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Liu T, Peng Y, Wu J, Lu S, He Y, Li X, Sun L, Song S, Zhang S, Li Z, Wang X, Zhang S, Liu M, Kou Z. Surveillance of avian influenza viruses in live bird markets of Shandong province from 2013 to 2019. Front Microbiol 2022; 13:1030545. [PMID: 36406436 PMCID: PMC9670132 DOI: 10.3389/fmicb.2022.1030545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
Avian influenza viruses (AIVs) seriously affect the poultry industry and pose a great threat to humans. Timely surveillance of AIVs is the basis for preparedness of the virus. This study reported the long-term surveillance of AIVs in the live bird market (LBM) of 16 cities in Shandong province from 2013 to 2019. A total of 29,895 samples were obtained and the overall positive rate of AIVs was 9.7%. The H9 was found to be the most predominant subtype in most of the time and contributed most to the monthly positve rate of AIVs as supported by the univariate and multivariate analysis, while H5 and H7 only circulated in some short periods. Then, the whole-genome sequences of 62 representative H9N2 viruses including one human isolate from a 7-year-old boy in were determined and they were genetically similar to each other with the median pairwise sequence identities ranging from 0.96 to 0.98 for all segments. The newly sequenced viruses were most similar to viruses isolated in chickens in mainland China, especially the provinces in Eastern China. Phylogenetic analysis showed that these newly sequenced H9N2 viruses belonged to the same clade for all segments except PB1. Nearly all of these viruses belonged to the G57 genotype which has dominated in China since 2010. Finally, several molecular markers associated with human adaptation, mammalian virulence, and drug resistance were identified in the newly sequenced H9N2 viruses. Overall, the study deepens our understanding of the epidemic and evolution of AIVs and provides a basis for effective control of AIVs in China.
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Affiliation(s)
- Ti Liu
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Julong Wu
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Shangwen Lu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Yujie He
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Xiyan Li
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lin Sun
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Shaoxia Song
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Shengyang Zhang
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Zhong Li
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Xianjun Wang
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Shu Zhang
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Mi Liu
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Mi Liu,
| | - Zengqiang Kou
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
- *Correspondence: Zengqiang Kou,
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2
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Massari S, Desantis J, Nizi MG, Cecchetti V, Tabarrini O. Inhibition of Influenza Virus Polymerase by Interfering with Its Protein-Protein Interactions. ACS Infect Dis 2021; 7:1332-1350. [PMID: 33044059 PMCID: PMC8204303 DOI: 10.1021/acsinfecdis.0c00552] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Influenza (flu) virus is a serious threat to global health with the potential to generate devastating pandemics. The availability of broad spectrum antiviral drugs is an unequaled weapon during pandemic events, especially when a vaccine is still not available. One of the most promising targets for the development of new antiflu therapeutics is the viral RNA-dependent RNA polymerase (RdRP). The assembly of the flu RdRP heterotrimeric complex from the individual polymerase acidic protein (PA), polymerase basic protein 1 (PB1), and polymerase basic protein 2 (PB2) subunits is a prerequisite for RdRP functions, such as mRNA synthesis and genome replication. In this Review, we report the known protein-protein interactions (PPIs) occurring by RdRP that could be disrupted by small molecules and analyze their benefits and drawbacks as drug targets. An overview of small molecules able to interfere with flu RdRP functions exploiting the PPI inhibition approach is described. In particular, an update on the most recent inhibitors targeting the well-consolidated RdRP PA-PB1 subunit heterodimerization is mainly reported, together with pioneer inhibitors targeting other virus-virus or virus-host interactions involving RdRP subunits. As demonstrated by the PA-PB1 interaction inhibitors discussed herein, the inhibition of flu RdRP functions by PPI disrupters clearly represents a valid means to identify compounds endowed with a broad spectrum of action and a reduced propensity to develop drug resistance, which are the main issues of antiviral drugs.
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Affiliation(s)
- Serena Massari
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Jenny Desantis
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123, Perugia, Italy
| | - Maria Giulia Nizi
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
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3
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Yin R, Zhang Y, Zhou X, Kwoh CK. Time series computational prediction of vaccines for influenza A H3N2 with recurrent neural networks. J Bioinform Comput Biol 2021; 18:2040002. [PMID: 32336247 DOI: 10.1142/s0219720020400028] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Influenza viruses are persistently threatening public health, causing annual epidemics and sporadic pandemics due to rapid viral evolution. Vaccines are used to prevent influenza infections but the composition of the influenza vaccines have to be updated regularly to ensure its efficacy. Computational tools and analyses have become increasingly important in guiding the process of vaccine selection. By constructing time-series training samples with splittings and embeddings, we develop a computational method for predicting suitable strains as the recommendation of the influenza vaccines using recurrent neural networks (RNNs). The Encoder-decoder architecture of RNN model enables us to perform sequence-to-sequence prediction. We employ this model to predict the prevalent sequence of the H3N2 viruses sampled from 2006 to 2017. The identity between our predicted sequence and recommended vaccines is greater than 98% and the Pepitope<0.2 indicates their antigenic similarity. The multi-step vaccine prediction further demonstrates the robustness of our method which achieves comparable results in contrast to single step prediction. The results show significant matches of the recommended vaccine strains to the circulating strains. We believe it would facilitate the process of vaccine selection and surveillance of seasonal influenza epidemics.
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Affiliation(s)
- Rui Yin
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Yu Zhang
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Xinrui Zhou
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
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4
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Kwon JH, Criado MF, Killmaster L, Ali MZ, Giasuddin M, Samad MA, Karim MR, Brum E, Hasan MZ, Lee DH, Spackman E, Swayne DE. Efficacy of two vaccines against recent emergent antigenic variants of clade 2.3.2.1a highly pathogenic avian influenza viruses in Bangladesh. Vaccine 2021; 39:2824-2832. [PMID: 33910774 DOI: 10.1016/j.vaccine.2021.04.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 01/12/2023]
Abstract
H5N1 highly pathogenic avian influenza viruses (HPAIVs) have caused outbreaks in poultry in Bangladesh since 2007. While clade 2.2.2 and 2.3.4.2 HPAIVs have not been detected since 2012, clade 2.3.2.1a viruses have caused continuous outbreaks since 2012 despite the use of vaccines. In this study, we evaluated the efficacy of two H5 vaccines licensed in Bangladesh, RE-6 inactivated vaccine, and a recombinant herpesvirus of turkeys vaccine with an H5 insert (rHVT-H5), for protection against recent field viruses in chickens. We selected three viruses for efficacy tests (A/chicken/Bangladesh/NRL-AI-3237/2017, A/crow/Bangladesh/NRL-AI-8471/2017 and A/chicken/Bangladesh/NRL-AI-8323/2017) from 36 H5 viruses isolated from Bangladesh between 2016 and 2018 by comparing the amino acid sequences at five antigenic sites (A-E) and analyzing hemagglutination inhibition (HI) titers with reference antisera. The RE-6 and rHVT-H5 vaccines both conferred 80-100% clinical protection (i.e. reduced morbidity and mortality) against the three challenge viruses with no significant differences in protection. In addition, both vaccines significantly decreased viral shedding from infected chickens as compared to challenge control chickens. Based on these metrics, the current licensed H5 vaccines protected chickens against the recent field viruses. However, the A/crow/Bangladesh/NRL-AI-8471/2017 virus exhibited antigenic divergence including: several unique amino acid changes in antigenic epitope sites A and B and was a serological outlier in cross HI tests as visualized on the antigenic map. The continuing emergence of such antigenic variants which could alter the dominant antigenicity of field viruses should be continuously monitored and vaccines should be updated if field efficacy declines.
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Affiliation(s)
- Jung-Hoon Kwon
- U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Miria Ferreira Criado
- U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; Current address: Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
| | - Lindsay Killmaster
- U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA
| | - Md Zulfekar Ali
- National Reference Laboratory for Avian Influenza, Animal Health Research Division, Bangladesh Livestock Research Institute, Savar, Dhaka 1341, Bangladesh
| | - Mohammad Giasuddin
- National Reference Laboratory for Avian Influenza, Animal Health Research Division, Bangladesh Livestock Research Institute, Savar, Dhaka 1341, Bangladesh
| | - Mohammed A Samad
- National Reference Laboratory for Avian Influenza, Animal Health Research Division, Bangladesh Livestock Research Institute, Savar, Dhaka 1341, Bangladesh
| | - Md Rezaul Karim
- National Reference Laboratory for Avian Influenza, Animal Health Research Division, Bangladesh Livestock Research Institute, Savar, Dhaka 1341, Bangladesh
| | - Eric Brum
- Emergency Centre for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO), Dhaka 1341, Bangladesh
| | - Md Zakiul Hasan
- Emergency Centre for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO), Dhaka 1341, Bangladesh
| | - Dong-Hun Lee
- Department of Pathobiology and Veterinary Science, the University of Connecticut, Storrs, CT 06269, USA
| | - Erica Spackman
- U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA
| | - David E Swayne
- U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA.
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5
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Wang Q, Sun Z, Li J, Qin T, Ma H, Chen S, Peng D, Liu X. Identification of a universal antigen epitope of influenza A virus using peptide microarray. BMC Vet Res 2021; 17:22. [PMID: 33413356 PMCID: PMC7792037 DOI: 10.1186/s12917-020-02725-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 12/15/2020] [Indexed: 02/08/2023] Open
Abstract
Background Hemagglutinin is a major surface protein in influenza A virus (IAV), and HA2 is relative conserved among different IAVs. It will be meaningful to identify broad-spectrum epitopes based on the HA2 protein. Results Overlapping peptides of the HA2 protein of the H5N1 IAV A/Mallard/Huadong/S/2005 were synthesized and loaded on modified silica gel film to form a microarray, and antisera against different subtypes of IAVs were used to screen universal epitopes. The selected epitope was further confirmed by western blotting using anti-peptide immune serum and viruses rescued with amino acid substitution. The results showed that 485-FYHKCDNECME-495 of the H5 14th peptide in HA2 had broad-spectrum binding activity with antisera against H1, H3, H4, H5, H6, H7, H8, H9, and H10 subtype IAV. Substitution of amino acids (K or D) in rescued viruses resulted in decreased serum binding, indicating that they were critical residues for serum binding activity. In Immune Epitope Database, some epitopes containing 14–4 peptide were confirmed as MHC-II-restricted CD4 T cell epitope and had effects on releasing IL-2 or IFN. Conclusion The identified epitope should be a novel universal target for detection and vaccine design and its ability to generate immune protection needs further exploration. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-020-02725-5.
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Affiliation(s)
- Qiuxia Wang
- College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, 225009, Jiangsu, People's Republic of China.,Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, 225009, Jiangsu, People's Republic of China
| | - Zhihao Sun
- College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, 225009, Jiangsu, People's Republic of China.,Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, 225009, Jiangsu, People's Republic of China
| | - Jingzhi Li
- Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215000, People's Republic of China
| | - Tao Qin
- College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, 225009, Jiangsu, People's Republic of China.,Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, 225009, Jiangsu, People's Republic of China
| | - Hongwei Ma
- Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215000, People's Republic of China
| | - Sujuan Chen
- College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China. .,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, 225009, Jiangsu, People's Republic of China. .,Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, 225009, Jiangsu, People's Republic of China. .,Joint Laboratory Safety of International Cooperation of Agriculture & Agricultural-Products, Yangzhou, Jiangsu, 225009, People's Republic of China.
| | - Daxin Peng
- College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China. .,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, 225009, Jiangsu, People's Republic of China. .,Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, 225009, Jiangsu, People's Republic of China. .,Joint Laboratory Safety of International Cooperation of Agriculture & Agricultural-Products, Yangzhou, Jiangsu, 225009, People's Republic of China.
| | - Xiufan Liu
- College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, 225009, Jiangsu, People's Republic of China.,Joint Laboratory Safety of International Cooperation of Agriculture & Agricultural-Products, Yangzhou, Jiangsu, 225009, People's Republic of China
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6
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Identification of genome-wide nucleotide sites associated with mammalian virulence in influenza A viruses. BIOSAFETY AND HEALTH 2020. [DOI: 10.1016/j.bsheal.2020.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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7
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Yin R, Luusua E, Dabrowski J, Zhang Y, Kwoh CK. Tempel: time-series mutation prediction of influenza A viruses via attention-based recurrent neural networks. Bioinformatics 2020; 36:2697-2704. [DOI: 10.1093/bioinformatics/btaa050] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/01/2020] [Accepted: 01/22/2020] [Indexed: 02/06/2023] Open
Abstract
Abstract
Motivation
Influenza viruses are persistently threatening public health, causing annual epidemics and sporadic pandemics. The evolution of influenza viruses remains to be the main obstacle in the effectiveness of antiviral treatments due to rapid mutations. The goal of this work is to predict whether mutations are likely to occur in the next flu season using historical glycoprotein hemagglutinin sequence data. One of the major challenges is to model the temporality and dimensionality of sequential influenza strains and to interpret the prediction results.
Results
In this article, we propose an efficient and robust time-series mutation prediction model (Tempel) for the mutation prediction of influenza A viruses. We first construct the sequential training samples with splittings and embeddings. By employing recurrent neural networks with attention mechanisms, Tempel is capable of considering the historical residue information. Attention mechanisms are being increasingly used to improve the performance of mutation prediction by selectively focusing on the parts of the residues. A framework is established based on Tempel that enables us to predict the mutations at any specific residue site. Experimental results on three influenza datasets show that Tempel can significantly enhance the predictive performance compared with widely used approaches and provide novel insights into the dynamics of viral mutation and evolution.
Availability and implementation
The datasets, source code and supplementary documents are available at: https://drive.google.com/drive/folders/15WULR5__6k47iRotRPl3H7ghi3RpeNXH.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rui Yin
- School of Computer Science and Engineering, Nanyang Technological University, Singapore
| | - Emil Luusua
- Faculty of Science and Engineering, Linköping University, Linköping, Sweden
| | - Jan Dabrowski
- School of Computer Science, Swansea University, Swansea, UK
| | - Yu Zhang
- School of Computer Science and Engineering, Nanyang Technological University, Singapore
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, Singapore
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8
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Detecting influenza and emerging avian influenza virus by influenza and pneumonia surveillance systems in a large city in China, 2005 to 2016. BMC Infect Dis 2019; 19:825. [PMID: 31533638 PMCID: PMC6751661 DOI: 10.1186/s12879-019-4405-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/25/2019] [Indexed: 11/25/2022] Open
Abstract
Background Detecting avian influenza virus has become an important public health strategy for controlling the emerging infectious disease. Methods The HIS (hospital information system) modified influenza surveillance system (ISS) and a newly built pneumonia surveillance system (PSS) were used to monitor the influenza viruses in Changsha City, China. The ISS was used to monitor outpatients in two sentinel hospitals and to detect mild influenza and avian influenza cases, and PSS was used to monitor inpatients in 49 hospitals and to detect severe and death influenza cases. Results From 2005 to 2016, there were 3,551,917 outpatients monitored by the ISS system, among whom 126,076 were influenza-like illness (ILI) cases, with the ILI proportion (ILI%) of 3.55%. After the HIS was used, the reported incident cases of ILI and ILI% were increased significantly. From March, 2009 to September, 2016, there were 5,491,560 inpatient cases monitored by the PSS system, among which 362,743 were pneumonia cases, with a proportion of 6.61%. Among pneumonia cases, about 10.55% (38,260/362,743) of cases were severe or death cases. The pneumonia incidence increased each year in the city. Among 15 avian influenza cases reported from January, 2005 to September, 2016, there were 26.7% (4/15) mild cases detected by the HIS-modified ISS system, while 60.0% (9/15) were severe or death cases detected by the PSS system. Two H5N1 severe cases were missed by the ISS system in January, 2009 when the PSS system was not available. Conclusions The HIS was able to improve the efficiency of the ISS for monitoring ILI and emerging avian influenza virus. However, the efficiency of the system needs to be verified in a wider area for a longer time span in China.
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9
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Sun J, Wang J, Yuan X, Wu X, Sui T, Wu A, Cheng G, Jiang T. Regulation of Early Host Immune Responses Shapes the Pathogenicity of Avian Influenza A Virus. Front Microbiol 2019; 10:2007. [PMID: 31572308 PMCID: PMC6749051 DOI: 10.3389/fmicb.2019.02007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/15/2019] [Indexed: 01/16/2023] Open
Abstract
Avian influenza A viruses (IAV) can cross the species barrier and cause disease in humans. Understanding the pathogenesis of avian IAV remains a challenge. Interferon-mediated antiviral responses and multiple cytokines production are important host cellular antiviral immunity against IAV infection. To elucidate the pathogenicity of avian IAV, a system approach was adopted to investigate dysregulation of the two host cellular antiviral immune responses in contrast with human IAV. As a result, we revealed that avian IAV not only disrupted normal early host cellular interferon-mediated antiviral responses, but also caused abnormal cytokines production through different pathways. For avian IAV infection, dysregulation of STAT2 was mainly responsible for abnormal cellular interferon-mediated antiviral responses, and IRF5 and NFKB1 played crucial roles in unusual cytokines production. In contrast, for human IAV infection, IRF1, IRF7, and STAT1 contributed to cellular cytokines production. Furthermore, differential activation of pattern recognition receptors (PRRs) likely led to avian IAV-related abnormal early host cellular antiviral immunity, where TLR7 and RIG-I were activated by avian and human IAV, respectively. Finally, a pathogenesis model was proposed that combined of early host cellular interferon-mediated antiviral responses with cytokines production could partly explain the pathogenicity of avian IAV. In conclusion, our study provides a new perspective of the pathogenesis of avian IAV, which will be helpful in preventing their infections in the future.
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Affiliation(s)
- Jiya Sun
- Suzhou Institute of Systems Medicine, Suzhou, China.,Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingfeng Wang
- Suzhou Institute of Systems Medicine, Suzhou, China.,Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuye Yuan
- Suzhou Institute of Systems Medicine, Suzhou, China.,Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiangwei Wu
- Suzhou Institute of Systems Medicine, Suzhou, China.,Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tianqi Sui
- Suzhou Institute of Systems Medicine, Suzhou, China.,Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Aiping Wu
- Suzhou Institute of Systems Medicine, Suzhou, China.,Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Genhong Cheng
- Suzhou Institute of Systems Medicine, Suzhou, China.,Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Taijiao Jiang
- Suzhou Institute of Systems Medicine, Suzhou, China.,Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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10
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Coronado L, Rios L, Frías MT, Amarán L, Naranjo P, Percedo MI, Perera CL, Prieto F, Fonseca-Rodriguez O, Perez LJ. Positive selection pressure on E2 protein of classical swine fever virus drives variations in virulence, pathogenesis and antigenicity: Implication for epidemiological surveillance in endemic areas. Transbound Emerg Dis 2019; 66:2362-2382. [PMID: 31306567 DOI: 10.1111/tbed.13293] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/08/2019] [Accepted: 07/07/2019] [Indexed: 12/14/2022]
Abstract
Classical swine fever (CSF), caused by CSF virus (CSFV), is considered one of the most important infectious diseases with devasting consequences for the pig industry. Recent reports describe the emergence of new CSFV strains resulting from the action of positive selection pressure, due mainly to the bottleneck effect generated by ineffective vaccination. Even though a decrease in the genetic diversity of the positively selected CSFV strains has been observed by several research groups, there is little information about the effect of this selective force on the virulence degree, antigenicity and pathogenicity of this type of strains. Hence, the aim of the current study was to determine the effect of the positive selection pressure on these three parameters of CSFV strains, emerged as result of the bottleneck effects induced by improper vaccination in a CSF-endemic area. Moreover, the effect of the positively selected strains on the epidemiological surveillance system was assessed. By the combination of in vitro, in vivo and immunoinformatic approaches, we revealed that the action of the positive selection pressure induces a decrease in virulence and alteration in pathogenicity and antigenicity. However, we also noted that the evolutionary process of CSFV, especially in segregated microenvironments, could contribute to the gain-fitness event, restoring the highly virulent pattern of the circulating strains. Besides, we denoted that the presence of low virulent strains selected by bottleneck effect after inefficient vaccination can lead to a relevant challenge for the epidemiological surveillance of CSF, contributing to under-reports of the disease, favouring the perpetuation of the virus in the field. In this study, B-cell and CTL epitopes on the E2 3D-structure model were also identified. Thus, the current study provides novel and significant insights into variation in virulence, pathogenesis and antigenicity experienced by CSFV strains after the positive selection pressure effect.
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Affiliation(s)
- Liani Coronado
- Centro Nacional de Sanidad Agropecuaria (CENSA), OIE Collaborating Centre for Diagnosis and Risk Analysis of the Caribbean Region, La Habana, Cuba
| | - Liliam Rios
- Reiman Cancer Research Laboratory, Faculty of Medicine, University of New Brunswick, Saint John, New Brunswick, Canada
| | - María Teresa Frías
- Centro Nacional de Sanidad Agropecuaria (CENSA), OIE Collaborating Centre for Diagnosis and Risk Analysis of the Caribbean Region, La Habana, Cuba
| | - Laymara Amarán
- National Laboratory for Veterinary Diagnostic (NLVD), La Habana, Cuba
| | | | - María Irian Percedo
- Centro Nacional de Sanidad Agropecuaria (CENSA), OIE Collaborating Centre for Diagnosis and Risk Analysis of the Caribbean Region, La Habana, Cuba
| | - Carmen Laura Perera
- Centro Nacional de Sanidad Agropecuaria (CENSA), OIE Collaborating Centre for Diagnosis and Risk Analysis of the Caribbean Region, La Habana, Cuba
| | - Felix Prieto
- National Laboratory for Veterinary Diagnostic (NLVD), La Habana, Cuba
| | | | - Lester J Perez
- Department of Clinical Veterinary Medicine, College of Veterinary Science, University of Illinois, Urbana, IL, USA.,College of Veterinary Science, Veterinary Diagnostic Laboratory (VDL), University of Illinois, Urbana, IL, USA
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11
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Dhingra MS, Artois J, Dellicour S, Lemey P, Dauphin G, Von Dobschuetz S, Van Boeckel TP, Castellan DM, Morzaria S, Gilbert M. Geographical and Historical Patterns in the Emergences of Novel Highly Pathogenic Avian Influenza (HPAI) H5 and H7 Viruses in Poultry. Front Vet Sci 2018; 5:84. [PMID: 29922681 PMCID: PMC5996087 DOI: 10.3389/fvets.2018.00084] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 04/03/2018] [Indexed: 01/28/2023] Open
Abstract
Over the years, the emergence of novel H5 and H7 highly pathogenic avian influenza viruses (HPAI) has been taking place through two main mechanisms: first, the conversion of a low pathogenic into a highly pathogenic virus, and second, the reassortment between different genetic segments of low and highly pathogenic viruses already in circulation. We investigated and summarized the literature on emerging HPAI H5 and H7 viruses with the aim of building a spatio-temporal database of all these recorded conversions and reassortments events. We subsequently mapped the spatio-temporal distribution of known emergence events, as well as the species and production systems that they were associated with, the aim being to establish their main characteristics. From 1959 onwards, we identified a total of 39 independent H7 and H5 LPAI to HPAI conversion events. All but two of these events were reported in commercial poultry production systems, and a majority of these events took place in high-income countries. In contrast, a total of 127 reassortments have been reported from 1983 to 2015, which predominantly took place in countries with poultry production systems transitioning from backyard to intensive production systems. Those systems are characterized by several co-circulating viruses, multiple host species, regular contact points in live bird markets, limited biosecurity within value chains, and frequent vaccination campaigns that impose selection pressures for emergence of novel reassortants. We conclude that novel HPAI emergences by these two mechanisms occur in different ecological niches, with different viral, environmental and host associated factors, which has implications in early detection and management and mitigation of the risk of emergence of novel HPAI viruses.
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Affiliation(s)
- Madhur S Dhingra
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium.,Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Jean Artois
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
| | - Simon Dellicour
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Gwenaelle Dauphin
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | | | - Thomas P Van Boeckel
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,Center for Disease Dynamics, Economics and Policy, Washington, DC, United States
| | | | - Subhash Morzaria
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Marius Gilbert
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium.,Fonds National de la Recherche Scientifique (FNRS), Brussels, Belgium
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12
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Tang Y, Wang Z, Huo C, Guo X, Yang G, Wang M, Tian H, Hu Y, Dong H. Antiviral effects of Shuanghuanglian injection powder against influenza A virus H5N1 in vitro and in vivo. Microb Pathog 2018; 121:318-324. [PMID: 29864534 DOI: 10.1016/j.micpath.2018.06.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/08/2018] [Accepted: 06/01/2018] [Indexed: 11/25/2022]
Abstract
The current study was to identify a protective role of Shuanghuanglian (SHL) injection powder in vitro and in vivo after H5N1 viral infection. Immunofluorescent staining was used to determine the susceptibility of rat intestinal mucosa microvascular endothelial cells (RIM-MVECs) to the H5N1 virus. Viral replication of RIM-MVECs was measured by transmission electron microscopy (TEM) a hemagglutination assay and real-time quantitative PCR. H5N1 virally infected RIM-MVECs, and BALB/c mice were treated with SHL to investigate its therapeutic effect. Animal survival and the weight of H5N1 virally infected BALB/c mice after SHL treatment was noted, and histology and real-time PCR applied to mouse lungs were used to confirm the anti-H5N1 viral effects of SHL. RIM-MVECs supported replication of the H5N1 virus in vitro. SHL treatment reduced viral titers in H5N1 virally infected RIM-MVECs and mouse lungs. SHL -treated mice survived compared to controls. Mild pathological changes, reduced inflammatory cell infiltration and fewer viral antigens were observed in the lungs of SHL-treated mice at days 3 and 6 post-infection. In conclusion, SHL may have the antiviral activity against the H5N1 virus infection by inhibiting viral replication and alleviating lung injury.
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Affiliation(s)
- Yuling Tang
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, PR China
| | - Zhaohua Wang
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, PR China
| | - Caiyun Huo
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, PR China
| | - Xiaotong Guo
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, PR China
| | - Guanghui Yang
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, PR China
| | - Ming Wang
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, PR China
| | - Haiyan Tian
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, PR China
| | - Yanxin Hu
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, PR China.
| | - Hong Dong
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Beijing University of Agriculture, Beijing, PR China.
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13
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Klingen TR, Reimering S, Guzmán CA, McHardy AC. In Silico Vaccine Strain Prediction for Human Influenza Viruses. Trends Microbiol 2017; 26:119-131. [PMID: 29032900 DOI: 10.1016/j.tim.2017.09.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/21/2017] [Accepted: 09/06/2017] [Indexed: 02/02/2023]
Abstract
Vaccines preventing seasonal influenza infections save many lives every year; however, due to rapid viral evolution, they have to be updated frequently to remain effective. To identify appropriate vaccine strains, the World Health Organization (WHO) operates a global program that continually generates and interprets surveillance data. Over the past decade, sophisticated computational techniques, drawing from multiple theoretical disciplines, have been developed that predict viral lineages rising to predominance, assess their suitability as vaccine strains, link genetic to antigenic alterations, as well as integrate and visualize genetic, epidemiological, structural, and antigenic data. These could form the basis of an objective and reproducible vaccine strain-selection procedure utilizing the complex, large-scale data types from surveillance. To this end, computational techniques should already be incorporated into the vaccine-selection process in an independent, parallel track, and their performance continuously evaluated.
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Affiliation(s)
- Thorsten R Klingen
- Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany; Co-first authors
| | - Susanne Reimering
- Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany; Co-first authors
| | - Carlos A Guzmán
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany; German Centre for Infection Research (DZIF)
| | - Alice C McHardy
- Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany; German Centre for Infection Research (DZIF).
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14
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Evolution of Influenza A Virus by Mutation and Re-Assortment. Int J Mol Sci 2017; 18:ijms18081650. [PMID: 28783091 PMCID: PMC5578040 DOI: 10.3390/ijms18081650] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 12/13/2022] Open
Abstract
Influenza A virus (IAV), a highly infectious respiratory pathogen, has continued to be a significant threat to global public health. To complete their life cycle, influenza viruses have evolved multiple strategies to interact with a host. A large number of studies have revealed that the evolution of influenza A virus is mainly mediated through the mutation of the virus itself and the re-assortment of viral genomes derived from various strains. The evolution of influenza A virus through these mechanisms causes worldwide annual epidemics and occasional pandemics. Importantly, influenza A virus can evolve from an animal infected pathogen to a human infected pathogen. The highly pathogenic influenza virus has resulted in stupendous economic losses due to its morbidity and mortality both in human and animals. Influenza viruses fall into a category of viruses that can cause zoonotic infection with stable adaptation to human, leading to sustained horizontal transmission. The rapid mutations of influenza A virus result in the loss of vaccine optimal efficacy, and challenge the complete eradication of the virus. In this review, we highlight the current understanding of influenza A virus evolution caused by the mutation and re-assortment of viral genomes. In addition, we discuss the specific mechanisms by which the virus evolves.
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