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Zhao S, Hu I, Lou J, Chong MK, Cao L, He D, Zee BC, Wang MH. The mechanism shaping the logistic growth of mutation proportion in epidemics at population scale. Infect Dis Model 2022; 8:107-121. [PMID: 36632179 PMCID: PMC9811219 DOI: 10.1016/j.idm.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/19/2022] [Accepted: 12/25/2022] [Indexed: 12/28/2022] Open
Abstract
Virus evolution is a common process of pathogen adaption to host population and environment. Frequently, a small but important fraction of virus mutations are reported to contribute to higher risks of host infection, which is one of the major determinants of infectious diseases outbreaks at population scale. The key mutations contributing to transmission advantage of a genetic variant often grow and reach fixation rapidly. Based on classic epidemiology theories of disease transmission, we proposed a mechanistic explanation of the process that between-host transmission advantage may shape the observed logistic curve of the mutation proportion in population. The logistic growth of mutation is further generalized by incorporating time-varying selective pressure to account for impacts of external factors on pathogen adaptiveness. The proposed model is implemented in real-world data of COVID-19 to capture the emerging trends and changing dynamics of the B.1.1.7 strains of SARS-CoV-2 in England. The model characterizes and establishes the underlying theoretical mechanism that shapes the logistic growth of mutation in population.
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Affiliation(s)
- Shi Zhao
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Inchi Hu
- Department of Information Systems, Business Statistics and Operations Management, Hong Kong University of Science and Technology, Hong Kong, China
| | - Jingzhi Lou
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China
| | - Marc K.C. Chong
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Lirong Cao
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Daihai He
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China
| | - Benny C.Y. Zee
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Maggie H. Wang
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China,CUHK Shenzhen Research Institute, Shenzhen, China,Corresponding author. JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China.
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2
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Lijuan Z, Fuchang W, Hongri L. A Stochastic SEIRS Epidemic Model with Infection Forces and Intervention Strategies. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:4538045. [PMID: 35047150 PMCID: PMC8763553 DOI: 10.1155/2022/4538045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/04/2021] [Indexed: 11/17/2022]
Abstract
The spread of epidemics has been extensively investigated using susceptible-exposed infectious-recovered-susceptible (SEIRS) models. In this work, we propose a SEIRS pandemic model with infection forces and intervention strategies. The proposed model is characterized by a stochastic differential equation (SDE) framework with arbitrary parameter settings. Based on a Markov semigroup hypothesis, we demonstrate the effect of the proliferation number R 0 S on the SDE solution. On the one hand, when R 0 S < 1, the SDE has an illness-free solution set under gentle additional conditions. This implies that the epidemic can be eliminated with a likelihood of 1. On the other hand, when R 0 S > 1, the SDE has an endemic stationary circulation under mild additional conditions. This prompts the stochastic regeneration of the epidemic. Also, we show that arbitrary fluctuations can reduce the infection outbreak. Hence, valuable procedures can be created to manage and control epidemics.
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Affiliation(s)
- Zhang Lijuan
- Institute of Disaster Prevention, Basic Course Teaching Department, Yanjiao Sanhe 065201, Hebei, China
| | - Wang Fuchang
- Institute of Disaster Prevention, Basic Course Teaching Department, Yanjiao Sanhe 065201, Hebei, China
| | - Liang Hongri
- Institute of Disaster Prevention, Basic Course Teaching Department, Yanjiao Sanhe 065201, Hebei, China
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3
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Wang D, Zhu W, Yang L, Shu Y. The Epidemiology, Virology, and Pathogenicity of Human Infections with Avian Influenza Viruses. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a038620. [PMID: 31964651 DOI: 10.1101/cshperspect.a038620] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Influenza is a global challenge, and future pandemics of influenza are inevitable. One of the lessons learned from past pandemics is that all pandemic influenza viruses characterized to date possess viral genes originating from avian influenza viruses (AIVs). During the past decades, a wide range of AIVs have overcome the species barrier and infected humans with different clinical manifestations ranging from mild illness to severe disease and even death. Understanding the mechanisms of infection in the context of clinical outcomes, the mechanism of interspecies transmission, and the molecular determinants that confer interspecies transmission is important for pandemic preparedness. Here, we summarize the epidemiology, virology, and pathogenicity of human infections with AIVs to further our understanding of interspecies transmission.
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Affiliation(s)
- Dayan Wang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health Commission of the People's Republic of China, Beijing 102206, P.R. China
| | - Wenfei Zhu
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health Commission of the People's Republic of China, Beijing 102206, P.R. China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health Commission of the People's Republic of China, Beijing 102206, P.R. China
| | - Yuelong Shu
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health Commission of the People's Republic of China, Beijing 102206, P.R. China.,School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong 510275, P.R. China
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4
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Arai Y, Watanabe Y. "Genetic tuning" of avian influenza virus host adaptation from birds to humans. BIOSAFETY AND HEALTH 2021; 3:78-80. [PMID: 33319189 PMCID: PMC7726760 DOI: 10.1016/j.bsheal.2020.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/13/2020] [Accepted: 11/29/2020] [Indexed: 12/23/2022] Open
Affiliation(s)
- Yasuha Arai
- Department of Infectious Diseases, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Yohei Watanabe
- Department of Infectious Diseases, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
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5
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Schreiber SJ, Ke R, Loverdo C, Park M, Ahsan P, Lloyd-Smith JO. Cross-scale dynamics and the evolutionary emergence of infectious diseases. Virus Evol 2021; 7:veaa105. [PMID: 35186322 PMCID: PMC8087961 DOI: 10.1093/ve/veaa105] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
When emerging pathogens encounter new host species for which they are poorly adapted, they must evolve to escape extinction. Pathogens experience selection on traits at multiple scales, including replication rates within host individuals and transmissibility between hosts. We analyze a stochastic model linking pathogen growth and competition within individuals to transmission between individuals. Our analysis reveals a new factor, the cross-scale reproductive number of a mutant virion, that quantifies how quickly mutant strains increase in frequency when they initially appear in the infected host population. This cross-scale reproductive number combines with viral mutation rates, single-strain reproductive numbers, and transmission bottleneck width to determine the likelihood of evolutionary emergence, and whether evolution occurs swiftly or gradually within chains of transmission. We find that wider transmission bottlenecks facilitate emergence of pathogens with short-term infections, but hinder emergence of pathogens exhibiting cross-scale selective conflict and long-term infections. Our results provide a framework to advance the integration of laboratory, clinical, and field data in the context of evolutionary theory, laying the foundation for a new generation of evidence-based risk assessment of emergence threats.
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Affiliation(s)
| | - Ruian Ke
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Claude Loverdo
- Laboratoire Jean Perrin, Sorbonne Université, CNRS, Paris 75005, France
| | - Miran Park
- Department of Ecology & Evolution, University of California, Los Angeles, CA 90095, USA
| | - Prianna Ahsan
- Department of Ecology & Evolution, University of California, Los Angeles, CA 90095, USA
| | - James O Lloyd-Smith
- Department of Ecology & Evolution, University of California, Los Angeles, CA 90095, USA
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6
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Li H, Chen X, Zhou SJ. Dauricine combined with clindamycin inhibits severe pneumonia co-infected by influenza virus H5N1 and Streptococcus pneumoniae in vitro and in vivo through NF-κB signaling pathway. J Pharmacol Sci 2018; 137:12-19. [PMID: 29769163 DOI: 10.1016/j.jphs.2018.01.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 01/14/2018] [Accepted: 01/18/2018] [Indexed: 11/29/2022] Open
Abstract
Dauricine, isolated from Menispermum dauricum, has been widely used for treatment of various diseases, including cardiac ischemia and inflammation-related diseases. However, little is known regarding to the effect of dauricine on severe pneumonia. Therefore, the aim was to investigate the effect of dauricine on severe pneumonia and its mechanism during progress. Herein, H5N1 and Streptococcus pneumoniae (D39) were conducted to induce severe pneumonia in both BEAS-2B cells and mice. In vitro, dauricine reversed the protein and mRNA expressions of TNF-α, IL-6 and IL-1β, examined by ELISA and qRT-PCR assay, respectively. In addition, the nuclear translocation of NF-κB/p65 and the phosphorylation expressions of IκBα and IKKα/β, examined by western blotting, were dose-dependently dropped by dauricine. However, dauricine had no significant effect on MAPKs, including JNK, ERK and p38. In vivo, dauricine significantly decreased MPO activity, the lung wet/dry weight ratio, the protein and mRNA expression of TNF-α, IL-6 and IL-1β, the expressions of NF-κB/p65, and attenuated the lung histological alterations. Besides, compared to dauricine alone, combined with clindamycin had more remarkably effects on severe pneumonia in vitro. Overall, the results suggested that dauricine, a relatively drug that targets NF-κB, in combination with clindamycin, maybe a novel therapeutic strategy for severe pneumonia.
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Affiliation(s)
- Hui Li
- Department of Critical Care Medicine, The Third Affiliated Hospital of Soochow University, The First People's Hospital of Changzhou, No. 185 Juqian Street, Changzhou 213003, Jiangsu, People's Republic of China
| | - Xin Chen
- Emergency Department, The Third Affiliated Hospital of Soochow University, The First People's Hospital of Changzhou, No. 185 Juqian Street, Changzhou 213003, Jiangsu, People's Republic of China
| | - Shu-Jun Zhou
- Department of Critical Care Medicine, The Third Affiliated Hospital of Soochow University, The First People's Hospital of Changzhou, No. 185 Juqian Street, Changzhou 213003, Jiangsu, People's Republic of China.
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7
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DiPiazza A, Richards K, Poulton N, Sant AJ. Avian and Human Seasonal Influenza Hemagglutinin Proteins Elicit CD4 T Cell Responses That Are Comparable in Epitope Abundance and Diversity. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2017; 24:e00548-16. [PMID: 28100497 PMCID: PMC5339641 DOI: 10.1128/cvi.00548-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 01/10/2017] [Indexed: 02/07/2023]
Abstract
Avian influenza viruses remain a significant concern due to their pandemic potential. Vaccine trials have suggested that humans respond poorly to avian influenza vaccines relative to seasonal vaccines. It is important to understand, first, if there is a general deficiency in the ability of avian hemagglutinin (HA) proteins to generate immune responses and, if so, what underlies this defect. This question is of particular interest because it has been suggested that in humans, the poor immunogenicity of H7 vaccines may be due to a paucity of CD4 T cell epitopes. Because of the generally high levels of cross-reactive CD4 T cells in humans, it is not possible to compare the inherent immunogenicities of avian and seasonal HA proteins in an unbiased manner. Here, we empirically examine the epitope diversity and abundance of CD4 T cells elicited by seasonal and avian HA proteins. HLA-DR1 and HLA-DR4 transgenic mice were vaccinated with purified HA proteins, and CD4 T cells to specific epitopes were identified and quantified. These studies revealed that the diversity and abundance of CD4 T cells specific for HA do not segregate on the basis of whether the HA was derived from human seasonal or avian influenza viruses. Therefore, we conclude that failure in responses to avian vaccines in humans is likely due to a lack of cross-reactive CD4 T cell memory perhaps coupled with competition with or suppression of naive, HA-specific CD4 T cells by memory CD4 T cells specific for more highly conserved proteins.
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Affiliation(s)
- Anthony DiPiazza
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Katherine Richards
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Nicholas Poulton
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Andrea J Sant
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
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8
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Genesis and Dissemination of Highly Pathogenic H5N6 Avian Influenza Viruses. J Virol 2017; 91:JVI.02199-16. [PMID: 28003485 DOI: 10.1128/jvi.02199-16] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/11/2016] [Indexed: 11/20/2022] Open
Abstract
Clade 2.3.4.4 highly pathogenic avian influenza viruses (H5Nx) have spread from Asia to other parts of the world. Since 2014, human infections with clade 2.3.4.4 highly pathogenic avian influenza H5N6 viruses have been continuously reported in China. To investigate the genesis of the virus, we analyzed 123 H5 or N6 environmental viruses sampled from live-poultry markets or farms from 2012 to 2015 in Mainland China. Our results indicated that clade 2.3.4.4 H5N2/N6/N8 viruses shared the same hemagglutinin gene as originated in early 2009. From 2012 to 2015, the genesis of highly pathogenic avian influenza H5N6 viruses occurred via two independent pathways. Three major reassortant H5N6 viruses (reassortants A, B, and C) were generated. Internal genes of reassortant A and B viruses and reassortant C viruses derived from clade 2.3.2.1c H5N1 and H9N2 viruses, respectively. Many mammalian adaption mutations and antigenic variations were detected among the three reassortant viruses. Considering their wide circulation and dynamic reassortment in poultry, we highly recommend close monitoring of the viruses in poultry and humans. IMPORTANCE Since 2014, clade 2.3.4.4 highly pathogenic avian influenza (H5Nx) viruses have caused many outbreaks in both wild and domestic birds globally. Severe human cases with novel H5N6 viruses in this group were also reported in China in 2014 and 2015. To investigate the genesis of the genetic diversity of these H5N6 viruses, we sequenced 123 H5 or N6 environmental viruses sampled from 2012 to 2015 in China. Sequence analysis indicated that three major reassortants of these H5N6 viruses had been generated by two independent evolutionary pathways. The H5N6 reassortant viruses had been detected in most provinces of southern China and neighboring countries. Considering the mammalian adaption mutations and antigenic variation detected, the spread of these viruses should be monitored carefully due to their pandemic potential.
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9
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Two Outbreak Sources of Influenza A (H7N9) Viruses Have Been Established in China. J Virol 2016; 90:5561-5573. [PMID: 27030268 DOI: 10.1128/jvi.03173-15] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/18/2016] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED Due to enzootic infections in poultry and persistent human infections in China, influenza A (H7N9) virus has remained a public health threat. The Yangtze River Delta region, which is located in eastern China, is well recognized as the original source for H7N9 outbreaks. Based on the evolutionary analysis of H7N9 viruses from all three outbreak waves since 2013, we identified the Pearl River Delta region as an additional H7N9 outbreak source. H7N9 viruses are repeatedly introduced from these two sources to the other areas, and the persistent circulation of H7N9 viruses occurs in poultry, causing continuous outbreak waves. Poultry movements may contribute to the geographic expansion of the virus. In addition, the AnH1 genotype, which was predominant during wave 1, was replaced by JS537, JS18828, and AnH1887 genotypes during waves 2 and 3. The establishment of a new source and the continuous evolution of the virus hamper the elimination of H7N9 viruses, thus posing a long-term threat of H7N9 infection in humans. Therefore, both surveillance of H7N9 viruses in humans and poultry and supervision of poultry movements should be strengthened. IMPORTANCE Since its occurrence in humans in eastern China in spring 2013, the avian H7N9 viruses have been demonstrating the continuing pandemic threat posed by the current influenza ecosystem in China. As the viruses are silently circulated in poultry, with potentially severe outcomes in humans, H7N9 virus activity in humans in China is very important to understand. In this study, we identified a newly emerged H7N9 outbreak source in the Pearl River Delta region. Both sources in the Yangtze River Delta region and the Pearl River Delta region have been established and found to be responsible for the H7N9 outbreaks in mainland China.
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10
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Huang G. Artificial infectious disease optimization: A SEIQR epidemic dynamic model-based function optimization algorithm. SWARM AND EVOLUTIONARY COMPUTATION 2016; 27:31-67. [PMID: 32288989 PMCID: PMC7104270 DOI: 10.1016/j.swevo.2015.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 08/05/2015] [Accepted: 09/21/2015] [Indexed: 05/04/2023]
Abstract
To solve some complicated function optimization problems, an artificial infectious disease optimization algorithm based on the SEIQR epidemic model is constructed, it is called as the SEIQR algorithm, or SEIQRA in short. The algorithm supposes that some human individuals exist in an ecosystem; each individual is characterized by a number of features; an infectious disease (SARS) exists in the ecosystem and spreads among individuals, the disease attacks only a part of features of an individual. Each infected individual may pass through such states as susceptibility (S), exposure (E), infection (I), quarantine (Q) and recovery (R). State S, E, I, Q and R can automatically and dynamically divide all people in the ecosystem into five classes, it provides the diversity for SEIQRA; that people can be attacked by the infectious disease and then transfer it to other people can cause information exchange among people, information exchange can make a person to transit from one state to another; state transitions can be transformed into operators of SEIQRA; the algorithm has 13 legal state transitions, which corresponds to 13 operators; the transmission rules of the infectious disease among people is just the logic to control state transitions of individuals among S, E, I, Q and R, it is just the synergy of SEIQRA, the synergy can be transformed into the logic structure of the algorithm. The 13 operators in the algorithm provide a native opportunity to integrate many operations with different purposes; these operations include average, differential, expansion, chevy, reflection and crossover. The 13 operators are executed equi-probably; a stable heart rhythm of the algorithm is realized. Because the infectious disease can only attack a small part of organs of a person when it spreads among people, the part variables iteration strategy (PVI) can be ingeniously applied, thus enabling the algorithm to possess of high performance of computation, high suitability for solving some kinds of complicated optimization problems, especially high dimensional optimization problems. Results show that SEIQRA has characteristics of strong search capability and global convergence, and has a high convergence speed for some complicated functions optimization problems.
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Affiliation(s)
- Guangqiu Huang
- School of Management, Xi'an University of Architecture and Technology, Xi'an 710055, China
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11
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Sha J, Chen X, Ren Y, Chen H, Wu Z, Ying D, Zhang Z, Liu S. Differences in the epidemiology and virology of mild, severe and fatal human infections with avian influenza A (H7N9) virus. Arch Virol 2016; 161:1239-59. [PMID: 26887968 PMCID: PMC7101734 DOI: 10.1007/s00705-016-2781-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 01/30/2016] [Indexed: 11/04/2022]
Abstract
A novel avian influenza A (H7N9) virus caused 5-10 % mild and 30.5 % fatal human infections as of December 10, 2015. In order to investigate the reason for the higher rate of fatal outcome of this infection, this study compared the molecular epidemiology and virology of avian influenza A (H7N9) viruses from mild (N = 14), severe (N = 50) and fatal (N = 35) cases, as well as from non-human hosts (N = 73). The epidemiological results showed that the average age of the people in the mild, severe and fatal groups was 27.6, 52 and 62 years old, respectively (p < 0.001). Males accounted for 42.9 % (6/14), 58.0 % (29/50), and 74.3 % (26/35) of cases in the mild, severe and fatal group respectively (p = 0.094). Median days from onset to start of antiviral treatment were 2, 5 and 7 days in the mild, severe and fatal group, respectively (p = 0.002). The median time from onset to discharge/death was 12, 40 and 19 days in the mild, severe and fatal group, respectively (p < 0.001). Analysis of whole genome sequences showed that PB2 (E627K), NA (R294K) and PA (V100A) mutations were markedly associated with an increased fatality rate, while HA (N276D) and PB2 (N559T) mutations were clearly related to mild cases. There were no differences in the genotypes, adaptation to mammalian hosts, and genetic identity between the three types of infection. In conclusion, advanced age and delayed confirmation of diagnosis and antiviral intervention were risk factors for death. Furthermore, PB2 (E627K), NA (R294K) and PA (V100A) mutations might contribute to a fatal outcome in human H7N9 infection.
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Affiliation(s)
- Jianping Sha
- Department of Gastroenterology, The 421 Hospital of Chinese People's Liberation Army, Guangzhou, People's Republic of China
| | - Xiaowen Chen
- Department of Senior Cadres, The 421 Hospital of Chinese People's Liberation Army, Guangzhou, People's Republic of China
| | - Yajin Ren
- Pharmacy Department, The 421 Hospital of Chinese People's Liberation Army, Guangzhou, People's Republic of China
| | - Haijun Chen
- Department of Infectious Diseases, Jinhua Municipal Central Hospital, Jinhua, People's Republic of China
| | - Zuqun Wu
- Department of Respiratory Medicine, Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, People's Republic of China
| | - Dong Ying
- Department of Oncology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Zhiruo Zhang
- School of Public Health, Shanghai Jiao Tong University, 227 South Chongqing Road, Huangpu District, Shanghai, 200025, People's Republic of China.
| | - Shelan Liu
- Department of Infectious Diseases, Zhejiang Provincial Centre for Disease Control and Prevention, 3399 Binsheng Road, Binjiang District, Hangzhou, 310051, Zhejiang Province, People's Republic of China.
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Zhu W, Zou X, Zhou J, Tang J, Shu Y. Residues 41V and/or 210D in the NP protein enhance polymerase activities and potential replication of novel influenza (H7N9) viruses at low temperature. Virol J 2015; 12:71. [PMID: 25940512 PMCID: PMC4434832 DOI: 10.1186/s12985-015-0304-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 04/29/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The influenza A (H7N9) virus emerged in the spring of 2013 in China. It contained six internal genes from Y280-like H9N2 viruses, which have co-circulated with G1-like lineage viruses throughout poultry in China. Accompanied with continuous reassortment among H7N9 and H9N2 viruses in poultry, it is possible for H7N9 viruses to acquire internal genes of G1-lineage viruses. Thus, it is important to evaluate potential impact of G1-like viruses on the H7N9 viruses. FINDINGS We used in vitro assays of polymerase activities and growth kinetics to evaluate the potential contribution of G1-like virus genes to the replication abilities of H7N9 viruses. Two mutations in the NP protein (41V and/or 210D) could enhance H7N9 RNP activities, especially at low temperature (33°C, which is similar to the temperature of human upper respiratory tract). Meanwhile, G1 viruses with V41I or D210E substitutions exhibited poor growth ability in the early infection stage at low temperature. The D210E substitution also reduced the replication ability of G1 virus at 12 and 24 hour post infection at 37°C. In both tested temperatures, V41I could compensate for the defective virus replication induced by the D210E mutation. CONCLUSIONS Mutations 41V and/or 210D in the NP protein conferred improved RNP activity in H7N9 viruses and promoted the replication ability of H9N2 viruses, particularly at lower temperature. Substitutions at these two positions may promote the replication ability of H7N9 viruses in low temperature and thus might contribute to viral transmissibility. While these two residues have not yet been observed in H7N9 viruses, attention should be devoted to these two residues.
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Affiliation(s)
- Wenfei Zhu
- National Institute for Viral Disease Control and Prevention, China CDC, Key Laboratory for Medical Virology, National Health and Family Planning Commission, 155 Changbai Road, Beijing, 102206, P.R China.
| | - Xiaohui Zou
- National Institute for Viral Disease Control and Prevention, China CDC, Key Laboratory for Medical Virology, National Health and Family Planning Commission, 155 Changbai Road, Beijing, 102206, P.R China.
| | - Jianfang Zhou
- National Institute for Viral Disease Control and Prevention, China CDC, Key Laboratory for Medical Virology, National Health and Family Planning Commission, 155 Changbai Road, Beijing, 102206, P.R China.
| | - Jing Tang
- National Institute for Viral Disease Control and Prevention, China CDC, Key Laboratory for Medical Virology, National Health and Family Planning Commission, 155 Changbai Road, Beijing, 102206, P.R China.
| | - Yuelong Shu
- National Institute for Viral Disease Control and Prevention, China CDC, Key Laboratory for Medical Virology, National Health and Family Planning Commission, 155 Changbai Road, Beijing, 102206, P.R China.
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13
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Farooqui A, Leon AJ, Huang L, Wu S, Cai Y, Lin P, Chen W, Fang X, Zeng T, Liu Y, Zhang L, Su T, Chen W, Ghedin E, Zhu H, Guan Y, Kelvin DJ. Genetic diversity of the 2013-14 human isolates of influenza H7N9 in China. BMC Infect Dis 2015; 15:109. [PMID: 25880069 PMCID: PMC4352237 DOI: 10.1186/s12879-015-0829-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 02/11/2015] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Influenza H7N9 has become an endemic pathogen in China where circulating virus is found extensively in wild birds and domestic poultry. Two epidemic waves of Human H7N9 infections have taken place in Eastern and South Central China during the years of 2013 and 2014. In this study, we report on the first four human cases of influenza H7N9 in Shantou, Guangdong province, which occurred during the second H7N9 wave, and the subsequent analysis of the viral isolates. METHODS Viral genomes were subjected to multisegment amplification and sequenced in an Illumina MiSeq. Later, phylogenetic analyses of influenza H7N9 viruses were performed to establish the evolutionary context of the disease in humans. RESULTS The sequences of the isolates from Shantou have closer evolutionary proximity to the predominant Eastern H7N9 cluster (similar to A/Shanghai/1/2013 (H7N9)) than to the Southern H7N9 cluster (similar to A/Guangdong/1/2013 (H7N9)). CONCLUSIONS Two distinct phylogenetic groups of influenza H7N9 circulate currently in China and cause infections in humans as a consequence of cross-species spillover from the avian disease. The Eastern cluster, which includes the four isolates from Shantou, presents a wide geographic distribution and overlaps with the more restricted area of circulation of the Southern cluster. Continued monitoring of the avian disease is of critical importance to better understand and predict the epidemiological behaviour of the human cases.
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Affiliation(s)
- Amber Farooqui
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong, 515041, China.
| | - Alberto J Leon
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong, 515041, China.
- Division of Experimental Therapeutics, University Health Network, Toronto, Ontario, Canada.
| | - Linxi Huang
- Intensive Care Unit, the First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China.
| | - Suwu Wu
- Intensive Care Unit, Shantou Central Hospital, Shantou, Guangdong, China.
| | - Yingmu Cai
- Department of Laboratory Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China.
| | - Pengzhou Lin
- Intensive Care Unit, the First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China.
| | - Weihong Chen
- Intensive Care Unit, Shantou Central Hospital, Shantou, Guangdong, China.
| | - Xibin Fang
- Intensive Care Unit, Shantou Central Hospital, Shantou, Guangdong, China.
| | - Tiansheng Zeng
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong, 515041, China.
| | - Yisu Liu
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong, 515041, China.
| | - Li Zhang
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong, 515041, China.
| | - Ting Su
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong, 515041, China.
| | - Weibin Chen
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong, 515041, China.
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, Global Institute of Public Health, New York University, New York, USA.
| | - Huachen Zhu
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China.
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China.
| | - Yi Guan
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China.
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China.
| | - David J Kelvin
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, 22 Xinling Road, Shantou, Guangdong, 515041, China.
- Division of Experimental Therapeutics, University Health Network, Toronto, Ontario, Canada.
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He B, Zheng BJ, Wang Q, Du L, Jiang S, Lu L. Adenovirus-based vaccines against avian-origin H5N1 influenza viruses. Microbes Infect 2015; 17:135-41. [PMID: 25479556 PMCID: PMC7110517 DOI: 10.1016/j.micinf.2014.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 11/18/2014] [Accepted: 11/18/2014] [Indexed: 02/03/2023]
Abstract
Since 1997, human infection with avian H5N1, having about 60% mortality, has posed a threat to public health. In this review, we describe the epidemiology of H5N1 transmission, advantages and disadvantages of different influenza vaccine types, and characteristics of adenovirus, finally summarizing advances in adenovirus-based H5N1 systemic and mucosal vaccines.
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Affiliation(s)
- Biao He
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China
| | - Bo-jian Zheng
- Department of Microbiology, University of Hong Kong, Pokfulam, Hong Kong 999077, China
| | - Qian Wang
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China; Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China.
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