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Muhammad Azami NA, Abdullah N, Kamalul Ariffin AS, Abdullah MS, Dauni A, Kamaruddin MA, Jamal R. Hepatitis B and influenza vaccination coverage in healthcare workers, the elderly, and patients with diabetes in Malaysia. Hum Vaccin Immunother 2023; 19:2170660. [PMID: 36728847 PMCID: PMC10012949 DOI: 10.1080/21645515.2023.2170660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Adult immunization remains to be a neglected issue in developing countries including Malaysia. This nationwide study determined the vaccination coverage of hepatitis B and influenza among Malaysia's healthcare workers (HCWs), the elderly (aged 60 y and above) and patients with diabetes, who are the participants of The Malaysia Cohort Program. The participants were categorized based on their occupation, age and medical history. Self-reported questionnaire was used to assess the participant's hepatitis B and influenza vaccination status. A Chi-square test and logistic regression analyses were performed to determine the risk factors associated with vaccination behavior. The hepatitis B vaccination coverage for healthcare workers, elderly, and patients with diabetes were 34.6%, 10.1% and 9.8%, respectively. The influenza vaccination coverage rates for healthcare workers, the elderly and patients with diabetes were 26.3%, 5.5% and 6.4%, respectively. The Chinese were more likely to be vaccinated against hepatitis B, while Malay was more likely to be vaccinated against influenza. Individuals with higher education and living in urban areas were more likely vaccinated than those with low education levels and who lived in rural areas. The low vaccination coverage for healthcare workers was alarming because hepatitis B and influenza were subsidized for the healthcare workers. The hepatitis B and influenza vaccination coverage among healthcare workers, elderly and patients with diabetes in Malaysia were low. Specific interventions such as educational and awareness programs should be conducted to increase the vaccination rate among adults, especially those at high risk.
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Affiliation(s)
| | - Noraidatulakma Abdullah
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | | | - Mohd Shaharom Abdullah
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Andri Dauni
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Mohd Arman Kamaruddin
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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2
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Heider A, Wedde M, Dürrwald R, Wolff T, Schweiger B. Molecular characterization and evolution dynamics of influenza B viruses circulating in Germany from season 1996/1997 to 2019/2020. Virus Res 2022; 322:198926. [PMID: 36096395 DOI: 10.1016/j.virusres.2022.198926] [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: 07/07/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 12/24/2022]
Abstract
Influenza B viruses are responsible for significant disease burden caused by viruses of both the Yamagata- and Victoria-lineage. Since the circulating patterns of influenza B viruses in different countries vary we investigated molecular properties and evolution dynamics of influenza B viruses circulating in Germany between 1996 and 2020. A change of the dominant lineage occurred in Germany in seven seasons in over past 25 years. A total of 676 sequences of hemagglutinin coding domain 1 (HA1) and 516 sequences of neuraminidase (NA) genes of Yamagata- and Victoria-lineage viruses were analyzed using time-scaled phylogenetic tree. Phylogenetic analysis demonstrated that Yamagata-lineage viruses are more diverse than the Victoria-lineage viruses and could be divided into nine genetic groups whereas Victoria-lineage viruses presented six genetic groups. Comparative phylogenetic analyses of both the HA and NA segments together revealed a number of inter-lineage as well as inter- and intra-clade reassortants. We identified key amino acid substitutions in major HA epitopes such as in four antigenic sites and receptor-binding sites (RBS) and in the regions close to them, with most substitutions in the 120-loop of both lineage viruses. Altogether, seventeen substitutions were fixed over time within the Yamagata-lineage with twelve of them in the antigenic sites. Thirteen substitutions were identified within the Victoria-lineage, with eleven of them in the antigenic sites. Moreover, all Victoria-lineage viruses of the 2017/2018 season were characterized by a deletion of two amino acids at the position 162-163 in the antigenic site of HA1. The viruses with triple deletion Δ162-164 were found in Germany since season 2018/2019. We highlighted the interplay between substitutions in the glycosylation sites and RBS and antigenic epitope during HA evolution. The results obtained underscore the need for continuous monitoring of circulating influenza B viruses. Early detection of strains with genetic and antigenic variation is essential to predict the circulation patterns for the following season. Such information is important for the development of optimal vaccines and strategies for prevention and control of influenza.
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Affiliation(s)
- Alla Heider
- Division of Influenza Viruses and Other Respiratory Viruses, National Reference Centre for Influenza, Robert Koch-Institute, Seestrasse 10, Berlin 13353, Germany.
| | - Marianne Wedde
- Division of Influenza Viruses and Other Respiratory Viruses, National Reference Centre for Influenza, Robert Koch-Institute, Seestrasse 10, Berlin 13353, Germany
| | - Ralf Dürrwald
- Division of Influenza Viruses and Other Respiratory Viruses, National Reference Centre for Influenza, Robert Koch-Institute, Seestrasse 10, Berlin 13353, Germany
| | - Thorsten Wolff
- Division of Influenza Viruses and Other Respiratory Viruses, National Reference Centre for Influenza, Robert Koch-Institute, Seestrasse 10, Berlin 13353, Germany
| | - Brunhilde Schweiger
- Division of Influenza Viruses and Other Respiratory Viruses, National Reference Centre for Influenza, Robert Koch-Institute, Seestrasse 10, Berlin 13353, Germany
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3
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Kou Z, Fan X, Li J, Shao Z, Qiang X. Using amino acid features to identify the pathogenicity of influenza B virus. Infect Dis Poverty 2022; 11:50. [PMID: 35509019 PMCID: PMC9066401 DOI: 10.1186/s40249-022-00974-0] [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: 02/18/2022] [Accepted: 04/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Influenza B virus can cause epidemics with high pathogenicity, so it poses a serious threat to public health. A feature representation algorithm is proposed in this paper to identify the pathogenicity phenotype of influenza B virus. METHODS The dataset included all 11 influenza virus proteins encoded in eight genome segments of 1724 strains. Two types of features were hierarchically used to build the prediction model. Amino acid features were directly delivered from 67 feature descriptors and input into the random forest classifier to output informative features about the class label and probabilistic prediction. The sequential forward search strategy was used to optimize the informative features. The final features for each strain had low dimensions and included knowledge from different perspectives, which were used to build the machine learning model for pathogenicity identification. RESULTS The 40 signature positions were achieved by entropy screening. Mutations at position 135 of the hemagglutinin protein had the highest entropy value (1.06). After the informative features were directly generated from the 67 random forest models, the dimensions for class and probabilistic features were optimized as 4 and 3, respectively. The optimal class features had a maximum accuracy of 94.2% and a maximum Matthews correlation coefficient of 88.4%, while the optimal probabilistic features had a maximum accuracy of 94.1% and a maximum Matthews correlation coefficient of 88.2%. The optimized features outperformed the original informative features and amino acid features from individual descriptors. The sequential forward search strategy had better performance than the classical ensemble method. CONCLUSIONS The optimized informative features had the best performance and were used to build a predictive model so as to identify the phenotype of influenza B virus with high pathogenicity and provide early risk warning for disease control.
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Affiliation(s)
- Zheng Kou
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, 510006, China.
| | - Xinyue Fan
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, 510006, China
| | - Junjie Li
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, 510006, China
| | - Zehui Shao
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, 510006, China
| | - Xiaoli Qiang
- School of Computer Science and Cyber Engineering, Guangzhou University, Guangzhou, 510006, China.
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4
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Phung VLH, Ueda K, Sahani M, Seposo XT, Wan Mahiyuddin WR, Honda A, Takano H. Investigation of association between smoke haze and under-five mortality in Malaysia, accounting for time lag, duration and intensity. Int J Epidemiol 2021; 51:155-165. [PMID: 34148080 DOI: 10.1093/ije/dyab100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/22/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Studies on the association between smoke haze (hereafter 'haze') and adverse health effects have increased in recent years due to extreme weather conditions and the increased occurrence of vegetation fires. The possible adverse health effects on under-five children (U5Y) is especially worrying due to their vulnerable condition. Despite continuous repetition of serious haze occurrence in Southeast Asia, epidemiological studies in this region remained scarce. Furthermore, no study had examined the association accounting for three important aspects (time lag, duration and intensity) concurrently. OBJECTIVE This study aimed to examine the association between haze and U5Y mortality in Malaysia, considering time lag, duration and intensity of exposure. METHODS We performed a time-stratified case-crossover study using a generalized additive model to examine the U5Y mortality related to haze in 12 districts in Malaysia, spanning from 2014 to 2016. A 'haze day' was characterized by intensity [based on concentrations of particulate matter (PM)] and duration (continuity of haze occurrence, up to 3 days). RESULTS We observed the highest but non-significant odds ratios (ORs) of U5Y mortality at lag 4 of Intensity-3. Lag patterns revealed the possibility of higher acuteness at prolonged and intensified haze. Stratifying the districts by the 95th-percentile of PM distribution, the 'low' category demonstrated marginal positive association at Intensity-2 Duration-3 [OR: 1.210 (95% confidence interval: 1.000, 1.464)]. CONCLUSIONS We found a null association between haze and U5Y mortality. The different lag patterns of the association observed over different duration and intensity suggest consideration of these aspects in future studies.
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Affiliation(s)
- Vera Ling Hui Phung
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan.,Center for Climate Change Adaptation, National Institute for Environmental Studies, Tsukuba, Japan
| | - Kayo Ueda
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan.,Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Mazrura Sahani
- Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Xerxes Tesoro Seposo
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan.,Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan.,School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Wan Rozita Wan Mahiyuddin
- Environmental Health Research Center, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Malaysia
| | - Akiko Honda
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan.,Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Hirohisa Takano
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan.,Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
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5
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Zhang C, Cui H, Wang Z, Dong S, Zhang C, Li J, Meng K, Sun Y, Liu J, Guo Z, Chen L. Pathogenicity and transmissibility assessment of two strains of human influenza virus isolated in China in 2018. J Int Med Res 2021; 49:300060520982832. [PMID: 33472481 PMCID: PMC7829534 DOI: 10.1177/0300060520982832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Influenza season occurs every year in China, but its presentation was unusual in the period from December 2017 to early 2018. During this period, influenza activity was increasing across the country and was much greater than during the same period in previous years, with great harm to people's health. METHODS In this study, we isolated two human influenza virus strains-A/Hebei/F076/2018(H1N1) and B/Hebei/16275B/2018-from patients with severe influenza in Hebei, China, during the flu season in January 2018, and explored their genetic characteristics, pathogenicity, and transmissibility. RESULTS A/Hebei/F076/2018(H1N1) belongs to the human-like H1N1 influenza virus lineage, whereas B/Hebei/16275B/2018 belongs to the Victoria lineage and is closely related to the World Health Organization reference strain B/Brisbane/60/2008. Pathogenicity tests revealed that A/Hebei/F076/2018(H1N1) replicated much more strongly in mice, with mice exhibiting 40% mortality, whereas B/Hebei/16275B/2018 was not lethal. Both viruses could be transmitted through direct contact and by the aerosol route between guinea pigs, but the H1N1 strain exhibited higher airborne transmissibility. CONCLUSIONS These results may contribute to the monitoring of influenza mutation and the prevention of an influenza outbreak.
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Affiliation(s)
- Cheng Zhang
- College of Veterinary Medicine, Hebei Agricultural University,
Baoding, Hebei, China
| | - Huan Cui
- College of Veterinary Medicine, Hebei Agricultural University,
Baoding, Hebei, China
| | - Zhongyi Wang
- Institute of Military Veterinary, Academy of Military Medical
Sciences, Changchun, Jilin, China
| | - Shishan Dong
- College of Veterinary Medicine, Hebei Agricultural University,
Baoding, Hebei, China
| | - Chunmao Zhang
- Institute of Military Veterinary, Academy of Military Medical
Sciences, Changchun, Jilin, China
| | - Jiaming Li
- Institute of Military Veterinary, Academy of Military Medical
Sciences, Changchun, Jilin, China
| | - Keyin Meng
- Institute of Military Veterinary, Academy of Military Medical
Sciences, Changchun, Jilin, China
| | - Yucheng Sun
- Institute of Military Veterinary, Academy of Military Medical
Sciences, Changchun, Jilin, China
| | - Juxiang Liu
- College of Veterinary Medicine, Hebei Agricultural University,
Baoding, Hebei, China
| | - Zhendong Guo
- Institute of Military Veterinary, Academy of Military Medical
Sciences, Changchun, Jilin, China
| | - Ligong Chen
- College of Veterinary Medicine, Hebei Agricultural University,
Baoding, Hebei, China
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6
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Sam IC, Noraini W, Sandhu SS, Norizah I, Selvanesan S, Thayan R, Yusof MA, Hassan A, Jafar FL, Chan YF. Seasonal influenza activity based on laboratory surveillance in Malaysia, 2011-2016. J Med Virol 2018; 91:498-502. [PMID: 30199092 DOI: 10.1002/jmv.25313] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/06/2018] [Indexed: 01/16/2023]
Abstract
Influenza seasonality in equatorial countries is little understood. Seasonal and alert influenza thresholds were determined for Malaysia, using laboratory-based data obtained from the Malaysia Influenza Surveillance System and a major teaching hospital, from 2011 to 2016. Influenza was present year-round, with no clear annual seasons. Variable periods of higher transmission occurred inconsistently, in November to December, January to March, July to September, or a combination of these. These coincide with seasons in the nearby southeast Asian countries or winter seasons of the northern and southern hemispheres. Changes in the predominant circulating influenza type were only sometimes associated with increased transmission. The data can provide public health interventions such as vaccines.
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Affiliation(s)
- I-Ching Sam
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Wan Noraini
- Disease Control Division, Ministry of Health Malaysia, Putrajaya, Malaysia
| | | | - Ismail Norizah
- Virology Section, National Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Malaysia
| | - Sengol Selvanesan
- Virology Section, National Public Health Laboratory, Ministry of Health Malaysia, Sungai Buloh, Malaysia
| | - Ravindran Thayan
- Virology Unit, Institute for Medical Research, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Mohd Apandi Yusof
- Virology Unit, Institute for Medical Research, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Ardalinah Hassan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Faizatul Lela Jafar
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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7
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Jennings L, Huang QS, Barr I, Lee PI, Kim WJ, Buchy P, Sanicas M, Mungall BA, Chen J. Literature review of the epidemiology of influenza B disease in 15 countries in the Asia-Pacific region. Influenza Other Respir Viruses 2018; 12:383-411. [PMID: 29127742 PMCID: PMC5907823 DOI: 10.1111/irv.12522] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2017] [Indexed: 01/06/2023] Open
Abstract
Influenza control strategies focus on the use of trivalent influenza vaccines containing two influenza A virus subtypes and one of the two circulating influenza type B lineages (Yamagata or Victoria). Mismatches between the vaccine B lineage and the circulating lineage have been regularly documented in many countries, including those in the Asia‐Pacific region. We conducted a literature review with the aim of understanding the relative circulation of influenza B viruses in Asia‐Pacific countries. PubMed and Western Pacific Region Index Medicus were searched for relevant articles on influenza type B published since 1990 in English language for 15 Asia‐Pacific countries. Gray literature was also accessed. From 4834 articles identified, 121 full‐text articles were analyzed. Influenza was reported as an important cause of morbidity in the Asia‐Pacific region, affecting all age groups. In all 15 countries, influenza B was identified and associated with between 0% and 92% of laboratory‐confirmed influenza cases in any one season/year. Influenza type B appeared to cause more illness in children aged between 1 and 10 years than in other age groups. Epidemiological data for the two circulating influenza type B lineages remain limited in several countries in the Asia‐Pacific, although the co‐circulation of both lineages was seen in countries where strain surveillance data were available. Mismatches between circulating B lineages and vaccine strains were observed in all countries with available data. The data suggest that a shift from trivalent to quadrivalent seasonal influenza vaccines could provide additional benefits by providing broader protection.
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Affiliation(s)
- Lance Jennings
- Canterbury District Health Board, Christchurch, New Zealand
| | - Qiu Sue Huang
- WHO National Influenza Centre, Institute of Environmental Science and Research, Porirua, New Zealand
| | - Ian Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, VIC, Australia
| | - Ping-Ing Lee
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan
| | - Woo Joo Kim
- Department of Internal Medicine, Korea University Guro Hospital, Seoul, Korea
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8
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Langat P, Raghwani J, Dudas G, Bowden TA, Edwards S, Gall A, Bedford T, Rambaut A, Daniels RS, Russell CA, Pybus OG, McCauley J, Kellam P, Watson SJ. Genome-wide evolutionary dynamics of influenza B viruses on a global scale. PLoS Pathog 2017; 13:e1006749. [PMID: 29284042 PMCID: PMC5790164 DOI: 10.1371/journal.ppat.1006749] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/10/2018] [Accepted: 11/13/2017] [Indexed: 12/14/2022] Open
Abstract
The global-scale epidemiology and genome-wide evolutionary dynamics of influenza B remain poorly understood compared with influenza A viruses. We compiled a spatio-temporally comprehensive dataset of influenza B viruses, comprising over 2,500 genomes sampled worldwide between 1987 and 2015, including 382 newly-sequenced genomes that fill substantial gaps in previous molecular surveillance studies. Our contributed data increase the number of available influenza B virus genomes in Europe, Africa and Central Asia, improving the global context to study influenza B viruses. We reveal Yamagata-lineage diversity results from co-circulation of two antigenically-distinct groups that also segregate genetically across the entire genome, without evidence of intra-lineage reassortment. In contrast, Victoria-lineage diversity stems from geographic segregation of different genetic clades, with variability in the degree of geographic spread among clades. Differences between the lineages are reflected in their antigenic dynamics, as Yamagata-lineage viruses show alternating dominance between antigenic groups, while Victoria-lineage viruses show antigenic drift of a single lineage. Structural mapping of amino acid substitutions on trunk branches of influenza B gene phylogenies further supports these antigenic differences and highlights two potential mechanisms of adaptation for polymerase activity. Our study provides new insights into the epidemiological and molecular processes shaping influenza B virus evolution globally.
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Affiliation(s)
- Pinky Langat
- Wellcome Trust Sanger Institute, Hinxton, United
Kingdom
| | - Jayna Raghwani
- Department of Zoology, University of Oxford, Oxford, United
Kingdom
| | - Gytis Dudas
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh,
United Kingdom
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research
Center, Seattle, Washington, United States of America
| | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics,
University of Oxford, Oxford, United Kingdom
| | | | - Astrid Gall
- Wellcome Trust Sanger Institute, Hinxton, United
Kingdom
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research
Center, Seattle, Washington, United States of America
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh,
United Kingdom
- Fogarty International Center, National Institutes of Health, Bethesda,
Maryland, United States of America
| | - Rodney S. Daniels
- Worldwide Influenza Centre, The Francis Crick Institute, London, United
Kingdom
| | - Colin A. Russell
- Department of Veterinary Medicine, University of Cambridge, Cambridge,
United Kingdom
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United
Kingdom
| | - John McCauley
- Worldwide Influenza Centre, The Francis Crick Institute, London, United
Kingdom
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Hinxton, United
Kingdom
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9
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Oong XY, Ng KT, Tan JL, Chan KG, Kamarulzaman A, Chan YF, Sam IC, Tee KK. Whole-Genome Phylogenetic Analysis of Influenza B/Phuket/3073/2013-Like Viruses and Unique Reassortants Detected in Malaysia between 2012 and 2014. PLoS One 2017; 12:e0170610. [PMID: 28129386 PMCID: PMC5271328 DOI: 10.1371/journal.pone.0170610] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/06/2017] [Indexed: 11/19/2022] Open
Abstract
Reassortment of genetic segments between and within influenza B lineages (Victoria and Yamagata) has been shown to generate novel reassortants with unique genetic characteristics. Based on hemagglutinin (HA) and neuraminidase (NA) genes, recent surveillance study has identified reassortment properties in B/Phuket/3073/2013-like virus, which is currently used in the WHO-recommended influenza vaccine. To understand the potential reassortment patterns for all gene segments, four B/Phuket/3073/2013-like viruses and two unique reassortants (one each from Yamagata and Victoria) detected in Malaysia from 2012-2014 were subjected to whole-genome sequencing. Each gene was phylogenetically classified into lineages, clades and sub-clades. Three B/Phuket/3073/2013-like viruses from Yamagata lineage were found to be intra-clade reassortants, possessing PA and NA genes derived from Stockholm/12-like sub-clade, while the remaining genes from Wisconsin/01-like sub-clade (both sub-clades were within Yamagata Clade 3/Yam-3). However, the other B/Phuket/3073/2013-like virus had NS gene that derived from Stockholm/12-like sub-clade instead of Wisconsin/01-like sub-clade. One inter-clade reassortant had Yamagata Clade 2/Yam-2-derived HA and NP, and its remaining genes were Yam-3-derived. Within Victoria Clade 1/Vic-1 in Victoria lineage, one virus had intra-clade reassortment properties: HA and PB2 from Vic-1B sub-clade, MP and NS from a unique sub-clade "Vic-1C", and the remaining genes from Vic-1A sub-clade. Although random reassortment event may generate unique reassortants, detailed phylogenetic classification of gene segments showed possible genetic linkage between PA and NA genes in B/Phuket/3073/2013-like viruses, which requires further investigation. Understanding on reassortment patterns in influenza B evolution may contribute to future vaccine design.
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Affiliation(s)
- Xiang Yong Oong
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kim Tien Ng
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Joon Ling Tan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Adeeba Kamarulzaman
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - I-Ching Sam
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
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10
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Oong XY, Ng KT, Lam TTY, Pang YK, Chan KG, Hanafi NS, Kamarulzaman A, Tee KK. Epidemiological and Evolutionary Dynamics of Influenza B Viruses in Malaysia, 2012-2014. PLoS One 2015; 10:e0136254. [PMID: 26313754 PMCID: PMC4552379 DOI: 10.1371/journal.pone.0136254] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/01/2015] [Indexed: 12/16/2022] Open
Abstract
Epidemiological and evolutionary dynamics of influenza B Victoria and Yamagata lineages remained poorly understood in the tropical Southeast Asia region, despite causing seasonal outbreaks worldwide. From 2012-2014, nasopharyngeal swab samples collected from outpatients experiencing acute upper respiratory tract infection symptoms in Kuala Lumpur, Malaysia, were screened for influenza viruses using a multiplex RT-PCR assay. Among 2,010/3,935 (51.1%) patients infected with at least one respiratory virus, 287 (14.3%) and 183 (9.1%) samples were tested positive for influenza A and B viruses, respectively. Influenza-positive cases correlate significantly with meteorological factors-total amount of rainfall, relative humidity, number of rain days, ground temperature and particulate matter (PM10). Phylogenetic reconstruction of haemagglutinin (HA) gene from 168 influenza B viruses grouped them into Yamagata Clade 3 (65, 38.7%), Yamagata Clade 2 (48, 28.6%) and Victoria Clade 1 (55, 32.7%). With neuraminidase (NA) phylogeny, 30 intra-clade (29 within Yamagata Clade 3, 1 within Victoria Clade 1) and 1 inter-clade (Yamagata Clade 2-HA/Yamagata Clade 3-NA) reassortants were identified. Study of virus temporal dynamics revealed a lineage shift from Victoria to Yamagata (2012-2013), and a clade shift from Yamagata Clade 2 to Clade 3 (2013-2014). Yamagata Clade 3 predominating in 2014 consisted of intra-clade reassortants that were closely related to a recent WHO vaccine candidate strain (B/Phuket/3073/2013), with the reassortment event occurred approximately 2 years ago based on Bayesian molecular clock estimation. Malaysian Victoria Clade 1 viruses carried H274Y substitution in the active site of neuraminidase, which confers resistance to oseltamivir. Statistical analyses on clinical and demographic data showed Yamagata-infected patients were older and more likely to experience headache while Victoria-infected patients were more likely to experience nasal congestion and sore throat. This study describes the evolution of influenza B viruses in Malaysia and highlights the importance of continuous surveillance for better vaccination policy in this region.
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Affiliation(s)
- Xiang Yong Oong
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kim Tien Ng
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Tommy Tsan-Yuk Lam
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - Yong Kek Pang
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Nik Sherina Hanafi
- Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Adeeba Kamarulzaman
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Keng Tee
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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