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Yang CR, Chang SY, Gong YN, Huang CG, Tung TH, Liu W, Chan TC, Hung KS, Shang HS, Tsai JJ, Kao CL, Wu HL, Daisy Liu LY, Lin WY, Fan YC, King CC, Ku CC. The emergence and successful elimination of SARS-CoV-2 dominant strains with increasing epidemic potential in Taiwan's 2021 outbreak. Heliyon 2023; 9:e22436. [PMID: 38107297 PMCID: PMC10724543 DOI: 10.1016/j.heliyon.2023.e22436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
Taiwan's experience with severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003 guided its development of strategies to defend against SARS-CoV-2 in 2020, which enabled the successful control of Coronavirus disease 2019 (COVID-19) cases from 2020 through March 2021. However, in late-April 2021, the imported Alpha variant began to cause COVID-19 outbreaks at an exceptional rate in Taiwan. In this study, we aimed to determine what epidemiological conditions enabled the SARS-CoV-2 Alpha variant strains to become dominant and decline later during a surge in the outbreak. In conjunction with contact-tracing investigations, we used our bioinformatics software, CoVConvert and IniCoV, to analyze whole-genome sequences of 101 Taiwan Alpha strains. Univariate and multivariable regression analyses revealed the epidemiological factors associated with viral dominance. Univariate analysis showed the dominant Alpha strains were preferentially selected in the surge's epicenter (p = 0.0024) through intensive human-to-human contact and maintained their dominance for 1.5 months until the Zero-COVID Policy was implemented. Multivariable regression found that the epidemic periods (p = 0.007) and epicenter (p = 0.001) were two significant factors associated with the dominant virus strains spread in the community. These dominant virus strains emerged at the outbreak's epicenter with frequent human-to-human contact and low vaccination coverage. The Level 3 Restrictions and Zero-COVID policy successfully controlled the outbreak in the community without city lockdowns. Our integrated method can identify the epidemiological conditions for emerging dominant virus with increasing epidemiological potential and support decision makers in rapidly containing outbreaks using public health measures that target fast-spreading virus strains.
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Affiliation(s)
- Chin-Rur Yang
- Graduate Institute of Immunology, College of Medicine, National Taiwan University, 1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan, ROC
| | - Sui-Yuan Chang
- Department (Dept.) of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan, ROC
- Dept. of Laboratory Medicine, National Taiwan University Hospital, Taipei, 10051, Taiwan, ROC
| | - Yu-Nong Gong
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, 33302, Taiwan, ROC
- Dept. of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 33302, Taiwan, ROC
| | - Chung-Guei Huang
- Dept. of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 33302, Taiwan, ROC
- Dept. of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, 33302, Taiwan, ROC
| | - Tsung-Hua Tung
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
- Dept. of Health, Taipei City Government, Taipei, Taiwan, ROC
| | - Wei Liu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
| | - Ta-Chien Chan
- Research Center for Humanities and Social Sciences, Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Kuo-Sheng Hung
- Center for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei, 11490, Taiwan, ROC
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Dept. of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, 11490, Taiwan, ROC
| | - Jih-Jin Tsai
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, ROC
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, 80756, Taiwan, ROC
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, 80756, Taiwan, ROC
| | - Chuan-Liang Kao
- Department (Dept.) of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan, ROC
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
| | - Hui-Lin Wu
- Hepatitis Research Center, National Taiwan University Hospital, Taipei, 10051, Taiwan, ROC
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan, ROC
| | - Li-Yu Daisy Liu
- Division of Biometry, Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan, ROC
| | - Wan-Yu Lin
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
| | - Yi-Chin Fan
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
| | - Chwan-Chuen King
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
| | - Chia-Chi Ku
- Graduate Institute of Immunology, College of Medicine, National Taiwan University, 1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan, ROC
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Yang M, Gong S, Huang S, Huo X, Wang W. Geographical characteristics and influencing factors of the influenza epidemic in Hubei, China, from 2009 to 2019. PLoS One 2023; 18:e0280617. [PMID: 38011126 PMCID: PMC10681244 DOI: 10.1371/journal.pone.0280617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 09/13/2023] [Indexed: 11/29/2023] Open
Abstract
Influenza is an acute respiratory infectious disease that commonly affects people and has an important impact on public health. Based on influenza incidence data from 103 counties in Hubei Province from 2009 to 2019, this study used time series analysis and geospatial analysis to analyze the spatial and temporal distribution characteristics of the influenza epidemic and its influencing factors. The results reveal significant spatial-temporal clustering of the influenza epidemic in Hubei Province. Influenza mainly occurs in winter and spring of each year (from December to March of the next year), with the highest incidence rate observed in 2019 and an overall upward trend in recent years. There were significant spatial and urban-rural differences in influenza prevalence in Hubei Province, with the eastern region being more seriously affected than the central and western regions, and the urban regions more seriously affected than the rural region. Hubei's influenza epidemic showed an obvious spatial agglomeration distribution from 2009 to 2019, with the strongest clustering in winter. The hot spot areas of interannual variation in influenza were mainly distributed in eastern and western Hubei, and the cold spot areas were distributed in north-central Hubei. In addition, the cold hot spot areas of influenza epidemics varied from season to season. The seasonal changes in influenza prevalence in Hubei Province are mainly governed by meteorological factors, such as temperature, sunshine, precipitation, humidity, and wind speed. Low temperature, less rain, less sunshine, low wind speed and humid weather will increase the risk of contracting influenza; the interannual changes and spatial differentiation of influenza are mainly influenced by socioeconomic factors, such as road density, number of health technicians per 1,000 population, urbanization rate and population density. The strength of influenza's influencing factors in Hubei Province exhibits significant spatial variation, but in general, the formation of spatial variation of influenza in Hubei Province is still the result of the joint action of socioeconomic factors and natural meteorological factors. Understanding the temporal and spatial distribution characteristics of influenza in Hubei Province and its influencing factors can provide a reasonable decision-making basis for influenza prevention and control and public health development in Hubei Province and can also effectively improve the scientific understanding of the public with respect to influenza and other respiratory infectious diseases to reduce the influenza incidence, which also has reference significance for the prevention and control of influenza and other respiratory infectious diseases in other countries or regions.
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Affiliation(s)
- Mengmeng Yang
- College of Urban and Environmental Sciences, Central China Normal University, Wuhan, China
| | - Shengsheng Gong
- College of Urban and Environmental Sciences, Central China Normal University, Wuhan, China
| | - Shuqiong Huang
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Xixiang Huo
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Wuwei Wang
- College of Urban and Environmental Sciences, Central China Normal University, Wuhan, China
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Shang S, Jia W, Zhang S, Su B, Cheng R, Li Y, Zhang N. Changes on local travel behaviors under travel reduction-related interventions during COVID-19 pandemic: a case study in Hong Kong. CITY AND BUILT ENVIRONMENT 2023; 1:5. [PMCID: PMC9985955 DOI: 10.1007/s44213-023-00006-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
The emerging Omicron variant poses a serious threat to human health. Public transports play a critical role in infection spread. Based on the data of nearly 4 billion smartcard uses, between January 1, 2019 and January 31, 2021 from the Mass Transit Railway Corporation of Hong Kong, we analyzed the subway travel behavior of different population groups (adults, children, students and senior citizens) due to the COVID-19 pandemic and human travel behavior under different interventions (e.g. work suspension, school closure). Due to the pandemic, the number of MTR passengers (the daily number of passengers in close proximity in subway carriages) decreased by 37.4% (40.8%) for adults, 80.3% (78.5%) for children, 71.6% (71.6%) for students, and 33.5% (36.1%) for senior citizens. Due to work from home (school suspension), the number of contacted adults (students/children) in the same carriage during the rush hours decreased by 39.6% (38.6%/43.2%). If all workers, students, and children were encouraged to commute avoiding rush hours, the possible repeated contacts during rush hour of adults, children and students decreased by 73.3%, 77.9% and 79.5%, respectively. Since adults accounted for 87.3% of the total number of subway passengers during the pandemic, work from home and staggered shift pattern of workers can reduce the infection risk effectively. Our objective is to find the changes of local travel behavior due to the pandemic. From the perspective of public transports, the results provide a scientific support for COVID-19 prevention and control in cities.
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Affiliation(s)
- Shujia Shang
- grid.28703.3e0000 0000 9040 3743Beijing Key Laboratory of Green Built Environment and Energy Efficient Technology, Beijing University of Technology, Beijing, China
| | - Wei Jia
- grid.194645.b0000000121742757Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China
| | - Shiyao Zhang
- grid.263817.90000 0004 1773 1790The Research Institute for Trustworthy Autonomous Systems, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Boni Su
- grid.467472.4China Electric Power Planning & Engineering Institute, Beijing, China
| | - Reynold Cheng
- grid.194645.b0000000121742757Department of Computer Science, The University of Hong Kong, Hong Kong, SAR China
| | - Yuguo Li
- grid.194645.b0000000121742757Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China ,grid.194645.b0000000121742757School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, SAR China
| | - Nan Zhang
- grid.28703.3e0000 0000 9040 3743Beijing Key Laboratory of Green Built Environment and Energy Efficient Technology, Beijing University of Technology, Beijing, China
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Tunnicliffe L, Warren‐Gash C. Investigating the effects of population density of residence and rural/urban classification on rate of influenza-like illness symptoms in England and Wales. Influenza Other Respir Viruses 2022; 16:1183-1190. [PMID: 35922884 PMCID: PMC9530544 DOI: 10.1111/irv.13032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Better understanding of risk factors for influenza could help improve seasonal and pandemic planning. There is a dearth of literature on area-level risk factors such as population density and rural/urban living. METHODS We used data from Flusurvey, an online community-based cohort that records influenza events. The study outcome was symptoms of influenza-like illness (ILI). Multivariable Poisson regression analysis was used to explore associations of both population density and rural/urban status with rate of ILI symptoms and whether these effects differed by vaccination status. RESULTS Of the 6177 study participants, the median age was 45 (IQR 32-57), 65.73% were female, and 66% reported at least one episode of ILI symptoms between 2011 and 2016. We found no evidence to suggest that the rate of ILI symptoms was higher in the medium [RR 1.02 (95% CI 0.95-1.09)] or high [RR 1.02 (95% CI 0.96-1.09)] population density group versus the low population density group. This was the same for the effect of urban living [RR 0.96 (95% CI 0.90-1.03)] versus rural living on symptom rate. There was weak evidence to suggest that the ILI symptom rate was lower in urban areas compared with rural areas among unvaccinated individuals only [RR 0.90 (95% CI 0.83-0.99)], whereas no difference was seen among vaccinated individuals [1.04 (95% CI 0.94-1.16)]. CONCLUSIONS Although neither population density nor rural/urban status was associated with ILI symptom rate in this community cohort, future research that incorporates activity and contact patterns will help to elucidate this relationship further.
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Affiliation(s)
- Louis Tunnicliffe
- Department of Non‐communicable Disease Epidemiology, Faculty of Epidemiology and Population HealthLondon School of Hygiene and Tropical MedicineLondonUK
| | - Charlotte Warren‐Gash
- Department of Non‐communicable Disease Epidemiology, Faculty of Epidemiology and Population HealthLondon School of Hygiene and Tropical MedicineLondonUK
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Ho PI, Liu W, Li TZR, Chan TC, Ku CC, Lien YH, Shen YHD, Chen JR, Yen MY, Tu YK, Lin WY, Compans R, Lee PI, King CC. Taiwan's Response to Influenza: A Seroepidemiological Evaluation of Policies and Implications for Pandemic Preparedness. Int J Infect Dis 2022; 121:226-237. [PMID: 35235824 DOI: 10.1016/j.ijid.2022.02.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES To evaluate class suspension and mass vaccination implemented among Taipei schoolchildren during the 2009 influenza pandemic and investigate factors affecting antibody responses. METHODS We conducted 2 cohort studies on: (1) 972 schoolchildren from November 2009-March 2010 to evaluate pandemic policies and (2) 935 schoolchildren from November 2011-March 2012 to verify factors in antibody waning. Anti-influenza H1N1pdm09 hemagglutination inhibition antibodies (HI-Ab) were measured from serum samples collected before vaccination, and at 1 and 4 months after vaccination. Factors affecting HI-Ab responses were investigated through logistic regression and generalized estimating equation. RESULTS Seroprevalence of H1N1pdm09 before vaccination was significantly higher among schoolchildren who experienced class suspensions than those who did not (59.6% vs 47.5%, p<0.05). Participating in after-school activities (adjusted odds ratio [aOR]=2.47, p=0.047) and having ≥3 hours per week of exercise (aOR=2.86, p=0.019) were significantly correlated with H1N1pdm09 infection. Two doses of the H1N1pdm09 vaccine demonstrated significantly better antibody persistence than 1 dose (HI-Ab geometric mean titer: 132.5 vs 88.6, p=0.047). Vaccine effectiveness after controlling for preexisting immunity was 86% (32%-97%). Exercise ≥3 hours per week and preexisting immunity were significantly associated with antibody waning/maintenance. CONCLUSIONS This study is the first to show that exercise and preexisting immunity may affect antibody waning. Further investigation is needed to identify immune correlates of protection.
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Affiliation(s)
- Pui-I Ho
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan
| | - Wei Liu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan
| | - Tiger Zheng-Rong Li
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan
| | - Ta-Chien Chan
- Research Center for Humanities & Social Sciences, Academia Sinica, Taipei, Taiwan
| | - Chia-Chi Ku
- Institute of Immunology, College of Medicine, NTU, Taipei, Taiwan
| | - Yu-Hui Lien
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan
| | - Ya-Hui Daphne Shen
- Department of Infection, Yuan's General Hospital, Kaohsiung City, Taiwan; StatPlus, Inc., Taipei, Taiwan
| | | | | | - Yu-Kang Tu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan
| | - Wan-Yu Lin
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan
| | - Richard Compans
- Department of Microbiology and Immunology and Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States of America (U.S.A.)
| | - Ping-Ing Lee
- Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.
| | - Chwan-Chuen King
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan.
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Bu L, Chen B, Xing L, Cai X, Liang S, Zhang L, Wang X, Song W. Generation of a pdmH1N1 2018 Influenza A Reporter Virus Carrying a mCherry Fluorescent Protein in the PA Segment. Front Cell Infect Microbiol 2022; 11:827790. [PMID: 35127568 PMCID: PMC8811159 DOI: 10.3389/fcimb.2021.827790] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 12/31/2021] [Indexed: 11/13/2022] Open
Abstract
Influenza A virus (IAV) is a major human pathogen associated with significant morbidity and mortality worldwide. Through serial passage in mice, we generated a recombinant pdmH1N1 2009 IAV, A/Guangdong/GLW/2018 (GLW/18-MA), which encodes an mCherry gene fused to the C-terminal of a polymerase acidic (PA) segment and demonstrated comparable growth kinetics to the wild-type. Nine mutations were identified in the GLW/18-MA genome: PA (I61M, E351G, and G631S), NP (E292G), HA1 (T164I), HA2 (N117S and P160S), NA (W61R), and NEP (K44R). The recombinant IAV reporter expresses mCherry, a red fluorescent protein, at a high level and maintains its genetic integrity after five generations of serial passages in Madin-Darby Canine Kidney cells (MDCK) cells. Moreover, the imaging is noninvasive and permits the monitoring of infection in living mice. Treatment with oseltamivir or baicalin followed by infection with the reporter IAV led to a decrease in fluorescent protein signal in living mice. This result demonstrates that the IAV reporter virus is a powerful tool to study viral pathogenicity and transmission and to develop and evaluate novel anti-viral drugs, inhibitors, and vaccines in the future.
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Affiliation(s)
- Ling Bu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Institute of Integration of Traditional and Western Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Boqian Chen
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lei Xing
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Institute of Integration of Traditional and Western Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xuejun Cai
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Institute of Integration of Traditional and Western Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shuhua Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Institute of Integration of Traditional and Western Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Liying Zhang
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
| | - Xinhua Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Institute of Integration of Traditional and Western Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wenjun Song
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Institute of Integration of Traditional and Western Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, and the Research Center of Infection and Immunology, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
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Akter S, Dhar TK, Rahman AIA, Uddin MK. Investigating the resilience of refugee camps to COVID-19: A case of Rohingya settlements in Bangladesh. J Migr Health 2021; 4:100052. [PMID: 34405195 PMCID: PMC8352112 DOI: 10.1016/j.jmh.2021.100052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/07/2021] [Accepted: 06/13/2021] [Indexed: 12/23/2022] Open
Abstract
Bangladesh Rohingya camps have hosted 65,000 refugees fled from Myanmar only since 2017. Their compromised living environment and limited physical and socioeconomic facilities make them highly sensitive to COVID-19. The Government of Bangladesh and international aid agencies have applied WHO's IPC (Infection, Prevention, and Control) guidelines to mitigate the transmission of COVID-19 outbreaks and enhance their resilience. However, Rohingyas often disregard these guidelines or become reluctant to follow them. Building on 10 in-depth interviews, 66 questionnaires, and observation, the study investigates the limitations and challenges of implementing these guidelines toward building community resilience. It assesses their resilience, focusingon Kutupalong camp, Cox's Bazar-one of the world's largest refugee camps. Findings reveal that Rohingya's past experience associated with their psychological trauma largely influences their current actions and demotivates them fromfollowing the health guidelines. Their deep mistrust of and disrespect to healthcare providers and aid agencies discourage them to follow the IPC. Also, insufficient built infrastructure and unhygienic living conditions, including improper WASH management, increase their risk to COVID-19. The study highlights a need for understanding their socio-psychological values and cultural narratives and recommends a set of guidelines for policymakers and aid agencies to build community resilience to COVID -19.
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Affiliation(s)
- Salma Akter
- Lecturer, Architecture Department, Premier University, Chittagong, Bangladesh
| | - Tapan Kumar Dhar
- Professor, Architecture Discipline Khulna University, Khulna Bangladesh
| | | | - Md. Kamal Uddin
- Civil Engineer, Volume 11, 20/c Amirbag, Mehedibag, Chittagong, Bangladesh
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Jo Y, Hong A, Sung H. Density or Connectivity: What Are the Main Causes of the Spatial Proliferation of COVID-19 in Korea? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:5084. [PMID: 34065031 PMCID: PMC8150374 DOI: 10.3390/ijerph18105084] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 01/01/2023]
Abstract
COVID-19 has sparked a debate on the vulnerability of densely populated cities. Some studies argue that high-density urban centers are more vulnerable to infectious diseases due to a higher chance of infection in crowded urban environments. Other studies, however, argue that connectivity rather than population density plays a more significant role in the spread of COVID-19. While several studies have examined the role of urban density and connectivity in Europe and the U.S., few studies have been conducted in Asian countries. This study aims to investigate the role of urban spatial structure on COVID-19 by comparing different measures of urban density and connectivity during the first eight months of the outbreak in Korea. Two measures of density were derived from the Korean census, and four measures of connectivity were computed using social network analysis of the Origin-Destination data from the 2020 Korea Transport Database. We fitted both OLS and negative binomial models to the number of confirmed COVID-19 patients and its infection rates at the county level, collected individually from regional government websites in Korea. Results show that both density and connectivity play an important role in the proliferation of the COVID-19 outbreak in Korea. However, we found that the connectivity measure, particularly a measure of network centrality, was a better indicator of COVID-19 proliferation than the density measures. Our findings imply that policies that take into account different types of connectivity between cities might be necessary to contain the outbreak in the early phase.
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Affiliation(s)
- Yun Jo
- Graduate School of Urban Studies, Hanyang University, Seoul 04763, Korea;
| | - Andy Hong
- Department of City & Metropolitan Planning, College of Architecture + Planning, University of Utah, Salt Lake City, UT 84112, USA;
- The George Institute for Global Health, Newtown, NSW 2042, Australia
| | - Hyungun Sung
- Graduate School of Urban Studies, Hanyang University, Seoul 04763, Korea;
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Arif M, Sengupta S. Nexus between population density and novel coronavirus (COVID-19) pandemic in the south Indian states: A geo-statistical approach. ENVIRONMENT, DEVELOPMENT AND SUSTAINABILITY 2021; 23:10246-10274. [PMID: 33144832 PMCID: PMC7596317 DOI: 10.1007/s10668-020-01055-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/14/2020] [Indexed: 05/05/2023]
Abstract
The unprecedented growth of the novel coronavirus (SARS-CoV-2) as a severe acute respiratory syndrome escalated to the coronavirus disease 2019 (COVID-19) pandemic. It has created an unanticipated global public health crisis that is spreading rapidly in India as well, posing a serious threat to 1350 million persons. Among the factors, population density is foremost in posing a challenge in controlling the COVID-19 contagion. In such extraordinary times, evidence-based knowledge is the prime requisite for pacifying the effect. In this piece, we have studied the district wise transmissions of the novel coronavirus in five south Indian states until 20th July 2020 and its relationship with their respective population density. The five states are purposefully selected for their records in better healthcare infrastructure vis-à-vis other states in India. The study uses Pearson's correlation coefficient to account for the direct impact of population density on COVID-19 transmission rate. Response surface methodology approach is used to validate the correlation between density and transmission rate and spatiotemporal dynamics is highlighted using Thiessen polygon method. The analysis has found that COVID-19 transmission in four states (Kerala, Tamil Nadu, Karnataka and Telangana) strongly hinges upon the spatial distribution of population density. In addition, the results indicate that the long-term impacts of the COVID-19 crisis are likely to differ with demographic density. In conclusion, those at the helm of affairs must take cognizance of the vulnerability clusters together across districts.
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Affiliation(s)
- Mohammad Arif
- Department of Geography, Visva-Bharati (A Central University), Santiniketan, West Bengal 731235 India
| | - Soumita Sengupta
- Department of Remote Sensing, Birla Institute of Technology, Mesra, Jharkhand 835215 India
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Baser O. Population density index and its use for distribution of Covid-19: A case study using Turkish data. Health Policy 2020; 125:148-154. [PMID: 33190934 PMCID: PMC7550260 DOI: 10.1016/j.healthpol.2020.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 09/20/2020] [Accepted: 10/04/2020] [Indexed: 11/25/2022]
Abstract
Since March 2020, many countries around the world have been experiencing a large outbreak of a novel coronavirus (2019-nCoV). Because there is a higher rate of contact between humans in cities with higher population weighted densities, Covid-19 spreads faster in these areas. In this study, we examined the relationship between population weighted density and the spread of Covid-19. Using data from Turkey, we calculated the elasticity of Covid-19 spread with respect to population weighted density to be 0.67 after controlling for other factors. In addition to the density, the proportion of people over 65, the per capita GDP, and the number of total health care workers in each city positively contributed to the case numbers, while education level and temperature had a negative effect. We suggested a policy measure on how to transfer health care workers from different areas to the areas with a possibility of wide spread.
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Affiliation(s)
- Onur Baser
- Department of Economics, MEF University, Ayazaga Cad. No:4 Maslak, 34396, Sariyer, Istanbul, Turkey; Medical School, University of Michigan, Department of Internal Medicine, 1500 East Medical Center Drive, Ann Arbor, MI, 48109, United States; John. D. Dingell VA Medical Center, 4646 John R Street, Detroit, MI, 48201, United States.
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Hamidi S, Ewing R, Sabouri S. Longitudinal analyses of the relationship between development density and the COVID-19 morbidity and mortality rates: Early evidence from 1,165 metropolitan counties in the United States. Health Place 2020. [PMID: 32738578 DOI: 10.1016/j.healthplace:2020.102378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
This longitudinal study aims to investigative the impacts of development density on the spread and mortality rates of COVID-19 in metropolitan counties in the United States. Multilevel Linear Modeling (MLM) is employed to model the infection rate and the mortality rate of COVID-19, accounting for the hierarchical (two-level) and longitudinal structure of the data. This study finds that large metropolitan size (measured in terms of population) leads to significantly higher COVID-19 infection rates and higher mortality rates. After controlling for metropolitan size and other confounding variables, county density leads to significantly lower infection rates and lower death rates. These findings recommend that urban planners and health professionals continue to advocate for compact development and continue to oppose urban sprawl for this and many other reasons documented in the literature, including the positive relationship between compact development and fitness and general health.
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Affiliation(s)
- Shima Hamidi
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, MD, 21205, USA.
| | - Reid Ewing
- Department of City and Metropolitan Planning, College of Architecture + Planning, University of Utah, 375S 1530 E, Salt Lake City, UT, 84112, USA.
| | - Sadegh Sabouri
- Department of City and Metropolitan Planning, College of Architecture + Planning, University of Utah, 375S 1530 E, Salt Lake City, UT, 84112, USA.
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Hamidi S, Ewing R, Sabouri S. Longitudinal analyses of the relationship between development density and the COVID-19 morbidity and mortality rates: Early evidence from 1,165 metropolitan counties in the United States. Health Place 2020; 64:102378. [PMID: 32738578 PMCID: PMC7315990 DOI: 10.1016/j.healthplace.2020.102378] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/05/2020] [Accepted: 06/16/2020] [Indexed: 11/11/2022]
Abstract
This longitudinal study aims to investigative the impacts of development density on the spread and mortality rates of COVID-19 in metropolitan counties in the United States. Multilevel Linear Modeling (MLM) is employed to model the infection rate and the mortality rate of COVID-19, accounting for the hierarchical (two-level) and longitudinal structure of the data. This study finds that large metropolitan size (measured in terms of population) leads to significantly higher COVID-19 infection rates and higher mortality rates. After controlling for metropolitan size and other confounding variables, county density leads to significantly lower infection rates and lower death rates. These findings recommend that urban planners and health professionals continue to advocate for compact development and continue to oppose urban sprawl for this and many other reasons documented in the literature, including the positive relationship between compact development and fitness and general health.
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Affiliation(s)
- Shima Hamidi
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, MD, 21205, USA.
| | - Reid Ewing
- Department of City and Metropolitan Planning, College of Architecture + Planning, University of Utah, 375S 1530 E, Salt Lake City, UT, 84112, USA.
| | - Sadegh Sabouri
- Department of City and Metropolitan Planning, College of Architecture + Planning, University of Utah, 375S 1530 E, Salt Lake City, UT, 84112, USA.
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Khan A, AlBalwi MA, AlAbdulkareem I, AlMasoud A, AlAsiri A, AlHarbi W, AlSehile F, El-Saed A, Balkhy HH. Atypical influenza A(H1N1)pdm09 strains caused an influenza virus outbreak in Saudi Arabia during the 2009-2011 pandemic season. J Infect Public Health 2019; 12:557-567. [PMID: 30799182 DOI: 10.1016/j.jiph.2019.01.067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/22/2019] [Accepted: 01/30/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The triple assortment influenza A(H1N1) virus emerged in spring 2009 and disseminated worldwide, including Saudi Arabia. This study was carried out to characterize Saudi influenza isolates in relation to the global strains and to evaluate the potential role of mutated residues in transmission, adaptation, and the pathogenicity of the virus. METHODS Nasopharyngeal samples (n = 6492) collected between September 2009 to March 2011 from patients with influenza-like illness were screened by PCR for influenza A(H1N1). Phylogenetic and Molecular evolutionary analysis were carried out to place the Saudi strains in relation to the global strains followed by Mutation analysis of surface and internal proteins. RESULTS Concatenated whole-genome phylogenetic analysis along with hemagglutinin (HA) signature changes, that is, Aspartic Acid (D) at position 187, P83S, S203T, and R223Q confirmed that the Saudi strains belong to the antigenic category of A/California/07/2009. However, phylogenetic analysis revealed unusual strains of A(H1N1) circulating in Saudi Arabia, not belonging to any of known clades, appearing in five distinct groups well supported by group-specific mutations and novel mutation complexes. These cases had characteristic inter- and intragroup substitution patterns while few of their closest matches showed up as sporadic cases the world over. Specific mutation patterns were detected within the functional domains of internal proteins PB2, PB1, PA, NP, NS1, and M2 having a putative role in viral fitness and virulence. Bayesian coalescent MCMC analysis revealed that Saudi strains belonged to cluster 2 of A(H1N1)pdm09 and spread a month later as compared to other strains of this cluster. CONCLUSION Influenza outbreak in Saudi Arabia during 2009-2011 was caused by atypical strains of influenza A(H1N1)pdm09, probably introduced in this community on multiple occasions. To understand the antigenic significance of these novel point mutations and mutation complexes require functional studies, which will be crucial for risk assessment of emergent strains and defining infection control measures.
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Affiliation(s)
- Anis Khan
- Department of Medical Genomics Research, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mohammed A AlBalwi
- Department of Medical Genomics Research, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; Department of Pathology & Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.
| | - Ibraheem AlAbdulkareem
- Intramural health sciences research, Princess Nourah Bint Abdulrahman university, Riyadh, Saudi Arabia
| | - Abdulrahman AlMasoud
- Department of Medical Genomics Research, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Abdulrahman AlAsiri
- Department of Medical Genomics Research, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Wardah AlHarbi
- Department of Medical Genomics Research, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Faisal AlSehile
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Aiman El-Saed
- Department of Infection Prevention & Control Department, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Hanan H Balkhy
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia; Department of Infection Prevention & Control Department, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
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Sitaras I, Rousou X, Peeters B, de Jong MC. Mutations in the haemagglutinin protein and their effect in transmission of highly pathogenic avian influenza (HPAI) H5N1 virus in sub-optimally vaccinated chickens. Vaccine 2016; 34:5512-5518. [DOI: 10.1016/j.vaccine.2016.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/29/2016] [Accepted: 10/03/2016] [Indexed: 10/20/2022]
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Sonnberg S, Ducatez MF, DeBeauchamp J, Crumpton JC, Rubrum A, Sharp B, Hall RJ, Peacey M, Huang S, Webby RJ. Pandemic Seasonal H1N1 Reassortants Recovered from Patient Material Display a Phenotype Similar to That of the Seasonal Parent. J Virol 2016; 90:7647-56. [PMID: 27279619 PMCID: PMC4988147 DOI: 10.1128/jvi.00772-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/06/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED We have previously shown that 11 patients became naturally coinfected with seasonal H1N1 (A/H1N1) and pandemic H1N1 (pdm/H1N1) during the Southern hemisphere winter of 2009 in New Zealand. Reassortment of influenza A viruses is readily observed during coinfection of host animals and in vitro; however, reports of reassortment occurring naturally in humans are rare. Using clinical specimen material, we show reassortment between the two coinfecting viruses occurred with high likelihood directly in one of the previously identified patients. Despite the lack of spread of these reassortants in the community, we did not find them to be attenuated in several model systems for viral replication and virus transmission: multistep growth curves in differentiated human bronchial epithelial cells revealed no growth deficiency in six recovered reassortants compared to A/H1N1 and pdm/H1N1 isolates. Two reassortant viruses were assessed in ferrets and showed transmission to aerosol contacts. This study demonstrates that influenza virus reassortants can arise in naturally coinfected patients. IMPORTANCE Reassortment of influenza A viruses is an important driver of virus evolution, but little has been done to address humans as hosts for the generation of novel influenza viruses. We show here that multiple reassortant viruses were generated during natural coinfection of a patient with pandemic H1N1 (2009) and seasonal H1N1 influenza A viruses. Though apparently fit in model systems, these reassortants did not become established in the wider population, presumably due to herd immunity against their seasonal H1 antigen.
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Affiliation(s)
| | | | | | | | - Adam Rubrum
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Bridgett Sharp
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Richard J Hall
- Institute of Environmental Science and Research, Upper Hutt, New Zealand
| | - Matthew Peacey
- Institute of Environmental Science and Research, Upper Hutt, New Zealand
| | - Sue Huang
- Institute of Environmental Science and Research, Upper Hutt, New Zealand
| | - Richard J Webby
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Ramírez-Salinas GL, García-Machorro J, Quiliano M, Zimic M, Briz V, Rojas-Hernández S, Correa-Basurto J. Molecular modeling studies demonstrate key mutations that could affect the ligand recognition by influenza AH1N1 neuraminidase. J Mol Model 2015; 21:292. [PMID: 26499499 DOI: 10.1007/s00894-015-2835-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 10/09/2015] [Indexed: 01/23/2023]
Abstract
The goal of this study was to identify neuraminidase (NA) residue mutants from human influenza AH1N1 using sequences from 1918 to 2012. Multiple alignment studies of complete NA sequences (5732) were performed. Subsequently, the crystallographic structure of the 1918 influenza (PDB ID: 3BEQ-A) was used as a wild-type structure and three-dimensional (3-D) template for homology modeling of the mutated selected NA sequences. The 3-D mutated NAs were refined using molecular dynamics (MD) simulations (50 ns). The refined 3-D models were used to perform docking studies using oseltamivir. Multiple sequence alignment studies showed seven representative mutations (A232V, K262R, V263I, T264V, S367L, S369N, and S369K). MD simulations applied to 3-D NAs showed that each NA had different active-site shapes according to structural surface visualization and docking results. Moreover, Cartesian principal component analyses (cPCA) show structural differences among these NA structures caused by mutations. These theoretical results suggest that the selected mutations that are located outside of the active site of NA could affect oseltamivir recognition and could be associated with resistance to oseltamivir.
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Affiliation(s)
- Gema L Ramírez-Salinas
- Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, 11340, México City, Mexico
| | - J García-Machorro
- Laboratorio de Medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Mexico, DF, 11340, México
| | - Miguel Quiliano
- Unidad de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Mirko Zimic
- Unidad de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Verónica Briz
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, España
| | - Saul Rojas-Hernández
- Laboratory of Immunology, School of Medicine, National Polytechnic Institute, Mexico, DF, Mexico
| | - J Correa-Basurto
- Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, 11340, México City, Mexico.
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Li YT, Ko HY, Lee CCD, Lai CY, Kao CL, Yang C, Wang WB, King CC. Phenotypic and Genetic Characterization of Avian Influenza H5N2 Viruses with Intra- and Inter-Duck Variations in Taiwan. PLoS One 2015; 10:e0133910. [PMID: 26263554 PMCID: PMC4532476 DOI: 10.1371/journal.pone.0133910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/02/2015] [Indexed: 12/19/2022] Open
Abstract
Background Human infections with avian influenza viruses (AIVs) have frequently raised global concerns of emerging, interspecies-transmissible viruses with pandemic potential. Waterfowl, the predominant reservoir of influenza viruses in nature, harbor precursors of different genetic lineages that have contributed to novel pandemic influenza viruses in the past. Methods Two duck influenza H5N2 viruses, DV518 and DV413, isolated through virological surveillance at a live-poultry market in Taiwan, showed phylogenetic relatedness but exhibited different replication capabilities in mammalian Madin-Darby Canine Kidney (MDCK) cells. This study characterizes the replication properties of the two duck H5N2 viruses and the determinants involved. Results The DV518 virus replicated more efficiently than DV413 in both MDCK and chicken DF1 cells. Interestingly, the infection of MDCK cells by DV518 formed heterogeneous plaques with great differences in size [large (L) and small (S)], and the two viral strains (p518-L and p518-S) obtained from plaque purification exhibited distinguishable replication kinetics in MDCK cells. Nonetheless, both plaque-purified DV518 strains still maintained their growth advantages over the plaque-purified p413 strain. Moreover, three amino acid substitutions in PA (P224S), PB2 (E72D), and M1 (A128T) were identified in intra-duck variations (p518-L vs p518-S), whereas other changes in HA (N170D), NA (I56T), and NP (Y289H) were present in inter-duck variations (DV518 vs DV413). Both p518-L and p518-S strains had the N170D substitution in HA, which might be related to their greater binding to MDCK cells. Additionally, polymerase activity assays on 293T cells demonstrated the role of vRNP in modulating the replication capability of the duck p518-L viruses in mammalian cells. Conclusion These results demonstrate that intra-host phenotypic variation occurs even within an individual duck. In view of recent human infections by low pathogenic AIVs, this study suggests possible determinants involved in the stepwise selection of virus variants from the duck influenza virus population which may facilitate inter-species transmission.
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Affiliation(s)
- Yao-Tsun Li
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan, Republic of China (R.O.C)
| | - Hui-Ying Ko
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan, Republic of China (R.O.C)
| | - Chang-Chun David Lee
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan, Republic of China (R.O.C)
| | - Ching-Yu Lai
- Graduate Institute of Microbiology, College of Medicine, NTU, Taipei, Taiwan, R.O.C
| | - Chuan-Liang Kao
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan, Republic of China (R.O.C)
| | - Chinglai Yang
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, 30322, United States of America
| | - Won-Bo Wang
- Graduate Institute of Microbiology, College of Medicine, NTU, Taipei, Taiwan, R.O.C
| | - Chwan-Chuen King
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan, Republic of China (R.O.C)
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Challenges and Strategies of Laboratory Diagnosis for Newly Emerging Influenza Viruses in Taiwan: A Decade after SARS. BIOMED RESEARCH INTERNATIONAL 2015; 2015:805306. [PMID: 26290876 PMCID: PMC4531154 DOI: 10.1155/2015/805306] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 07/08/2015] [Indexed: 12/15/2022]
Abstract
Since the first case of severe acute respiratory syndrome (SARS) in Taiwan was identified in March 2003, viral respiratory infections, in particular the influenza virus, have become a national public health concern. Taiwan would face a serious threat of public health problems if another SARS epidemic overlapped with a flu outbreak. After SARS, the Taiwan Centers for Disease Control accelerated and strengthened domestic research on influenza and expanded the exchange of information with international counterparts. The capacity of influenza A to cross species barriers presents a potential threat to human health. Given the mutations of avian flu viruses such as H7N9, H6N1, and H10N8, all countries, including Taiwan, must equip themselves to face a possible epidemic or pandemic. Such preparedness requires global collaboration.
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Early detection for cases of enterovirus- and influenza-like illness through a newly established school-based syndromic surveillance system in Taipei, January 2010 ~ August 2011. PLoS One 2015; 10:e0122865. [PMID: 25875080 PMCID: PMC4398411 DOI: 10.1371/journal.pone.0122865] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 02/16/2015] [Indexed: 11/19/2022] Open
Abstract
School children may transmit pathogens with cluster cases occurring on campuses and in families. In response to the 2009 influenza A (H1N1) pandemic, Taipei City Government officials developed a School-based Infectious Disease Syndromic Surveillance System (SID-SSS). Teachers and nurses from preschools to universities in all 12 districts within Taipei are required to daily report cases of symptomatic children or sick leave requests through the SID-SSS. The pre-diagnosis at schools is submitted firstly as common pediatric disease syndrome-groups and re-submitted after confirmation by physicians. We retrieved these data from January 2010 to August 2011 for spatio-temporal analysis and evaluated the temporal trends with cases obtained from both the Emergency Department-based Syndromic Surveillance System (ED-SSS) and the Longitudinal Health Insurance Database 2005 (LHID2005). Through the SID-SSS, enterovirus-like illness (EVI) and influenza-like illness (ILI) were the two most reported syndrome groups (77.6% and 15.8% among a total of 19,334 cases, respectively). The pre-diagnosis judgments made by school teachers and nurses showed high consistency with physicians' clinical diagnoses for EVI (97.8%) and ILI (98.9%). Most importantly, the SID-SSS had better timeliness with earlier peaks of EVI and ILI than those in the ED-SSS. Furthermore, both of the syndrome groups in these two surveillance systems had the best correlation reaching 0.98 and 0.95, respectively (p<0.01). Spatio-temporal analysis observed the patterns of EVI and ILI both diffuse from the northern suburban districts to central Taipei, with ILI spreading faster. This novel system can identify early suspected cases of two important pediatric infections occurring at schools, and clusters from schools/families. It was also cost-effective (95.5% of the operation cost reduced and 59.7% processing time saved). The timely surveillance of mild EVI and ILI cases integrated with spatial analysis may help public health decision-makers with where to target for enhancing surveillance and prevention measures to minimize severe cases.
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Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. J Virol 2014; 88:13269-83. [PMID: 25210166 PMCID: PMC4249111 DOI: 10.1128/jvi.01636-14] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The influenza pandemic that emerged in 2009 provided an unprecedented opportunity to study adaptation of a virus recently acquired from an animal source during human transmission. In the United Kingdom, the novel virus spread in three temporally distinct waves between 2009 and 2011. Phylogenetic analysis of complete viral genomes showed that mutations accumulated over time. Second- and third-wave viruses replicated more rapidly in human airway epithelial (HAE) cells than did the first-wave virus. In infected mice, weight loss varied between viral isolates from the same wave but showed no distinct pattern with wave and did not correlate with viral load in the mouse lungs or severity of disease in the human donor. However, second- and third-wave viruses induced less alpha interferon in the infected mouse lungs. NS1 protein, an interferon antagonist, had accumulated several mutations in second- and third-wave viruses. Recombinant viruses with the third-wave NS gene induced less interferon in human cells, but this alone did not account for increased virus fitness in HAE cells. Mutations in HA and NA genes in third-wave viruses caused increased binding to α-2,6-sialic acid and enhanced infectivity in human mucus. A recombinant virus with these two segments replicated more efficiently in HAE cells. A mutation in PA (N321K) enhanced polymerase activity of third-wave viruses and also provided a replicative advantage in HAE cells. Therefore, multiple mutations allowed incremental changes in viral fitness, which together may have contributed to the apparent increase in severity of A(H1N1)pdm09 influenza virus during successive waves. IMPORTANCE Although most people infected with the 2009 pandemic influenza virus had mild or unapparent symptoms, some suffered severe and devastating disease. The reasons for this variability were unknown, but the numbers of severe cases increased during successive waves of human infection in the United Kingdom. To determine the causes of this variation, we studied genetic changes in virus isolates from individual hospitalized patients. There were no consistent differences between these viruses and those circulating in the community, but we found multiple evolutionary changes that in combination over time increased the virus's ability to infect human cells. These adaptations may explain the remarkable ability of A(H1N1)pdm09 virus to continue to circulate despite widespread immunity and the apparent increase in severity of influenza over successive waves of infection.
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Sitaras I, Kalthoff D, Beer M, Peeters B, de Jong MCM. Immune escape mutants of Highly Pathogenic Avian Influenza H5N1 selected using polyclonal sera: identification of key amino acids in the HA protein. PLoS One 2014; 9:e84628. [PMID: 24586231 PMCID: PMC3934824 DOI: 10.1371/journal.pone.0084628] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 11/16/2013] [Indexed: 11/19/2022] Open
Abstract
Evolution of Avian Influenza (AI) viruses--especially of the Highly Pathogenic Avian Influenza (HPAI) H5N1 subtype--is a major issue for the poultry industry. HPAI H5N1 epidemics are associated with huge economic losses and are sometimes connected to human morbidity and mortality. Vaccination (either as a preventive measure or as a means to control outbreaks) is an approach that splits the scientific community, due to the risk of it being a potential driving force in HPAI evolution through the selection of mutants able to escape vaccination-induced immunity. It is therefore essential to study how mutations are selected due to immune pressure. To this effect, we performed an in vitro selection of mutants from HPAI A/turkey/Turkey/1/05 (H5N1), using immune pressure from homologous polyclonal sera. After 42 rounds of selection, we identified 5 amino acid substitutions in the Haemagglutinin (HA) protein, most of which were located in areas of antigenic importance and suspected to be prone to selection pressure. We report that most of the mutations took place early in the selection process. Finally, our antigenic cartography studies showed that the antigenic distance between the selected isolates and their parent strain increased with passage number.
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Affiliation(s)
- Ioannis Sitaras
- Quantitative Veterinary Epidemiology, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
- Department of Virology, Central Veterinary Institute of Wageningen University and Research Centre, Lelystad, The Netherlands
| | - Donata Kalthoff
- Institute of Diagnostic Virology, Friedrich-Loeffler Institut, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler Institut, Greifswald-Insel Riems, Germany
| | - Ben Peeters
- Department of Virology, Central Veterinary Institute of Wageningen University and Research Centre, Lelystad, The Netherlands
| | - Mart C. M. de Jong
- Quantitative Veterinary Epidemiology, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
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Abstract
UNLABELLED The noncovalent interactions that mediate trimerization of the influenza hemagglutinin (HA) are important determinants of its biological activities. Recent studies have demonstrated that mutations in the HA trimer interface affect the thermal and pH sensitivities of HA, suggesting a possible impact on vaccine stability (). We used size exclusion chromatography analysis of recombinant HA ectodomain to compare the differences among recombinant trimeric HA proteins from early 2009 pandemic H1N1 viruses, which dissociate to monomers, with those of more recent virus HAs that can be expressed as trimers. We analyzed differences among the HA sequences and identified intermolecular interactions mediated by the residue at position 374 (HA0 numbering) of the HA2 subdomain as critical for HA trimer stability. Crystallographic analyses of HA from the recent H1N1 virus A/Washington/5/2011 highlight the structural basis for this observed phenotype. It remains to be seen whether more recent viruses with this mutation will yield more stable vaccines in the future. IMPORTANCE Hemagglutinins from the early 2009 H1N1 pandemic viruses are unable to maintain a trimeric complex when expressed in a recombinant system. However, HAs from 2010 and 2011 strains are more stable, and our work highlights that the improvement in stability can be attributed to an E374K substitution in the HA2 subunit of the stalk that emerged naturally in the circulating viruses.
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Radomski JP, Płoński P, Zagórski-Ostoja W. The hemagglutinin mutation E391K of pandemic 2009 influenza revisited. Mol Phylogenet Evol 2014; 70:29-36. [DOI: 10.1016/j.ympev.2013.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 08/25/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
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Evolution of the hemagglutinin protein of the new pandemic H1N1 influenza virus: maintaining optimal receptor binding by compensatory substitutions. J Virol 2013; 87:13868-77. [PMID: 24109242 DOI: 10.1128/jvi.01955-13] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pandemic influenza A H1N1 (pH1N1) virus emerged in 2009. In the subsequent 4 years, it acquired several genetic changes in its hemagglutinin (HA). Mutations may be expected while virus is adapting to the human host or upon evasion from adaptive immune responses. However, pH1N1 has not displayed any major antigenic changes so far. We examined the effect of the amino acid substitutions found to be most frequently occurring in the pH1N1 HA protein before 1 April 2012 on the receptor-binding properties of the virus by using recombinant soluble HA trimers. Two changes (S186P and S188T) were shown to increase the receptor-binding avidity of HA, whereas two others (A137T and A200T) decreased binding avidity. Construction of an HA protein tree revealed the worldwide emergence of several HA variants during the past few influenza seasons. Strikingly, two major variants harbor combinations of substitutions (S186P/A137T and S188T/A200T, respectively) with opposite individual effects on binding. Stepwise reconstruction of the HA proteins of these variants demonstrated that the mutations that increase receptor-binding avidity are compensated for by the acquisition of subsequent mutations. The combination of these substitutions restored the receptor-binding properties (avidity and specificity) of these HA variants to those of the parental virus. The results strongly suggest that the HA of pH1N1 was already optimally adapted to the human host upon its emergence in April 2009. Moreover, these results are in agreement with a recent model for antigenic drift, in which influenza A virus mutants with high and low receptor-binding avidity alternate.
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Pham VL, Nakayama M, Itoh Y, Ishigaki H, Kitano M, Arikata M, Ishida H, Kitagawa N, Shichinohe S, Okamatsu M, Sakoda Y, Tsuchiya H, Nakamura S, Kida H, Ogasawara K. Pathogenicity of pandemic H1N1 influenza A virus in immunocompromised cynomolgus macaques. PLoS One 2013; 8:e75910. [PMID: 24086663 PMCID: PMC3781065 DOI: 10.1371/journal.pone.0075910] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 08/20/2013] [Indexed: 01/20/2023] Open
Abstract
Pandemic (H1N1) 2009 influenza virus spread throughout the world since most people did not have immunity against the virus. In the post pandemic phase when many humans might possess immunity against the pandemic virus, one of the concerns is infection in immunocompromised people. Therefore, we used an immunosuppressed macaque model to examine pathogenicity of the pandemic (H1N1) 2009 virus under an immunocompromised condition. The virus in nasal samples of immunosuppressed macaques infected with the pandemic (H1N1) 2009 virus was detected longer after infection than was the virus in nasal samples of immunocompetent macaques. As expected, not only virus amounts but also virus propagation sites in the immunosuppressed macaques were larger than those in lungs of the immunocompetent macaques when they were infected with the pandemic virus. Immunosuppressed macaques possessed low levels of immune cells producing cytokines and chemokines, but levels of inflammatory cytokines/chemokine interleukin (IL)-6, IL-18, and monocyte chemotactic protein (MCP)-1 in lungs of the immunosuppressed macaques were higher than those in lungs of the immunocompetent macaques, though the differences were not statistically significant. Therefore, under an immunosuppressive condition, the pandemic influenza (H1N1) 2009 virus might cause more severe morbidity with high cytokine/chemokine production by the host innate immune system than that seen in macaques under the immunocompetent condition.
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Affiliation(s)
- Van Loi Pham
- Division of Pathology and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Misako Nakayama
- Division of Pathology and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Yasushi Itoh
- Division of Pathology and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
- * E-mail:
| | - Hirohito Ishigaki
- Division of Pathology and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Mitsutaka Kitano
- Division of Pathology and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Masahiko Arikata
- Division of Pathology and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
- Department of Otorhinolaryngology-Head and Neck Surgery, Shiga University of Medical Science, Otsu, Japan
| | - Hideaki Ishida
- Division of Pathology and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Naoko Kitagawa
- Division of Pathology and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Shintaro Shichinohe
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Masatoshi Okamatsu
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Hideaki Tsuchiya
- Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Japan
| | - Shinichiro Nakamura
- Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Japan
| | - Hiroshi Kida
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kazumasa Ogasawara
- Division of Pathology and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
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26
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Moussi AE, Kacem MABH, Pozo F, Ledesma J, Cuevas MT, Casas I, Slim A. Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. Diagn Pathol 2013; 8:124. [PMID: 23902660 PMCID: PMC3751102 DOI: 10.1186/1746-1596-8-124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 03/10/2013] [Indexed: 01/24/2023] Open
Abstract
Background The novel pandemic A (H1N1) pdm09 virus was first identified in Mexico in April 2009 and since then it spread worldwide over a short period of time. Although the virus infection is generally associated with mild disease and a relatively low mortality, it is projected that mutations in specific regions of the viral genome, especially within the receptor binding domain of the haemagglutinin (HA) protein could result in more virulent virus stains, leading to a more severe pathogenicity. Methods To monitor the genetic polymorphisms at position 222 of Haemagglutinin of influenza A(H1N1)pdm09 viruses from both outpatients with mild influenza and individuals with severe disease requiring hospitalization, during 2009–2010 and 2010–2011 seasons, a sequence-based genotypic assessment of viral populations to understand the prevalence of D222G mutation. Results The D222G was identified in clinical specimens from 3 out of 42 cases analyzed in Tunisia with severe outcome (7%). Interestingly, in one fatal case out of four viruses taken from fatal cases studied (25%). Also this mutation was found in one mild case out of 8 mild cases studied (0.1%). D222E substitution was found in virus taken from one patient with severe clinical syndrome (2%) out of 42 severe cases analyzed and E374K substitution was found in two severe cases (4%) out of 42 severe cases studied. Conclusions A specific mutation in the viral haemagglutinin (D222G) was found in fatal, severe and mild case. Further virological, clinical and epidemiological investigations are needed to ascertain the role of this and other mutations that may alter the virulence and transmissibility of the pandemic influenza A (H1N1)pdm09. Virtual Slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1027334947811255
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Affiliation(s)
- Awatef El Moussi
- National Influenza Centre-Tunis, Unit Virology, Microbiology Laboratory, Charles Nicolle’s Hospital, Tunis, Tunisia
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27
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Jiménez-Alberto A, Alvarado-Facundo E, Ribas-Aparicio RM, Castelán-Vega JA. Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. PLoS One 2013; 8:e70005. [PMID: 23894575 PMCID: PMC3720954 DOI: 10.1371/journal.pone.0070005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 06/17/2013] [Indexed: 12/17/2022] Open
Abstract
Hemagglutinin is the major surface glycoprotein of influenza viruses. It participates in the initial steps of viral infection through receptor binding and membrane fusion events. The influenza pandemic of 2009 provided a unique scenario to study virus evolution. We performed molecular dynamics simulations with four hemagglutinin variants that appeared throughout the 2009 influenza A (H1N1) pandemic. We found that variant 1 (S143G, S185T) likely arose to avoid immune recognition. Variant 2 (A134T), and variant 3 (D222E, P297S) had an increased binding affinity for the receptor. Finally, variant 4 (E374K) altered hemagglutinin stability in the vicinity of the fusion peptide. Variants 1 and 4 have become increasingly predominant, while variants 2 and 3 declined as the pandemic progressed. Our results show some of the different strategies that the influenza virus uses to adapt to the human host and provide an example of how selective pressure drives antigenic drift in viral proteins.
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MESH Headings
- Adaptation, Physiological/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/metabolism
- Humans
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/metabolism
- Influenza A Virus, H1N1 Subtype/physiology
- Influenza Pandemic, 1918-1919
- Influenza, Human/epidemiology
- Influenza, Human/virology
- Molecular Dynamics Simulation
- Molecular Epidemiology
- Static Electricity
- Surface Properties
- Thermodynamics
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Affiliation(s)
- Alicia Jiménez-Alberto
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Distrito Federal, Mexico City, Mexico
| | - Esmeralda Alvarado-Facundo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Distrito Federal, Mexico City, Mexico
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, Maryland, United States of America
| | - Rosa María Ribas-Aparicio
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Distrito Federal, Mexico City, Mexico
| | - Juan A. Castelán-Vega
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Distrito Federal, Mexico City, Mexico
- * E-mail:
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28
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Lan YC, Su MC, Chen CH, Huang SH, Chen WL, Tien N, Lin CW. Epidemiology of pandemic influenza A/H1N1 virus during 2009-2010 in Taiwan. Virus Res 2013; 177:46-54. [PMID: 23886669 DOI: 10.1016/j.virusres.2013.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 06/14/2013] [Accepted: 07/11/2013] [Indexed: 11/15/2022]
Abstract
Outbreak of swine-origin influenza A/H1N1 virus (pdmH1N1) occurred in 2009. Taiwanese authorities implemented nationwide vaccinations with pdmH1N1-specific inactivated vaccine as of November 2009. This study evaluates prevalence, HA phylogenetic relationship, and transmission dynamic of influenza A and B viruses in Taiwan in 2009-2010. Respiratory tract specimens were analyzed for influenza A and B viruses. The pdmH1N1 peaked in November 2009, was predominant from August 2009 to January 2010, then sharply dropped in February 2010. Significant prevalence peaks of influenza B in April-June of 2010 and H3N2 virus in July and August were observed. Highest percentage of pdmH1N1- and H3N2-positive cases appeared among 11-15-year-olds; influenza B-positive cases were dominant among those 6-10 years old. Maximum likelihood phylogenetic trees showed 11 unique clusters of pdmH1N1, seasonal H3N2 influenza A and B viruses, as well as transmission clusters and mixed infections of influenza strains in Taiwan. The 2009 pdmH1N1 virus was predominant in Taiwan from August 2009 to January 2010; seasonal H3N2 influenza A and B viruses exhibited small prevalence peaks after nationwide vaccinations. Phylogenetic evidence indicated transmission clusters and multiple independent clades of co-circulating influenza A and B strains in Taiwan.
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Affiliation(s)
- Yu-Ching Lan
- Department of Health Risk Management, School of Public, China Medical University, Taichung, Taiwan
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29
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Chandra S, Kassens-Noor E, Kuljanin G, Vertalka J. A geographic analysis of population density thresholds in the influenza pandemic of 1918-19. Int J Health Geogr 2013; 12:9. [PMID: 23425498 PMCID: PMC3641965 DOI: 10.1186/1476-072x-12-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 01/13/2013] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Geographic variables play an important role in the study of epidemics. The role of one such variable, population density, in the spread of influenza is controversial. Prior studies have tested for such a role using arbitrary thresholds for population density above or below which places are hypothesized to have higher or lower mortality. The results of such studies are mixed. The objective of this study is to estimate, rather than assume, a threshold level of population density that separates low-density regions from high-density regions on the basis of population loss during an influenza pandemic. We study the case of the influenza pandemic of 1918-19 in India, where over 15 million people died in the short span of less than one year. METHODS Using data from six censuses for 199 districts of India (n=1194), the country with the largest number of deaths from the influenza of 1918-19, we use a sample-splitting method embedded within a population growth model that explicitly quantifies population loss from the pandemic to estimate a threshold level of population density that separates low-density districts from high-density districts. RESULTS The results demonstrate a threshold level of population density of 175 people per square mile. A concurrent finding is that districts on the low side of the threshold experienced rates of population loss (3.72%) that were lower than districts on the high side of the threshold (4.69%). CONCLUSIONS This paper introduces a useful analytic tool to the health geographic literature. It illustrates an application of the tool to demonstrate that it can be useful for pandemic awareness and preparedness efforts. Specifically, it estimates a level of population density above which policies to socially distance, redistribute or quarantine populations are likely to be more effective than they are for areas with population densities that lie below the threshold.
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Affiliation(s)
- Siddharth Chandra
- Asian Studies Center, Michigan State University, 427 N Shaw Lane, Room 301, East Lansing, MI, 48824, USA
| | - Eva Kassens-Noor
- Urban and Transport Planning in the School of Planning, Design, and Construction and Global Urban Studies Program, 552 W Circle Drive, Room 201E, East Lansing, MI, 48824, USA
| | - Goran Kuljanin
- Department of Psychology, Psychology Building 316 Physics Room 262, East Lansing, MI, 48824, USA
| | - Joshua Vertalka
- Department of Geography, 673 Auditorium Road, Room 116, East Lansing, MI, 48824, USA
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30
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Phenotypic differences in virulence and immune response in closely related clinical isolates of influenza A 2009 H1N1 pandemic viruses in mice. PLoS One 2013; 8:e56602. [PMID: 23441208 PMCID: PMC3575477 DOI: 10.1371/journal.pone.0056602] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/14/2013] [Indexed: 01/07/2023] Open
Abstract
To capture the possible genotypic and phenotypic differences of the 2009 influenza A virus H1N1 pandemic (H1N1pdm) strains circulating in adult hospitalized patients, we isolated and sequenced nine H1N1pdm viruses from patients hospitalized during 2009–2010 with severe influenza pneumonia in Kentucky. Each viral isolate was characterized in mice along with two additional H1N1 pandemic strains and one seasonal strain to assess replication and virulence. All isolates showed similar levels of replication in nasal turbinates and lung, but varied in their ability to cause morbidity. Further differences were identified in cytokine and chemokine responses. IL-6 and KC were expressed early in mice infected with strains associated with higher virulence. Strains that showed lower pathogenicity in mice had greater IFNγ, MIG, and IL-10 responses. A principal component analysis (PCA) of the cytokine and chemokine profiles revealed 4 immune response phenotypes that correlated with the severity of disease. A/KY/180/10, which showed the greatest virulence with a rapid onset of disease progression, was compared in additional studies with A/KY/136/09, which showed low virulence in mice. Analyses comparing a low (KY/136) versus a high (KY/180) virulent isolate showed a significant difference in the kinetics of infection within the lower respiratory tract and immune responses. Notably by 4 DPI, virus titers within the lung, bronchoalveolar lavage fluid (BALf), and cells within the BAL (BALc) revealed that the KY/136 replicated in BALc, while KY/180 replication persisted in lungs and BALc. In summary, our studies suggest four phenotypic groups based on immune responses that result in different virulence outcomes in H1N1pdm isolates with a high degree of genetic similarity. In vitro studies with two of these isolates suggested that the more virulent isolate, KY/180, replicates productively in macrophages and this may be a key determinant in tipping the response toward a more severe disease progression.
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