scholarly journals Predicting Cross-Species Infection of Swine Influenza Virus with Representation Learning of Amino Acid Features

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Zheng Kou ◽  
Junjie Li ◽  
Xinyue Fan ◽  
Saeed Kosari ◽  
Xiaoli Qiang
Keyword(s):  
Amino Acid ◽  
High Performance ◽  
Swine Influenza Virus ◽  
Swine Influenza ◽  
Representation Learning ◽  
Influenza Viruses ◽  
Feature Representation ◽  
Specific Information ◽  
Feature Representations ◽  
Probabilistic Information

Swine influenza viruses (SIVs) can unforeseeably cross the species barriers and directly infect humans, which pose huge challenges for public health and trigger pandemic risk at irregular intervals. Computational tools are needed to predict infection phenotype and early pandemic risk of SIVs. For this purpose, we propose a feature representation algorithm to predict cross-species infection of SIVs. We built a high-quality dataset of 1902 viruses. A feature representation learning scheme was applied to learn feature representations from 64 well-trained random forest models with multiple feature descriptors of mutant amino acid in the viral proteins, including compositional information, position-specific information, and physicochemical properties. Class and probabilistic information were integrated into the feature representations, and redundant features were removed by feature space optimization. High performance was achieved using 20 informative features and 22 probabilistic information. The proposed method will facilitate SIV characterization of transmission phenotype.

scholarly journals A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs

2017 ◽  
Vol 91 (21) ◽  
Author(s):  
Zeng Wang ◽  
Huanliang Yang ◽  
Yan Chen ◽  
Shiyu Tao ◽  
Liling Liu ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Amino Acid ◽  
Glutamic Acid ◽  
Guinea Pigs ◽  
Swine Influenza Virus ◽  
Virus Transmission ◽  
Swine Influenza ◽  
Influenza Viruses ◽  
Single Amino Acid ◽  
Efficient Transmission

ABSTRACT Efficient transmission from human to human is the prerequisite for an influenza virus to cause a pandemic; however, the molecular determinants of influenza virus transmission are still largely unknown. In this study, we explored the molecular basis for transmission of Eurasian avian-like H1N1 (EAH1N1) swine influenza viruses by comparing two viruses that are genetically similar but differ in their transmissibility in guinea pigs: the A/swine/Guangxi/18/2011 virus (GX/18) is highly transmissible by respiratory droplet in guinea pigs, whereas the A/swine/Heilongjiang/27/2012 virus (HLJ/27) does not transmit in this animal model. We used reverse genetics to generate a series of reassortants and mutants in the GX/18 background and tested their transmissibility in guinea pigs. We found that a single-amino-acid substitution of glycine (G) for glutamic acid (E) at position 225 (E225G) in the HA1 protein completely abolished the respiratory droplet transmission of GX/18, whereas the substitution of E for G at the same position (G225E) in HA1 enabled HLJ/27 to transmit in guinea pigs. We investigated the underlying mechanism and found that viruses bearing 225E in HA1 replicated more rapidly than viruses bearing 225G due to differences in assembly and budding efficiencies. Our study indicates that the amino acid 225E in HA1 plays a key role in EAH1N1 swine influenza virus transmission and provides important information for evaluating the pandemic potential of field influenza virus strains. IMPORTANCE Efficient transmission among humans is a prerequisite for a novel influenza virus to cause a human pandemic. Transmissibility of influenza viruses is a polygenic trait, and understanding the genetic determinants for transmissibility will provide useful insights for evaluating the pandemic potential of influenza viruses in the field. Several amino acids in the hemagglutinin (HA) protein of influenza viruses have been shown to be important for transmissibility, usually by increasing virus affinity for human-type receptors. In this study, we explored the genetic basis of the transmissibility difference between two Eurasian avian-like H1N1 (EAH1N1) swine influenza viruses in guinea pigs and found that the amino acid glutamic acid at position 225 in the HA1 protein plays a critical role in the transmission of EAH1N1 virus by increasing the efficiency of viral assembly and budding.

scholarly journals Key Molecular Factors in Hemagglutinin and PB2 Contribute to Efficient Transmission of the 2009 H1N1 Pandemic Influenza Virus

2012 ◽  
Vol 86 (18) ◽  
pp. 9666-9674 ◽  
Author(s):  
Ying Zhang ◽  
Qianyi Zhang ◽  
Yuwei Gao ◽  
Xijun He ◽  
Huihui Kong ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Amino Acid ◽  
Guinea Pigs ◽  
Influenza Pandemic ◽  
Swine Influenza Virus ◽  
Swine Influenza ◽  
Influenza Viruses ◽  
Human Virus ◽  
2009 H1n1 ◽  
Droplet Transmission

Animal influenza viruses pose a clear threat to public health. Transmissibility among humans is a prerequisite for a novel influenza virus to cause a human pandemic. A novel reassortant swine influenza virus acquired sustained human-to-human transmissibility and caused the 2009 influenza pandemic. However, the molecular aspects of influenza virus transmission remain poorly understood. Here, we show that an amino acid in hemagglutinin (HA) is important for the 2009 H1N1 influenza pandemic virus (2009/H1N1) to bind to human virus receptors and confer respiratory droplet transmissibility in mammals. We found that the change from glutamine (Q) to arginine (R) at position 226 of HA, which causes a switch in receptor-binding preference from human α-2,6 to avian α-2,3 sialic acid, resulted in a virus incapable of respiratory droplet transmission in guinea pigs and reduced the virus's ability to replicate in the lungs of ferrets. The change from alanine (A) to threonine (T) at position 271 of PB2 also abolished the virus's respiratory droplet transmission in guinea pigs, and this mutation, together with the HA Q226R mutation, abolished the virus's respiratory droplet transmission in ferrets. Furthermore, we found that amino acid 271A of PB2 plays a key role in virus acquisition of the mutation at position 226 of HA that confers human receptor recognition. Our results highlight the importance of both the PB2 and HA genes on the adaptation and transmission of influenza viruses in humans and provide important insights for monitoring and evaluating the pandemic potential of field influenza viruses.

scholarly journals Semantic Relationships Guided Representation Learning for Facial Action Unit Recognition

2019 ◽  
Vol 33 ◽  
pp. 8594-8601 ◽  
Author(s):  
Guanbin Li ◽  
Xin Zhu ◽  
Yirui Zeng ◽  
Qing Wang ◽  
Liang Lin
Keyword(s):  
Neural Network ◽  
Facial Expressions ◽  
Mutual Exclusion ◽  
Representation Learning ◽  
Feature Representation ◽  
Semantic Relationship ◽  
Action Unit ◽  
Facial Action ◽  
Feature Representations ◽  
Regional Feature

Facial action unit (AU) recognition is a crucial task for facial expressions analysis and has attracted extensive attention in the field of artificial intelligence and computer vision. Existing works have either focused on designing or learning complex regional feature representations, or delved into various types of AU relationship modeling. Albeit with varying degrees of progress, it is still arduous for existing methods to handle complex situations. In this paper, we investigate how to integrate the semantic relationship propagation between AUs in a deep neural network framework to enhance the feature representation of facial regions, and propose an AU semantic relationship embedded representation learning (SRERL) framework. Specifically, by analyzing the symbiosis and mutual exclusion of AUs in various facial expressions, we organize the facial AUs in the form of structured knowledge-graph and integrate a Gated Graph Neural Network (GGNN) in a multi-scale CNN framework to propagate node information through the graph for generating enhanced AU representation. As the learned feature involves both the appearance characteristics and the AU relationship reasoning, the proposed model is more robust and can cope with more challenging cases, e.g., illumination change and partial occlusion. Extensive experiments on the two public benchmarks demonstrate that our method outperforms the previous work and achieves state of the art performance.

scholarly journals Swine-Origin H1 Influenza Viruses Isolated from Humans Exhibit Sustained Infectivity in an Aerosol State

2019 ◽  
Vol 85 (10) ◽  
Author(s):  
Joanna A. Pulit-Penaloza ◽  
Jessica A. Belser ◽  
Terrence M. Tumpey ◽  
Taronna R. Maines
Keyword(s):  
Influenza Virus ◽  
Swine Influenza Virus ◽  
Virus Transmission ◽  
Swine Influenza ◽  
Influenza Viruses ◽  
Aerosol State ◽  
The Stability ◽  
Higher Doses ◽  
Enhanced Stability

ABSTRACT The relative importance of influenza virus transmission via aerosols is not fully understood, but experimental data suggest that aerosol transmission may represent a critical mode of influenza virus spread among humans. Decades ago, prototypical laboratory strains of influenza were shown to persist in aerosols; however, there is a paucity of data available covering currently circulating influenza viruses, which differ significantly from their predecessors. In this study, we evaluated the longevity of influenza viruses in aerosols generated in the laboratory. We selected a panel of H1 viruses that exhibit diverse transmission profiles in the ferret model, including four human isolates of swine origin (referred to as variant) and a seasonal strain. By measuring the ratio of viral RNA to infectious virus maintained in aerosols over time, we show that influenza viruses known to transmit efficiently through the air display enhanced stability in an aerosol state for prolonged periods compared to those viruses that do not transmit as efficiently. We then assessed whether H1 influenza virus was still capable of infecting and causing disease in ferrets after being aged in suspended aerosols. Ferrets exposed to very low levels of influenza virus (≤17 PFU) in aerosols aged for 15 or 30 min became infected, with five of six ferrets shedding virus in nasal washes at titers on par with ferrets who inhaled higher doses of unaged influenza virus. We describe here an underreported characteristic of influenza viruses, stability in aerosols, and make a direct connection to the role this characteristic plays in influenza transmission. IMPORTANCE Each time a swine influenza virus transmits to a human, it provides an opportunity for the virus to acquire adaptations needed for sustained human-to-human transmission. Here, we use aerobiology techniques to test the stability of swine-origin H1 subtype viruses in aerosols and evaluate their infectivity in ferrets. Our results show that highly transmissible influenza viruses display enhanced stability in an aerosol state compared to viruses that do not transmit as efficiently. Similar to human-adapted strains, swine-origin influenza viruses are infectious in ferrets at low doses even after prolonged suspension in the air. These data underscore the risk of airborne swine-origin influenza viruses and support the need for continued surveillance and refinement of innovative laboratory methods to investigate mammalian exposure to inhaled pathogens. Determination of the molecular markers that affect the longevity of airborne influenza viruses will improve our ability to quickly identify emerging strains that present the greatest threat to public health.

scholarly journals Mutations in the NS1 Protein of Swine Influenza Virus Impair Anti-Interferon Activity and Confer Attenuation in Pigs

2005 ◽  
Vol 79 (12) ◽  
pp. 7535-7543 ◽  
Author(s):  
Alicia Solórzano ◽  
Richard J. Webby ◽  
Kelly M. Lager ◽  
Bruce H. Janke ◽  
Adolfo García-Sastre ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Nonstructural Protein ◽  
Swine Influenza Virus ◽  
Swine Influenza ◽  
Influenza Viruses ◽  
Model Systems ◽  
Ns1 Protein ◽  
Wild Type ◽  
Virulence Attenuation

ABSTRACT It has been shown previously that the nonstructural protein NS1 of influenza virus is an alpha/beta interferon (IFN-α/β) antagonist, both in vitro and in experimental animal model systems. However, evidence of this function in a natural host has not yet been obtained. Here we investigated the role of the NS1 protein in the virulence of a swine influenza virus (SIV) isolate in pigs by using reverse genetics. The virulent wild-type A/Swine/Texas/4199-2/98 (TX/98) virus and various mutants encoding carboxy-truncated NS1 proteins were rescued. Growth properties of TX/98 viruses with mutated NS1, induction of IFN in tissue culture, and virulence-attenuation in pigs were analyzed and compared to those of the recombinant wild-type TX/98 virus. Our results indicate that deletions in the NS1 protein decrease the ability of the TX/98 virus to prevent IFN-α/β synthesis in pig cells. Moreover, all NS1 mutant viruses were attenuated in pigs, and this correlated with the amount of IFN-α/β induced in vitro. These data suggest that the NS1 protein of SIV is a virulence factor. Due to their attenuation, NS1-mutated swine influenza viruses might have a great potential as live attenuated vaccine candidates against SIV infections of pigs.

scholarly journals Effect of health seeking interval on outcome in swine flu cases attended a tertiary care hospital in southern Rajasthan region of India

2019 ◽  
Vol 6 (7) ◽  
pp. 2910
Author(s):  
Shalabh Sharma ◽  
Yogesh Kumar Singhal
Keyword(s):  
Influenza Virus ◽  
Clinical Care ◽  
Swine Influenza Virus ◽  
Swine Influenza ◽  
Influenza Viruses ◽  
Swine Flu ◽  
Care Hospital ◽  
Health Seeking ◽  
Early Presentation ◽  
Number Of Patients

Background: Swine flu influenza is an infection by H1N1 type of swine influenza virus. Swine influenza virus or swine-origin influenza virus (SIV or S-OIV) is a strain of the family of influenza viruses that’s endemic in swine (pigs). Early diagnosis and treatment is key approach to control the morbidity and mortality associated with swine flu which can be achieved by improving health seeking behaviour of community. Understanding of behaviour of community is essential for planning strategies for prevention and control. Aim of this study is to establish a relation between healthcare interval and outcome of swine flu.Methods: A complete data of all the patients visiting swine flu OPDs, swine flu wards and ICU were maintained for year 2015. Each patient visiting either the swine flu OPD or the swine flu ward, who was suspected clinically to be H1N1 positive were tested for real time PCR. Data was collected in a standardized pre-structured questionnaire.Results: Out of 1247 samples tested for rt-PCR, number of patients found to be swine positive was 491 (39.37%). Total 267 patients were admitted in swine flu ward and ICU, out of them 62 was expired. Clinical care intervals of more than 5 days from onset of symptoms to swab collection, diagnosis and admission were more in female and rural population. Mean duration between onset of symptom to hospitalization, swab collection and diagnosis was significantly higher in deceased patients than survived.Conclusions: Early presentation to healthcare facility is associated with better prognosis and outcome. After patient report to the health care setup, early sample collection and diagnosis help to reduce mortality.

scholarly journals Resurrected ancestral influenza A viruses recapitulate the avian-to-mammalian adaptation of European avian-like swine influenza virus

2021 ◽  
Author(s):  
Wen Su ◽  
Rhodri Harfoot ◽  
Yvonne Su ◽  
Jennifer DeBeauchamp ◽  
Udayan Joseph ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Avian Influenza ◽  
Influenza A ◽  
Swine Influenza Virus ◽  
Swine Influenza ◽  
Polymerase Activity ◽  
Influenza Viruses ◽  
Mammalian Host ◽  
Influenza A Viruses ◽  
Sequence Reconstruction

Abstract The emergence of a pandemic influenza virus may be better anticipated if we better understand the evolutionary steps taken by avian influenza viruses as they adapt to mammals. We used ancestral sequence reconstruction to resurrect viruses representing initial adaptive stages of the European avian-like H1N1 virus as it transitioned from avian to swine hosts. We demonstrate that efficient transmissibility in pigs was gained through stepwise adaptation after 1983. These time-dependent adaptations resulted in changes in hemagglutinin receptor binding specificity and increased viral polymerase activity. An NP-R351K mutation under strong positive selection increased the transmissibility of a reconstructed virus. The stepwise-adaptation of a wholly avian influenza virus to a mammalian host suggests a window where targeted intervention may have highest impact. Successful intervention will, however, require strategic coordination of surveillance and risk assessment activities to identify these adapting viruses and guide pandemic preparedness resources.

scholarly journals Simultaneous infection with porcine reproductive and respiratory syndrome and influenza viruses abrogates clinical protection induced by live attenuated porcine reproductive and respiratory syndrome vaccination

2021 ◽  
Author(s):  
Tiphany Chrun ◽  
Emmanuel Atangana Maze ◽  
Eleni Vatzia ◽  
Veronica Martini ◽  
Basu Paudyal ◽  
...  
Keyword(s):  
Swine Influenza Virus ◽  
Swine Influenza ◽  
Cost Effective ◽  
Influenza Viruses ◽  
H3n2 Virus ◽  
Economic Losses ◽  
Respiratory Syndrome Virus ◽  
Upper Respiratory Tract ◽  
Live Virus ◽  
Clinical Protection

The porcine respiratory disease complex (PRDC) is responsible for significant economic losses in the pig industry worldwide. Porcine reproductive and respiratory syndrome virus (PRRSV) and swine influenza virus are major viral contributors to PRDC. Vaccines are cost-effective measures for controlling PRRS, however, their efficacy in the context of co-infections has been poorly investigated. In this study, we aimed to determine the effect of PRRSV-2 and swine influenza H3N2 virus co-infection on the efficacy of PRRSV modified live virus (MLV) vaccination, which is widely used in the field. Following simultaneous challenge with contemporary PRRSV-2 and H3N2 field isolates, we found that the protective effect of PRRS MLV vaccination on clinical disease and pathology was abrogated, although viral load was unaffected and antibody responses were enhanced. In contrast, co-infection in non-immunized animals reduced PRRSV-2 viremia and H3N2 virus load in the upper respiratory tract and potentiated T cell responses against both PRRSV-2 and H3N2 in the lung. Further analysis suggested that an upregulation of inhibitory cytokines gene expression in the lungs of vaccinated pigs may have influenced responses to H3N2 and PRRSV-2. These findings provide important insights into the effect of viral co-infections on PRRS vaccine efficacy that may help identity more effective vaccination strategies against PRDC in the field.

scholarly journals Cellular Innate Immunity against PRRSV and Swine Influenza Viruses

2019 ◽  
Vol 6 (1) ◽  
pp. 26 ◽  
Author(s):  
Elisa Crisci ◽  
Lorenzo Fraile ◽  
Maria Montoya
Keyword(s):  
Innate Immunity ◽  
T Cells ◽  
Natural Killer ◽  
Swine Influenza Virus ◽  
Swine Influenza ◽  
Γδ T Cells ◽  
Influenza Viruses ◽  
Production Costs ◽  
Respiratory Syndrome Virus

Porcine respiratory disease complex (PRDC) is a polymicrobial syndrome that results from a combination of infectious agents, such as environmental stressors, population size, management strategies, age, and genetics. PRDC results in reduced performance as well as increased mortality rates and production costs in the pig industry worldwide. This review focuses on the interactions of two enveloped RNA viruses—porcine reproductive and respiratory syndrome virus (PRRSV) and swine influenza virus (SwIV)—as major etiological agents that contribute to PRDC within the porcine cellular innate immunity during infection. The innate immune system of the porcine lung includes alveolar and parenchymal/interstitial macrophages, neutrophils (PMN), conventional dendritic cells (DC) and plasmacytoid DC, natural killer cells, and γδ T cells, thus the in vitro and in vivo interactions between those cells and PRRSV and SwIV are reviewed. Likewise, the few studies regarding PRRSV-SwIV co-infection are illustrated together with the different modulation mechanisms that are induced by the two viruses. Alterations in responses by natural killer (NK), PMN, or γδ T cells have not received much attention within the scientific community as their counterpart antigen-presenting cells and there are numerous gaps in the knowledge regarding the role of those cells in both infections. This review will help in paving the way for future directions in PRRSV and SwIV research and enhancing the understanding of the innate mechanisms that are involved during infection with these viruses.

Sign in / Sign up

Export Citation Format

Share Document