome sequencing was successful for 66% of the samples, whilst the most relevant genome segments for epidemiological surveillance (corresponding to the hemagglutinin and neuraminidase) were sequenced with at least 93% coverage (and a minimum 10x) for 98% of the samples. Low coverage for some samples is likely due to an initial low viral RNA concentration in the original sample. The proposed methodology is especially suitable for sequencing a large number of samples, when genetic data is urgently required for strains characterization, and may also be useful for variant analysis.

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