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Gun L, Haixian P, Yumiao R, Han T, Jingqi L, Liguang Z. Codon usage characteristics of PB2 gene in influenza A H7N9 virus from different host species. INFECTION GENETICS AND EVOLUTION 2018; 65:430-435. [PMID: 30179716 DOI: 10.1016/j.meegid.2018.08.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 08/02/2018] [Accepted: 08/30/2018] [Indexed: 12/13/2022]
Abstract
The influenza A H7N9 virus is a highly contagious virus which can only infect poultry before early 2013. But after that time, it widely caused human infections in China and brought Southeast Asia great threaten in the public health area. The coding gene for polymerase basic protein 2 (PB2) in influenza A H7N9 virus encodes the PB2 protein, which is a part of the RNA polymerase. The enzyme lacks a correction function during its own replication process, so the mutation frequency of the influenza A H7N9 virus gene is high and the PB2 gene is also included. To investigate the codon usages characteristics of PB2 gene, gene sequences of 12 kinds of poultry are downloaded form the gene bank (NCBI) and their codon usage characteristics such as the effective number of codons (ENC), the evolutionary relationship of the sequences, the codon adaptation index (CAI), the correspondence analysis (COA), the relative synonymous codon usage (RSCU) and their PR2-bias are compared and studied. The value of these reults showed that there is a low codon usage bias in the PB2 gene. Then, the differences between the codon usages of PB2 gene from 12 kinds of poultry are compared and their potential applications are discussed. These results could lay a foundation for other further study on the evolution of H7N9.
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Affiliation(s)
- Li Gun
- Department of Biomedical Engineering, School of Electronics and Information Engineering, Xi'an Technological University, Xi'an, Shaanxi Province, China.
| | - Pan Haixian
- Department of Biomedical Engineering, School of Electronics and Information Engineering, Xi'an Technological University, Xi'an, Shaanxi Province, China
| | - Ren Yumiao
- Department of Biomedical Engineering, School of Electronics and Information Engineering, Xi'an Technological University, Xi'an, Shaanxi Province, China
| | - Tian Han
- Department of Biomedical Engineering, School of Electronics and Information Engineering, Xi'an Technological University, Xi'an, Shaanxi Province, China
| | - Lu Jingqi
- Department of Biomedical Engineering, School of Electronics and Information Engineering, Xi'an Technological University, Xi'an, Shaanxi Province, China
| | - Zhang Liguang
- Department of Biomedical Engineering, School of Electronics and Information Engineering, Xi'an Technological University, Xi'an, Shaanxi Province, China
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2
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Su S, Gu M, Liu D, Cui J, Gao GF, Zhou J, Liu X. Epidemiology, Evolution, and Pathogenesis of H7N9 Influenza Viruses in Five Epidemic Waves since 2013 in China. Trends Microbiol 2017; 25:713-728. [PMID: 28734617 DOI: 10.1016/j.tim.2017.06.008] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 01/30/2023]
Abstract
H7N9 influenza viruses were first isolated in 2013 and continue to cause human infections. H7N9 infections represent an ongoing public health threat that has resulted in 1344 cases with 511 deaths as of April 9, 2017. This highlights the continued threat posed by the current poultry trade and live poultry market system in China. Until now, there have been five H7N9 influenza epidemic waves in China; however, the steep increase in the number of humans infected with H7N9 viruses observed in the fifth wave, beginning in October 2016, the spread into western provinces, and the emergence of highly pathogenic (HP) H7N9 influenza outbreaks in chickens and infection in humans have caused domestic and international concern. In this review, we summarize and compare the different waves of H7N9 regarding their epidemiology, pathogenesis, evolution, and characteristic features, and speculate on factors behind the recent increase in the number of human cases and sudden outbreaks in chickens. The continuous evolution of the virus poses a long-term threat to public health and the poultry industry, and thus it is imperative to strengthen prevention and control strategies.
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Affiliation(s)
- Shuo Su
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Min Gu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Di Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jie Cui
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Jiyong Zhou
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China; Collaborative Innovation Center and State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University, Hangzhou 310003, China.
| | - Xiufan Liu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu, 225009, China; Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, Yangzhou, Jiangsu, 225009, China.
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Fang S, Wang X, Dong F, Jin T, Liu G, Lu X, Peng B, Wu W, Liu H, Kong D, Tang X, Qin Y, Mei S, Xie X, He J, Ma H, Zhang R, Cheng J. Genomic characterization of influenza A (H7N9) viruses isolated in Shenzhen, Southern China, during the second epidemic wave. Arch Virol 2016; 161:2117-32. [PMID: 27169600 DOI: 10.1007/s00705-016-2872-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 04/24/2016] [Indexed: 10/21/2022]
Abstract
There were three epidemic waves of human infection with avian influenza A (H7N9) virus in 2013-2014. While many analyses of the genomic origin, evolution, and molecular characteristics of the influenza A (H7N9) virus have been performed using sequences from the first epidemic wave, genomic characterization of the virus from the second epidemic wave has been comparatively less reported. In this study, an in-depth analysis was performed with respect to the genomic characteristics of 11 H7N9 virus strains isolated from confirmed cases and four H7N9 virus strains isolated from environmental samples in Shenzhen during the second epidemic wave. Phylogenetic analysis demonstrated that six internal segments of the influenza A (H7N9) virus isolated from confirmed cases and environmental samples in Shenzhen were clustered into two different clades and that the origin of the influenza A (H7N9) virus isolated from confirmed cases in Shenzhen was different from that of viruses isolated during the first wave. In addition, H9N2 viruses, which were prevalent in southern China, played an important role in the reassortment of the influenza A (H7N9) virus isolated in Shenzhen. HA-R47K and -T122A, PB2-V139I, PB1-I397M, and NS1-T216P were the signature amino acids of the influenza A (H7N9) virus isolated from confirmed cases in Shenzhen. We found that the HA, NA, M, and PA genes of the A(H7N9) viruses underwent positive selection in the human population. Therefore, enhanced surveillance should be carried out to determine the origin and mode of transmission of the novel influenza A (H7N9) virus and to facilitate the formulation of effective policies for prevention and containment of a human infection epidemics.
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Affiliation(s)
- Shisong Fang
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Xin Wang
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Fangyuan Dong
- College of Medicine, Jinan University, 601 Huangpu Avenue West, Guangzhou, China
| | - Tao Jin
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Guang Liu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xing Lu
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Bo Peng
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Weihua Wu
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Hui Liu
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Dongfeng Kong
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Xiujuan Tang
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Yanmin Qin
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Shujiang Mei
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Xu Xie
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Jianfan He
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Hanwu Ma
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Renli Zhang
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China.
| | - Jinquan Cheng
- Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong, China.
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Mammalian Pathogenesis and Transmission of H7N9 Influenza Viruses from Three Waves, 2013-2015. J Virol 2016; 90:4647-4657. [PMID: 26912620 DOI: 10.1128/jvi.00134-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/18/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Three waves of human infection with H7N9 influenza viruses have concluded to date, but only viruses within the first wave (isolated between March and September 2013) have been extensively studied in mammalian models. While second- and third-wave viruses remain closely linked phylogenetically and antigenically, even subtle molecular changes can impart critical shifts in mammalian virulence. To determine if H7N9 viruses isolated from humans during 2013 to 2015 have maintained the phenotype first identified among 2013 isolates, we assessed the ability of first-, second-, and third-wave H7N9 viruses isolated from humans to cause disease in mice and ferrets and to transmit among ferrets. Similar to first-wave viruses, H7N9 viruses from 2013 to 2015 were highly infectious in mice, with lethality comparable to that of the well-studied A/Anhui/1/2013 virus. Second- and third-wave viruses caused moderate disease in ferrets, transmitted efficiently to cohoused, naive contact animals, and demonstrated limited transmissibility by respiratory droplets. All H7N9 viruses replicated efficiently in human bronchial epithelial cells, with subtle changes in pH fusion threshold identified between H7N9 viruses examined. Our results indicate that despite increased genetic diversity and geographical distribution since their initial detection in 2013, H7N9 viruses have maintained a pathogenic phenotype in mammals and continue to represent an immediate threat to public health. IMPORTANCE H7N9 influenza viruses, first isolated in 2013, continue to cause human infection and represent an ongoing public health threat. Now entering the fourth wave of human infection, H7N9 viruses continue to exhibit genetic diversity in avian hosts, necessitating continuous efforts to monitor their pandemic potential. However, viruses isolated post-2013 have not been extensively studied, limiting our understanding of potential changes in virus-host adaptation. In order to ensure that current research with first-wave H7N9 viruses still pertains to more recently isolated strains, we compared the relative virulence and transmissibility of H7N9 viruses isolated during the second and third waves, through 2015, in the mouse and ferret models. Our finding that second- and third-wave viruses generally exhibit disease in mammals comparable to that of first-wave viruses strengthens our ability to extrapolate research from the 2013 viruses to current public health efforts. These data further contribute to our understanding of molecular determinants of pathogenicity, transmissibility, and tropism.
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Farooqui A, Liu W, Zeng T, Liu Y, Zhang L, Khan A, Wu X, Wu R, Wu S, Huang L, Cai Y, Kelvin AA, Paquette SG, Hu K, Zheng N, Chen H, Xu S, Lin C, Sun P, Yao Z, Wang J, Ma H, Zhu Z, Lin P, Chen W, Fang X, Bermejo-Martin JF, Leon AJ, Kelvin DJ. Probable Hospital Cluster of H7N9 Influenza Infection. N Engl J Med 2016; 374:596-8. [PMID: 26863372 DOI: 10.1056/nejmc1505359] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
| | | | | | - Yisu Liu
- Shantou University Medical College, Shantou, China
| | - Li Zhang
- Shantou University Medical College, Shantou, China
| | - Adnan Khan
- Shantou University Medical College, Shantou, China
| | - Xiuming Wu
- Second Affiliated Hospital, Shantou, China
| | - Renhua Wu
- Second Affiliated Hospital, Shantou, China
| | - Suwu Wu
- Shantou Central Hospital, Shantou, China
| | | | - Yingmu Cai
- First Affiliated Hospital, Shantou, China
| | | | | | - Kezhao Hu
- Second Affiliated Hospital, Shantou, China
| | | | | | - Sheng Xu
- Second Affiliated Hospital, Shantou, China
| | | | - Peng Sun
- Second Affiliated Hospital, Shantou, China
| | | | - Jun Wang
- Second Affiliated Hospital, Shantou, China
| | - Huanjie Ma
- Second Affiliated Hospital, Shantou, China
| | | | | | | | | | | | | | - David J Kelvin
- International Institute of Infection and Immunity, Shantou, China.
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Farooqui A, Huang L, Wu S, Cai Y, Su M, Lin P, Chen W, Fang X, Zhang L, Liu Y, Zeng T, Paquette SG, Khan A, Kelvin AA, Kelvin DJ. Assessment of Antiviral Properties of Peramivir against H7N9 Avian Influenza Virus in an Experimental Mouse Model. Antimicrob Agents Chemother 2015; 59:7255-64. [PMID: 26369969 PMCID: PMC4649212 DOI: 10.1128/aac.01885-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/03/2015] [Indexed: 02/05/2023] Open
Abstract
The H7N9 influenza virus causes a severe form of disease in humans. Neuraminidase inhibitors, including oral oseltamivir and injectable peramivir, are the first choices of antiviral treatment for such cases; however, the clinical efficacy of these drugs is questionable. Animal experimental models are essential for understanding the viral replication kinetics under the selective pressure of antiviral agents. This study demonstrates the antiviral activity of peramivir in a mouse model of H7N9 avian influenza virus infection. The data show that repeated administration of peramivir at 30 mg/kg of body weight successfully eradicated the virus from the respiratory tract and extrapulmonary tissues during the acute response, prevented clinical signs of the disease, including neuropathy, and eventually protected mice against lethal H7N9 influenza virus infection. Early treatment with peramivir was found to be associated with better disease outcomes.
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Affiliation(s)
- Amber Farooqui
- Division of Immunology, International Institute of Infection and Immunity, University Health Network & Shantou University Medical College, Shantou, China Division of Experimental Therapeutics, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou, Guangdong, China
| | - Linxi Huang
- Infectious Diseases Department, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Suwu Wu
- Intensive Care Unit, Shantou Central Hospital, Shantou, China
| | - Yingmu Cai
- Department of Laboratory Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Min Su
- Department of Pathology, Shantou University Medical College, Shantou, China
| | - Pengzhou Lin
- Infectious Diseases Department, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Weihong Chen
- Intensive Care Unit, Shantou Central Hospital, Shantou, China
| | - Xibin Fang
- Intensive Care Unit, Shantou Central Hospital, Shantou, China
| | - Li Zhang
- Division of Immunology, International Institute of Infection and Immunity, University Health Network & Shantou University Medical College, Shantou, China
| | - Yisu Liu
- Division of Immunology, International Institute of Infection and Immunity, University Health Network & Shantou University Medical College, Shantou, China
| | - Tiansheng Zeng
- Division of Immunology, International Institute of Infection and Immunity, University Health Network & Shantou University Medical College, Shantou, China
| | - Stephane G Paquette
- Division of Experimental Therapeutics, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Adnan Khan
- Division of Immunology, International Institute of Infection and Immunity, University Health Network & Shantou University Medical College, Shantou, China Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou, Guangdong, China
| | - Alyson A Kelvin
- Division of Experimental Therapeutics, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - David J Kelvin
- Division of Immunology, International Institute of Infection and Immunity, University Health Network & Shantou University Medical College, Shantou, China Division of Experimental Therapeutics, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou, Guangdong, China Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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Li X, Pushko P, Tretyakova I. Recombinant Hemagglutinin and Virus-Like Particle Vaccines for H7N9 Influenza Virus. ACTA ACUST UNITED AC 2015; 6. [PMID: 26523241 DOI: 10.4172/2157-7560.1000287] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cases of H7N9 human infection were caused by a novel, avian-origin H7N9 influenza A virus that emerged in eastern China in 2013. Clusters of human disease were identified in many cities in China, with mortality rates approaching 30%. Pandemic concerns were raised, as historically, influenza pandemics were caused by introduction of novel influenza A viruses into immunologically naïve human population. Currently, there are no approved human vaccines for H7N9 viruses. Recombinant protein vaccine approaches have advantages in safety and manufacturing. In this review, we focused on evaluation of the expression of recombinant hemagglutinin (rHA) proteins as candidate vaccines for H7N9 influenza, with the emphasis on the role of oligomeric and particulate structures in immunogenicity and protection. Challenges in preparation of broadly protective influenza vaccines are discussed, and examples of broadly protective vaccines are presented including rHA stem epitope vaccines, as well as recently introduced experimental multi-HA VLP vaccines.
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Affiliation(s)
- Xiaohui Li
- Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, PR China 200240 ; Genor Biopharma Co., Ltd. 1690 Zhangheng Road, Shanghai, PR China 201203
| | - Peter Pushko
- Medigen, Inc., 8420 Gas House Pike, Suite S, Frederick, MD, U.S.A
| | - Irina Tretyakova
- Medigen, Inc., 8420 Gas House Pike, Suite S, Frederick, MD, U.S.A
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