Computational identification of physicochemical signatures for host tropism of influenza A virus

2018 ◽  
Vol 16 (06) ◽  
pp. 1840023 ◽  
Author(s):  
Rui Yin ◽  
Xinrui Zhou ◽  
Jie Zheng ◽  
Chee Keong Kwoh
Keyword(s):  
Influenza A ◽  
High Performance ◽  
Computational Models ◽  
Prediction Models ◽  
Migratory Birds ◽  
Economic Loss ◽  
Influenza Viruses ◽  
Species Barrier ◽  
Van Der Waals Volume ◽  
Host Tropism

Avian influenza viruses from migratory birds have managed to cross host species barriers and infected various hosts like human and swine. Epidemics and pandemics might occur when influenza viruses are adapted to humans, causing deaths and enormous economic loss. Receptor-binding specificity of the virus is one of the key factors for the transmission of influenza viruses across species. The determination of host tropism and understanding of molecular properties would help identify the mechanism why zoonotic influenza viruses can cross species barrier and infect humans. In this study, we have constructed computational models for host tropism prediction on human-adapted subtypes of influenza HA proteins using random forest. The feature vectors of the prediction models were generated based on seven physicochemical properties of amino acids from influenza sequences of three major hosts. Feature aggregation and associative rules were further applied to select top 20 features and extract host-associated physicochemical signatures on the combined model of nonspecific subtypes. The prediction model achieved high performance ([Formula: see text], [Formula: see text], [Formula: see text]). Support and confidence rates were calculated for the host class-association rules. The results indicated that secondary structure and normalized Van der Waals volume were identified as more important physicochemical signatures in determining the host tropism.

scholarly journals Modern application and prospects of the stable isotopes  method for studying avian influenza A virus transmission   in migratory birds

2019 ◽  
Vol 14 (3) ◽  
pp. 92-100
Author(s):  
O. R. Druzyaka ◽  
A. V. Druzyaka ◽  
M. A. Gulyaeva ◽  
F. Huettmann ◽  
A. M. Shestopalov
Keyword(s):  
Stable Isotopes ◽  
Avian Influenza ◽  
Influenza A Virus ◽  
Influenza A ◽  
Bird Migration ◽  
Migratory Birds ◽  
Influenza Viruses ◽  
Migration Routes ◽  
Viral Pathogen ◽  
Avian Influenza A Virus

Aim. The circulation and transmission of pathogens is a global biological phenomenon that is closely associated with bird migration. This analysis was carried out with  the aim of understanding and assessing the prospects of using the stable isotope  method to study the circulation and transmission of the avian influenza A virus via  migratory birds. Discussion. Insufficient data on the distances of migration of infected birds and their  interpopulational relationships leaves open the question of the transmission of highly pathogenic influenza viruses (HSV) in the wild bird population. A deeper study of  the role of migrations in the spread of HSV may possibly allow the more effective  investigation of the transmission of the viral pathogen between individuals at migration stopover sites and the clarification of global migration routes. New methodological approaches are providing a more complete picture of the geography and phenology of migrations, as well as of the consequences of migratory behavior for species biology. The study of the quantitative component of migratory flows based on  the analysis of the content of stable isotopes (SIMS) in bird tissues seems very promising. This method is being applied to the solution of various environmental issues,  including the study of animal migrations.   Conclusion. Based on data from the scientific literature, it is shown that SIMS is  promising for the clarification of bird migration routes and the quantification of their  intensity. The resolving power of the method is sufficient to determine the migration  pathways of carriers of viral pathogens on the scale of zoogeographic subdomains  and in even further detail. However, to date, there have been few such studies: in  Russia they have not been conducted at all. The increased use of the SIMS methodology may possibly reveal new ways in which viral infections are spread via birds.  

scholarly journals Independence of Evolutionary and Mutational Rates after Transmission of Avian Influenza Viruses to Swine

1999 ◽  
Vol 73 (3) ◽  
pp. 1878-1884 ◽  
Author(s):  
J. Stech ◽  
X. Xiong ◽  
C. Scholtissek ◽  
R. G. Webster
Keyword(s):  
New York ◽  
Avian Influenza ◽  
Influenza A ◽  
Swine Influenza ◽  
Influenza Viruses ◽  
Mutation Rates ◽  
Influenza A Viruses ◽  
Species Barrier ◽  
H1n1 Strain ◽  
Serologic Evidence

ABSTRACT In 1979, an H1N1 avian influenza virus crossed the species barrier, establishing a new lineage in European swine. Because there is no direct or serologic evidence of previous H1N1 strains in these pigs, these isolates provide a model for studying early evolution of influenza viruses. The evolutionary rates of both the coding and noncoding changes of the H1N1 swine strains are higher than those of human and classic swine influenza A viruses. In addition, early H1N1 swine isolates show a marked plaque heterogeneity that consistently appears after a few passages. The presence of a mutator mutation was postulated (C. Scholtissek, S. Ludwig, and W. M. Fitch, Arch. Virol. 131:237–250, 1993) to account for these observations and the successful establishment of an avian H1N1 strain in swine. To address this question, we calculated the mutation rates of A/Mallard/New York/6750/78 (H2N2) and A/Swine/Germany/2/81 (H1N1) by using the frequency of amantadine-resistant mutants. To account for the inherent variability of estimated mutation rates, we used a probabilistic model for the statistical analysis. The resulting estimated mutation rates of the two strains were not significantly different. Therefore, an increased mutation rate due to the presence of a mutator mutation is unlikely to have led to the successful introduction of avian H1N1 viruses in European swine.

scholarly journals Wild Birds in Live Birds Markets: Potential Reservoirs of Enzootic Avian Influenza Viruses and Antimicrobial Resistant Enterobacteriaceae in Northern Egypt

Pathogens ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 196 ◽  
Author(s):  
Nehal M. Nabil ◽  
Ahmed M. Erfan ◽  
Maram M. Tawakol ◽  
Naglaa M. Haggag ◽  
Mahmoud M. Naguib ◽  
...  
Keyword(s):  
Influenza A ◽  
Migratory Birds ◽  
Wild Birds ◽  
Influenza Viruses ◽  
Northern Coast ◽  
Influenza A Viruses ◽  
E Coli ◽  
Ha Gene ◽  
Live Bird

Wild migratory birds are often implicated in the introduction, maintenance, and global dissemination of different pathogens, such as influenza A viruses (IAV) and antimicrobial-resistant (AMR) bacteria. Trapping of migratory birds during their resting periods at the northern coast of Egypt is a common and ancient practice performed mainly for selling in live bird markets (LBM). In the present study, samples were collected from 148 wild birds, representing 14 species, which were being offered for sale in LBM. All birds were tested for the presence of AIV and enterobacteriaceae. Ten samples collected from Northern Shoveler birds (Spatula clypeata) were positive for IAV and PCR sub-typing and pan HA/NA sequencing assays detected H5N8, H9N2, and H6N2 viruses in four, four, and one birds, respectively. Sequencing of the full haemagglutinin (HA) gene revealed a high similarity with currently circulating IAV in Egypt. From all the birds, E. coli was recovered from 37.2% and Salmonella from 20.2%, with 66–96% and 23–43% isolates being resistant to at least one of seven selected critically important antimicrobials (CIA), respectively. The presence of enzootic IAV and the wide prevalence of AMR enterobacteriaceae in wild birds highlight the potential role of LBM in the spread of different pathogens from and to wild birds. Continued surveillance of both AIV and antimicrobial-resistant enterobacteriaceae in wild birds’ habitats is urgently needed.

scholarly journals Influenza A Virus Strains Differ in Sensitivity to the Antiviral Action of Mx-GTPase

2008 ◽  
Vol 82 (7) ◽  
pp. 3624-3631 ◽  
Author(s):  
Jan Dittmann ◽  
Silke Stertz ◽  
Daniel Grimm ◽  
John Steel ◽  
Adolfo García-Sastre ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Influenza Viruses ◽  
Host Responses ◽  
Influenza A Viruses ◽  
Species Barrier ◽  
Spanish Flu ◽  
Avian Origin ◽  
Flu Virus ◽  
Virus Strains

ABSTRACT Interferon-mediated host responses are of great importance for controlling influenza A virus infections. It is well established that the interferon-induced Mx proteins possess powerful antiviral activities toward most influenza viruses. Here we analyzed a range of influenza A virus strains for their sensitivities to murine Mx1 and human MxA proteins and found remarkable differences. Virus strains of avian origin were highly sensitive to Mx1, whereas strains of human origin showed much weaker responses. Artificial reassortments of the viral components in a minireplicon system identified the viral nucleoprotein as the main target structure of Mx1. Interestingly, the recently reconstructed 1918 H1N1 “Spanish flu” virus was much less sensitive than the highly pathogenic avian H5N1 strain A/Vietnam/1203/04 when tested in a minireplicon system. Importantly, the human 1918 virus-based minireplicon system was almost insensitive to inhibition by human MxA, whereas the avian influenza A virus H5N1-derived system was well controlled by MxA. These findings suggest that Mx proteins provide a formidable hurdle that hinders influenza A viruses of avian origin from crossing the species barrier to humans. They further imply that the observed insensitivity of the 1918 virus-based replicon to the antiviral activity of human MxA is a hitherto unrecognized characteristic of the “Spanish flu” virus that may contribute to the high virulence of this unusual pandemic strain.

scholarly journals Genetic characterization of highly pathogenic avian influenza A (H5N8) virus isolated from domestic geese in Iraq, 2018

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Nahla Muhammad Saeed ◽  
Peshnyar Muhammad Atta Rashid ◽  
Hiewa Othman Dyary
Keyword(s):  
Molecular Markers ◽  
Influenza A ◽  
Migratory Birds ◽  
Mammalian Species ◽  
Influenza Viruses ◽  
Genetic Characteristics ◽  
Ha Gene ◽  
North Iraq ◽  
Group B

Abstract Background Influenza viruses are a continuous threat to avian and mammalian species, causing epidemics and pandemics. After the circulation of H5N1 in 2006, 2015, and 2016 in Iraq, an H5N8 influenza virus emerged in domestic geese in Sulaymaniyah Province, Iraq. This study analyzed the genetic characteristics of the Iraqi H5N8 viruses. Results An HPAI virus subtype H5N8 was identified from domestic backyard geese in the Kurdistan Region, north Iraq. Phylogenic analyses of the hemagglutinin (HA) and neuraminidase (NA) genes indicated that Iraq H5N8 viruses belonged to clade 2.3.4.4 group B and clustered with isolates from Iran, Israel, and Belgium. Genetic analysis of the HA gene indicated molecular markers for avian-type receptors. Characterization of the NA gene showed that the virus had sensitive molecular markers for antiviral drugs. Conclusions This is the first study ever on H5N8 in Iraq, and it is crucial to understand the epidemiology of the viruses in Iraq and the Middle East. The results suggest a possible role of migratory birds in the introduction of HPAI subtype H5N8 into Iraq.

scholarly journals In vivo evasion of MxA by avian influenza viruses requires human signature in the viral nucleoprotein

2017 ◽  
Vol 214 (5) ◽  
pp. 1239-1248 ◽  
Author(s):  
Christoph M. Deeg ◽  
Ebrahim Hassan ◽  
Pascal Mutz ◽  
Lara Rheinemann ◽  
Veronika Götz ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Transgenic Mice ◽  
Influenza A ◽  
Influenza Viruses ◽  
Influenza A Viruses ◽  
Avian Influenza Viruses ◽  
Species Barrier ◽  
Human Virus ◽  
Adaptive Mutations

Zoonotic transmission of influenza A viruses can give rise to devastating pandemics, but currently it is impossible to predict the pandemic potential of circulating avian influenza viruses. Here, we describe a new mouse model suitable for such risk assessment, based on the observation that the innate restriction factor MxA represents an effective species barrier that must be overcome by zoonotic viruses. Our mouse lacks functional endogenous Mx genes but instead carries the human MX1 locus as a transgene. Such transgenic mice were largely resistant to highly pathogenic avian H5 and H7 influenza A viruses, but were almost as susceptible to infection with influenza viruses of human origin as nontransgenic littermates. Influenza A viruses that successfully established stable lineages in humans have acquired adaptive mutations which allow partial MxA escape. Accordingly, an engineered avian H7N7 influenza virus carrying a nucleoprotein with signature mutations typically found in human virus isolates was more virulent in transgenic mice than parental virus, demonstrating that a few amino acid changes in the viral target protein can mediate escape from MxA restriction in vivo. Similar mutations probably need to be acquired by emerging influenza A viruses before they can spread in the human population.

scholarly journals IAV-CNN: a 2D convolutional neural network model to predict antigenic variants of influenza A virus

2020 ◽  
Author(s):  
Rui Yin ◽  
Nyi Nyi Thwin ◽  
Pei Zhuang ◽  
Yu Zhang ◽  
Zhuoyi Lin ◽  
...  
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Influenza A ◽  
Computational Models ◽  
Rapid Evolution ◽  
Predictive Performance ◽  
Influenza Viruses ◽  
Distributed Representation ◽  
Similar Distribution ◽  
Feature Maps

The rapid evolution of influenza viruses constantly leads to the emergence of novel influenza strains that are capable of escaping from population immunity. The timely determination of antigenic variants is critical to vaccine design. Empirical experimental methods like hemagglutination inhibition (HI) assays are time-consuming and labor-intensive, requiring live viruses. Recently, many computational models have been developed to predict the antigenic variants without considerations of explicitly modeling the interdependencies between the channels of feature maps. Moreover, the influenza sequences consisting of similar distribution of residues will have high degrees of similarity and will affect the prediction outcome. Consequently, it is challenging but vital to determine the importance of different residue sites and enhance the predictive performance of influenza antigenicity. We have proposed a 2D convolutional neural network (CNN) model to infer influenza antigenic variants (IAV-CNN). Specifically, we introduce a new distributed representation of amino acids, named ProtVec that can be applied to a variety of downstream proteomic machine learning tasks. After splittings and embeddings of influenza strains, a 2D squeeze-and-excitation CNN architecture is constructed that enables networks to focus on informative residue features by fusing both spatial and channel-wise information with local receptive fields at each layer. Experimental results on three influenza datasets show IAV-CNN achieves state-of-the-art performance combing the new distributed representation with our proposed architecture. It outperforms both traditional machine algorithms with the same feature representations and the majority of existing models in the independent test data. Therefore we believe that our model can be served as a reliable and robust tool for the prediction of antigenic variants.

UBIQUITOUS REASSORTMENTS IN INFLUENZA A VIRUSES

2008 ◽  
Vol 06 (05) ◽  
pp. 981-999 ◽  
Author(s):  
XIU-FENG WAN ◽  
MUFIT OZDEN ◽  
GUOHUI LIN
Keyword(s):  
Influenza A ◽  
Matrix Protein ◽  
Minimum Spanning Tree ◽  
Migratory Birds ◽  
Rna Virus ◽  
Influenza Pandemic ◽  
Influenza Viruses ◽  
Influenza A Viruses ◽  
H5n1 Avian Influenza Virus ◽  
Pandemic Strains

The influenza A virus is a negative-stranded RNA virus composed of eight segmented RNA molecules, including polymerases (PB2, PB1, PA), hemagglutinin (HA), nucleoprotein (NP), neuraminidase (NA), matrix protein (MP), and nonstructure gene (NS). The influenza A viruses are notorious for rapid mutations, frequent reassortments, and possible recombinations. Among these evolutionary events, reassortments refer to exchanges of discrete RNA segments between co-infected influenza viruses, and they have facilitated the generation of pandemic and epidemic strains. Thus, identification of reassortments will be critical for pandemic and epidemic prevention and control. This paper presents a reassortment identification method based on distance measurement using complete composition vector (CCV) and segment clustering using a minimum spanning tree (MST) algorithm. By applying this method, we identified 34 potential reassortment clusters among 2,641 PB2 segments of influenza A viruses. Among the 83 serotypes tested, at least 56 (67.46%) exchanged their fragments with another serotype of influenza A viruses. These identified reassortments involve 1,957 H2N1 and 1,968 H3N2 influenza pandemic strains as well as H5N1 avian influenza virus isolates, which have generated the potential for a future pandemic threat. More frequent reassortments were found to occur in wild birds, especially migratory birds. This MST clustering program is written in Java and will be available upon request.

scholarly journals Isolation and Characterization of a Distinct Influenza A Virus from Egyptian Bats

2018 ◽  
Vol 93 (2) ◽  
Author(s):  
Ahmed Kandeil ◽  
Mokhtar R. Gomaa ◽  
Mahmoud M. Shehata ◽  
Ahmed N. El Taweel ◽  
Sara H. Mahmoud ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Mdck Cells ◽  
Genomic Analysis ◽  
Cross Reactivity ◽  
Influenza Viruses ◽  
Avian Host ◽  
Influenza A Viruses ◽  
Species Barrier ◽  
Isolation And Characterization

ABSTRACT Recently, two genetically distinct influenza viruses were detected in bats in Guatemala and Peru. We conducted influenza A virus surveillance among four bat species in Egypt. Out of 1,202 swab specimens, 105 were positive by real-time PCR. A virus was successfully isolated in eggs and propagated in MDCK cells in the presence of N-tosyl-l-phenylalanine chloromethyl ketone-treated trypsin. Genomic analysis revealed that the virus was phylogenetically distinct from all other influenza A viruses. Analysis of the hemagglutinin gene suggested a common ancestry with other H9 viruses, and the virus showed a low level of cross-reactivity with serum raised against H9N2 viruses. Bats were seropositive for the isolated viruses. The virus replicated in the lungs of experimentally infected mice. While it is genetically distinct, this virus shares several avian influenza virus characteristics suggesting a more recent avian host origin. IMPORTANCE Through surveillance, we isolated and characterized an influenza A virus from Egyptian fruit bats. This virus had an affinity to avian-like receptors but was also able to infect mice. Our findings indicate that bats may harbor a diversity of influenza A viruses. Such viruses may have the potential to cross the species barrier to infect other species, including domestic birds, mammals, and, possibly, humans.

scholarly journals Weighing serological evidence of human exposure to animal influenza viruses − a literature review

2016 ◽  
Vol 21 (44) ◽  
Author(s):  
Reina Saapke Sikkema ◽  
Gudrun Stephanie Freidl ◽  
Erwin de Bruin ◽  
Marion Koopmans
Keyword(s):  
Avian Influenza ◽  
Human Exposure ◽  
Influenza A ◽  
Swine Influenza ◽  
Influenza Viruses ◽  
Influenza Surveillance ◽  
Low Grade ◽  
Surveillance Systems ◽  
Serological Evidence ◽  
Species Barrier

Assessing influenza A virus strains circulating in animals and their potential to cross the species barrier and cause human infections is important to improve human influenza surveillance and preparedness. We reviewed studies describing serological evidence of human exposure to animal influenza viruses. Comparing serological data is difficult due to a lack of standardisation in study designs and in laboratory methods used in published reports. Therefore, we designed a scoring system to assess and weigh specificity of obtained serology results in the selected articles. Many studies report reliable evidence of antibodies to swine influenza viruses among persons occupationally exposed to pigs. Most avian influenza studies target H5, H7 and H9 subtypes and most serological evidence of human exposure to avian influenza viruses is reported for these subtypes. Avian influenza studies receiving a low grade in this review often reported higher seroprevalences in humans compared with studies with a high grade. Official surveillance systems mainly focus on avian H5 and H7 viruses. Swine influenza viruses and avian subtypes other than H5 and H7 (emphasising H9) should be additionally included in official surveillance systems. Surveillance efforts should also be directed towards understudied geographical areas, such as Africa and South America.

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