scholarly journals Sequence characteristics and phylogenetic analysis of H9N2 subtype avian influenza A viruses detected from poultry and the environment in China, 2018

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12512
Author(s):  
Xiaoyi Gao ◽  
Naidi Wang ◽  
Yuhong Chen ◽  
Xiaoxue Gu ◽  
Yuanhui Huang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Avian Influenza ◽  
Influenza A ◽  
Mammalian Species ◽  
Glycosylation Site ◽  
Global Public Health ◽  
Influenza A Viruses ◽  
H9n2 Subtype ◽  
Avian Influenza A Virus ◽  
High Conservation

H9N2 subtype avian influenza A virus (AIV) is a causative agent that poses serious threats to both the poultry industry and global public health. In this study, we performed active surveillance to identify H9N2 AIVs from poultry (chicken, duck, and goose) and the environment of different regions in China, and we phylogenetically characterized the sequences. AIV subtype-specific reverse transcription polymerase chain reaction (RT-PCR) showed that 5.43% (83/1529) samples were AIV positive, and 87.02% (67/77) of which were H9N2 AIVs. Phylogenetic analysis revealed that all H9N2 field viruses belonged to the Y280-like lineage, exhibiting 93.9–100% and 94.6–100% of homology in the hemagglutinin (HA) gene and 94.4–100% and 96.3–100% in the neuraminidase (NA) gene, at the nucleotide (nt) and amino acid (aa) levels, respectively. All field viruses shared relatively lower identities with vaccine strains, ranging from 89.4% to 97.7%. The aa sequence at the cleavage site (aa 333–340) in HA of all the isolated H9N2 AIVs was PSRSSRG/L, which is a characteristic of low pathogenic avian influenza virus (LPAIV). Notably, all the H9N2 field viruses harbored eight glycosylation sites, whereas a glycosylation site 218 NRT was missing and a new site 313 NCS was inserted. All field viruses had NGLMR as their receptor binding sites (RBS) at aa position 224–229, showing high conservation with many recently-isolated H9N2 strains. All H9N2 field isolates at position 226 had the aa Leucine (L), indicating their ability to bind to sialic acid (SA) α, a 2–6 receptor of mammals that poses the potential risk of transmission to humans. Our results suggest that H9N2 AIVs circulating in poultry populations that have genetic variation and the potential of infecting mammalian species are of great significance when monitoring H9N2 AIVs in China.

scholarly journals Comparative sequence, antigenic and phylogenetic analysis of avian influenza (H9N2) surface proteins isolated in Pakistan between 1999 and 2008

2011 ◽  
Vol 5 (06) ◽  
pp. 413-424 ◽  
Author(s):  
Azeem Mehmood Butt ◽  
Samerene Siddique ◽  
Shifa Tahir ◽  
Izza Nasrullah ◽  
Mureed Hussain ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Avian Influenza ◽  
Viral Entry ◽  
Influenza A ◽  
Genomic Structure ◽  
Glycosylation Site ◽  
Surface Proteins ◽  
Host Immune System ◽  
Influenza A Viruses ◽  
Substitution Mutations

Introduction: Influenza A viruses possess a unique genomic structure which leads to genetic instability, especially in products of neuraminidase and hemagglutinin genes. These surface proteins play major roles in viral entry and release, and in the activation of the host immune system. Methodology: This study involved an in silico sequence, phylogenetic and antigenic analyses of hemagglutinin and neuraminidase proteins of avian influenza A (H9N2) strains that circulated in Pakistan's poultry flocks from 1999 to 2008 and determined variations among these sequences at different levels. Results: Sequence and phylogenetic analysis revealed a large number of similar substitution mutations and close evolutionary relation among sequences of both proteins. Changes were observed in the N-glycosylation sites of both surface proteins, along with the appearance of a new glycosylation site in the neuraminidase sequence isolated in 2007. Epitopes for hemagglutinin remained conserved, whereas for neuraminidase, epitopes from older strains reappeared in present sequences. Conclusions: Because of the rapid mutating nature of avian influenza subtype H9N2, constant surveillance of annual sequence variations is important. Preventive measures and vaccine products can be evaluated by keeping track of changes that may lead to reassortment among different circulating strains in Pakistan's commercial poultry flocks or in humans.

scholarly journals Characterization of a Human H5N1 Influenza A Virus Isolated in 2003

2005 ◽  
Vol 79 (15) ◽  
pp. 9926-9932 ◽  
Author(s):  
Kyoko Shinya ◽  
Masato Hatta ◽  
Shinya Yamada ◽  
Ayato Takada ◽  
Shinji Watanabe ◽  
...  
Keyword(s):  
Hong Kong ◽  
Avian Influenza ◽  
Influenza A Virus ◽  
Influenza A ◽  
Mainland China ◽  
Virus Infections ◽  
Influenza A Viruses ◽  
H5n1 Avian Influenza Virus ◽  
H5n1 Influenza ◽  
Avian Influenza A Virus

ABSTRACT In 2003, H5N1 avian influenza virus infections were diagnosed in two Hong Kong residents who had visited the Fujian province in mainland China, affording us the opportunity to characterize one of the viral isolates, A/Hong Kong/213/03 (HK213; H5N1). In contrast to H5N1 viruses isolated from humans during the 1997 outbreak in Hong Kong, HK213 retained several features of aquatic bird viruses, including the lack of a deletion in the neuraminidase stalk and the absence of additional oligosaccharide chains at the globular head of the hemagglutinin molecule. It demonstrated weak pathogenicity in mice and ferrets but caused lethal infection in chickens. The original isolate failed to produce disease in ducks but became more pathogenic after five passages. Taken together, these findings portray the HK213 isolate as an aquatic avian influenza A virus without the molecular changes associated with the replication of H5N1 avian viruses in land-based poultry such as chickens. This case challenges the view that adaptation to land-based poultry is a prerequisite for the replication of aquatic avian influenza A viruses in humans.

scholarly journals Molecular Basis for the Generation in Pigs of Influenza A Viruses with Pandemic Potential

1998 ◽  
Vol 72 (9) ◽  
pp. 7367-7373 ◽  
Author(s):  
Toshihiro Ito ◽  
J. Nelson S. S. Couceiro ◽  
Sørge Kelm ◽  
Linda G. Baum ◽  
Scott Krauss ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Influenza A ◽  
Influenza Viruses ◽  
Structural Basis ◽  
Human Populations ◽  
Influenza A Viruses ◽  
Human Virus ◽  
Surface Receptors ◽  
Virus Receptors ◽  
Avian Influenza A Virus

ABSTRACT Genetic and biologic observations suggest that pigs may serve as “mixing vessels” for the generation of human-avian influenza A virus reassortants, similar to those responsible for the 1957 and 1968 pandemics. Here we demonstrate a structural basis for this hypothesis. Cell surface receptors for both human and avian influenza viruses were identified in the pig trachea, providing a milieu conducive to viral replication and genetic reassortment. Surprisingly, with continued replication, some avian-like swine viruses acquired the ability to recognize human virus receptors, raising the possibility of their direct transmission to human populations. These findings help to explain the emergence of pandemic influenza viruses and support the need for continued surveillance of swine for viruses carrying avian virus genes.

scholarly journals Molecular Analysis of H7 Avian Influenza Viruses from Australia and New Zealand: Genetic Diversity and Relationships from 1976 to 2007

2010 ◽  
Vol 84 (19) ◽  
pp. 9957-9966 ◽  
Author(s):  
Dieter Bulach ◽  
Rebecca Halpin ◽  
David Spiro ◽  
Laura Pomeroy ◽  
Daniel Janies ◽  
...  
Keyword(s):  
New Zealand ◽  
Avian Influenza ◽  
Influenza A ◽  
Influenza Viruses ◽  
Full Genome Sequencing ◽  
Influenza A Viruses ◽  
Independent Evolution ◽  
Avian Influenza A Virus ◽  
Geographic Regions ◽  
Genetic Pool

ABSTRACT Full-genome sequencing of 11 Australian and 1 New Zealand avian influenza A virus isolate (all subtype H7) has enabled comparison of the sequences of each of the genome segments to those of other subtype H7 avian influenza A viruses. The inference of phylogenetic relationships for each segment has been used to develop a model of the natural history of these viruses in Australia. Phylogenetic analysis of the hemagglutinin segment indicates that the Australian H7 isolates form a monophyletic clade. This pattern is consistent with the long-term, independent evolution that is, in this instance, associated with geographic regions. On the basis of the analysis of the other H7 hemagglutinin sequences, three other geographic regions for which similar monophyletic clades have been observed were confirmed. These regions are Eurasia plus Africa, North America, and South America. Analysis of the neuraminidase sequences from the H7N1, H7N3, and H7N7 genomes revealed the same region-based relationships. This pattern of independent evolution of Australian isolates is supported by the results of analysis of each of the six remaining genomic segments. These results, in conjunction with the occurrence of five different combinations of neuraminidase subtypes (H7N2, H7N3, H7N4, H7N6, H7N7) among the 11 Australian isolates, suggest that the maintenance host(s) is nearly exclusively associated with Australia. The single lineage of Australian H7 hemagglutinin sequences, despite the occurrence of multiple neuraminidase types, suggests the existence of a genetic pool from which a variety of reassortants arise rather than the presence of a small number of stable viral clones. This pattern of evolution is likely to occur in each of the regions mentioned above.

scholarly journals Avian Influenza A Virus Associations in Wild, Terrestrial Mammals: A Review of Potential Synanthropic Vectors to Poultry Facilities

Viruses ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 1352
Author(s):  
J. Jeffrey Root ◽  
Susan A. Shriner
Keyword(s):  
Influenza A ◽  
Mammalian Species ◽  
Influenza A Viruses ◽  
Wild Mammals ◽  
Terrestrial Mammals ◽  
Poultry Facilities ◽  
Avian Influenza A Virus ◽  
Potential Risks ◽  
Virus Adaptation ◽  
Reservoir Hosts

The potential role of wild mammals in the epidemiology of influenza A viruses (IAVs) at the farm-side level has gained increasing consideration over the past two decades. In some instances, select mammals may be more likely to visit riparian areas (both close and distant to farms) as well as poultry farms, as compared to traditional reservoir hosts, such as waterfowl. Of significance, many mammalian species can successfully replicate and shed multiple avian IAVs to high titers without prior virus adaptation and often can shed virus in greater quantities than synanthropic avian species. Within this review, we summarize and discuss the potential risks that synanthropic mammals could pose by trafficking IAVs to poultry operations based on current and historic literature.

scholarly journals Protection against a Lethal Avian Influenza A Virus in a Mammalian System

1999 ◽  
Vol 73 (2) ◽  
pp. 1453-1459 ◽  
Author(s):  
Janice M. Riberdy ◽  
Kirsten J. Flynn ◽  
Juergen Stech ◽  
Robert G. Webster ◽  
John D. Altman ◽  
...  
Keyword(s):  
T Cell ◽  
Avian Influenza ◽  
Influenza A Virus ◽  
Influenza A ◽  
Influenza Pandemic ◽  
Immune Memory ◽  
H3n2 Virus ◽  
Influenza A Viruses ◽  
Cell Responses ◽  
Avian Influenza A Virus

ABSTRACT The question of how best to protect the human population against a potential influenza pandemic has been raised by the recent outbreak caused by an avian H5N1 virus in Hong Kong. The likely strategy would be to vaccinate with a less virulent, laboratory-adapted H5N1 strain isolated previously from birds. Little attention has been given, however, to dissecting the consequences of sequential exposure to serologically related influenza A viruses using contemporary immunology techniques. Such experiments with the H5N1 viruses are limited by the potential risk to humans. An extremely virulent H3N8 avian influenza A virus has been used to infect both immunoglobulin-expressing (Ig+/+) and Ig−/− mice primed previously with a laboratory-adapted H3N2 virus. The cross-reactive antibody response was very protective, while the recall of CD8+ T-cell memory in the Ig−/− mice provided some small measure of resistance to a low-dose H3N8 challenge. The H3N8 virus also replicated in the respiratory tracts of the H3N2-primed Ig+/+ mice, generating secondary CD8+ and CD4+ T-cell responses that may contribute to recovery. The results indicate that the various components of immune memory operate together to provide optimal protection, and they support the idea that related viruses of nonhuman origin can be used as vaccines.

scholarly journals Genotype turnover by reassortment of replication complex genes from avian Influenza A virus

2006 ◽  
Vol 87 (10) ◽  
pp. 2803-2815 ◽  
Author(s):  
Catherine A. Macken ◽  
Richard J. Webby ◽  
William J. Bruno
Keyword(s):  
Avian Influenza ◽  
Influenza A Virus ◽  
Influenza A ◽  
Genetic Material ◽  
Influenza A Viruses ◽  
Replication Complex ◽  
H5n1 Influenza ◽  
New Genotype ◽  
Avian Influenza A Virus ◽  
Rapid Generation

Reassortment among the RNA segments of Influenza A virus caused the two most recent human influenza pandemics; recently, reassortment has generated viral genotypes associated with outbreaks of avian H5N1 influenza in Asia and Europe. A statistical analysis has been developed for the systematic identification and characterization of reassortant viruses. The analysis was applied to the genes of the replication complex of 152 avian influenza A viruses isolated between 1966 and 2004 from predominantly terrestrial and domestic aquatic avian species. The results indicated that reassortment among these genes was pervasive throughout this period and throughout both the Eurasian and North American lineages of the virus. Evidence is presented that the circulating genotypes of the replication complex are being replaced continually by novel genotypes created by reassortment. No constraints for coordinated reassortment among genes of the replication complex were evident; rather, reassortment almost always proceeded one segment at a time. A maximum-likelihood estimate of the rate of reassortment was derived. For significantly diverged Asian avian influenza A viruses from the period 1991–2004, it was estimated that the median duration between creation of a new genotype and its next segment reassortment was 3 years. Reassortments that introduced previously unobserved influenza genetic material were detected. These findings point to substantial potential for rapid generation of novel avian influenza A viruses, emphasizing the importance of intensive surveillance of these host species in preparation for a possible pandemic.

scholarly journals Avian influenza A virus susceptibility, infection, transmission, and antibody kinetics in European starlings

2021 ◽  
Vol 17 (8) ◽  
pp. e1009879
Author(s):  
Jeremy W. Ellis ◽  
J. Jeffrey Root ◽  
Loredana M. McCurdy ◽  
Kevin T. Bentler ◽  
Nicole L. Barrett ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Influenza A ◽  
Reservoir Host ◽  
Influenza A Viruses ◽  
European Starlings ◽  
Transmission Experiment ◽  
Poultry Facilities ◽  
Field Samples ◽  
Transmission Study ◽  
Avian Influenza A Virus

Avian influenza A viruses (IAVs) pose risks to public, agricultural, and wildlife health. Bridge hosts are spillover hosts that share habitat with both maintenance hosts (e.g., mallards) and target hosts (e.g., poultry). We conducted a comprehensive assessment of European starlings (Sturnus vulgaris), a common visitor to both urban and agricultural environments, to assess whether this species might act as a potential maintenance or bridge host for IAVs. First, we experimentally inoculated starlings with a wild bird IAV to investigate susceptibility and replication kinetics. Next, we evaluated whether IAV might spill over to starlings from sharing resources with a widespread IAV reservoir host. We accomplished this using a specially designed transmission cage to simulate natural environmental transmission by exposing starlings to water shared with IAV-infected mallards (Anas platyrhynchos). We then conducted a contact study to assess intraspecies transmission between starlings. In the initial experimental infection study, all inoculated starlings shed viral RNA and seroconverted. All starlings in the transmission study became infected and shed RNA at similar levels. All but one of these birds seroconverted, but detectable antibodies were relatively transient, falling to negative levels in a majority of birds by 59 days post contact. None of the contact starlings in the intraspecies transmission experiment became infected. In summary, we demonstrated that starlings may have the potential to act as IAV bridge hosts if they share water with IAV-infected waterfowl. However, starlings are unlikely to act as maintenance hosts due to limited, if any, intraspecies transmission. In addition, starlings have a relatively brief antibody response which should be considered when interpreting serology from field samples. Further study is needed to evaluate the potential for transmission from starlings to poultry, a possibility enhanced by starling’s behavioral trait of forming very large flocks which can descend on poultry facilities when natural resources are scarce.

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