1
|
Matsuzaki Y, Sugawara K, Kidoguchi Y, Kadowaki Y, Shimotai Y, Katsushima Y, Katsushima F, Tanaka S, Matoba Y, Komabayashi K, Aoki Y, Mizuta K. Genetic Reassortment in a Child Coinfected with Two Influenza B Viruses, B/Yamagata Lineage and B/Victoria-Lineage Strains. Viruses 2024; 16:983. [PMID: 38932274 PMCID: PMC11209448 DOI: 10.3390/v16060983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
We identified a child coinfected with influenza B viruses of B/Yamagata and B/Victoria lineages, in whom we analyzed the occurrence of genetic reassortment. Plaque purification was performed using a throat swab specimen from a 9-year-old child, resulting in 34 well-isolated plaques. The genomic composition of eight gene segments (HA, NA, PB1, PB2, PA, NP, M, and NS genes) for each plaque was determined at the lineage level. Of the 34 plaques, 21 (61.8%) had B/Phuket/3073/2013 (B/Yamagata)-like sequences in all gene segments, while the other 13 (38.2%) were reassortants with B/Texas/02/2013 (B/Victoria)-like sequences in 1-5 of the 8 segments. The PB1 segment had the most B/Victoria lineage genes (23.5%; 8 of 34 plaques), while PB2 and PA had the least (2.9%; 1 of 34 plaques). Reassortants with B/Victoria lineage genes in 2-5 segments showed the same level of growth as viruses with B/Yamagata lineage genes in all segments. However, reassortants with B/Victoria lineage genes only in the NA, PB1, NP, or NS segments exhibited reduced or undetectable growth. We demonstrated that various gene reassortments occurred in a child. These results suggest that simultaneous outbreaks of two influenza B virus lineages increase genetic diversity and could promote the emergence of new epidemic strains.
Collapse
Affiliation(s)
- Yoko Matsuzaki
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan; (K.S.); (Y.K.); (Y.K.); (Y.S.)
| | - Kanetsu Sugawara
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan; (K.S.); (Y.K.); (Y.K.); (Y.S.)
| | - Yuko Kidoguchi
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan; (K.S.); (Y.K.); (Y.K.); (Y.S.)
| | - Yoko Kadowaki
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan; (K.S.); (Y.K.); (Y.K.); (Y.S.)
| | - Yoshitaka Shimotai
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan; (K.S.); (Y.K.); (Y.K.); (Y.S.)
| | - Yuriko Katsushima
- Katsushima Pediatric Clinic, Yamagata 990-2461, Japan; (Y.K.); (F.K.)
| | - Fumio Katsushima
- Katsushima Pediatric Clinic, Yamagata 990-2461, Japan; (Y.K.); (F.K.)
| | - Shizuka Tanaka
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata 990-0031, Japan; (S.T.); (Y.M.); (K.K.); (Y.A.); (K.M.)
| | - Yohei Matoba
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata 990-0031, Japan; (S.T.); (Y.M.); (K.K.); (Y.A.); (K.M.)
| | - Kenichi Komabayashi
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata 990-0031, Japan; (S.T.); (Y.M.); (K.K.); (Y.A.); (K.M.)
| | - Yoko Aoki
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata 990-0031, Japan; (S.T.); (Y.M.); (K.K.); (Y.A.); (K.M.)
| | - Katsumi Mizuta
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata 990-0031, Japan; (S.T.); (Y.M.); (K.K.); (Y.A.); (K.M.)
| |
Collapse
|
2
|
Karpuj MV, Shaytov DR, Shemer-Avni Y, Gideon M, Frenkel ZM, Sivan S. Comparative Bioinformatic Analysis Reveals Conserved Regions in SARS-CoV-2 Genome for RAPID Pandemic Response. Int J Mol Sci 2024; 25:5764. [PMID: 38891951 PMCID: PMC11172030 DOI: 10.3390/ijms25115764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 06/21/2024] Open
Abstract
In the face of the SARS-CoV-2 pandemic, characterized by the virus's rapid mutation rates, developing timely and targeted therapeutic and diagnostic interventions presents a significant challenge. This study utilizes bioinformatic analyses to pinpoint conserved genomic regions within SARS-CoV-2, offering a strategic advantage in the fight against this and future pathogens. Our approach has enabled the creation of a diagnostic assay that is not only rapid, reliable, and cost-effective but also possesses a remarkable capacity to detect a wide array of current and prospective variants with unmatched precision. The significance of our findings lies in the demonstration that focusing on these conserved genomic sequences can significantly enhance our preparedness for and response to emerging infectious diseases. By providing a blueprint for the development of versatile diagnostic tools and therapeutics, this research paves the way for a more effective global pandemic response strategy.
Collapse
Affiliation(s)
- Marcela Viviana Karpuj
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel 2161002, Israel
| | - D. R. Shaytov
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel 2161002, Israel
| | - Yonat Shemer-Avni
- Laboratory of Clinical Virology, Soroka University Medical Center, Beer-Sheva 84101, Israel
| | - Michael Gideon
- Department of Neurosurgery, Soroka Medical Center, Beer-Sheva 84101, Israel
| | - Zakharia M. Frenkel
- Department of Software Engineering, Braude College of Engineering, Karmiel 2161002, Israel
| | - Sarit Sivan
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel 2161002, Israel
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Ng KT, Ng LJ, Oong XY, Chook JB, Chan KG, Takebe Y, Kamarulzaman A, Tee KK. Application of a VP4/VP2-inferred transmission clusters in estimating the impact of interventions on rhinovirus transmission. Virol J 2022; 19:36. [PMID: 35246187 PMCID: PMC8894564 DOI: 10.1186/s12985-022-01762-w] [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: 08/31/2021] [Accepted: 02/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite the clinical burden attributable to rhinovirus (RV) infections, the RV transmission dynamics and the impact of interventions on viral transmission remain elusive. METHODS A total of 3,935 nasopharyngeal specimens were examined, from which the VP4/VP2 gene was sequenced and genotyped. RV transmission clusters were reconstructed using the genetic threshold of 0.005 substitutions/site, estimated from the global VP4/VP2 sequences. A transmission cluster is characterized by the presence of at least two individuals (represent by nodes), whose viral sequences are genetically linked (represent by undirected edges) at the estimated genetic distance threshold supported by bootstrap value of ≥ 90%. To assess the impact of facemask, pleconaril and social distancing on RV transmission clusters, trials were simulated for interventions with varying efficacy and were evaluated based on the reduction in the number of infected patients (nodes) and the reduction in the number of nodes-connecting edges. The putative impact of intervention strategies on RV transmission clusters was evaluated through 10,000 simulations. RESULTS A substantial clustering of 168 RV transmission clusters of varying sizes were observed. This suggests that RV disease burden observed in the population was largely due to multiple sub-epidemics, predominantly driven by RV-A, followed by RV-C and -B. No misclassification of RV species and types were observed, suggesting the specificity and sensitivity of the analysis. Through 10,000 simulations, it was shown that social distancing may be effective in decelerating RV transmission, by removing more than 95% of nodes and edges within the RV transmission clusters. However, facemask removed less than 8% and 66% of nodes and edges, respectively, conferring moderate advantage in limiting RV transmission. CONCLUSION Here, we presented a network-based approach of which the degree of RV spread that fuel disease transmission in the region was mapped for the first time. The utilization of RV transmission clusters in assessing the putative impact of interventions on disease transmission at the population level was demonstrated.
Collapse
Affiliation(s)
- Kim Tien Ng
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.,Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Liang Jie Ng
- Faculty of Information Science and Technology, Multimedia University, Melaka, Malaysia
| | - Xiang Yong Oong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jack Bee Chook
- School of Medical and Life Sciences, Sunway University, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yutaka Takebe
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.,AIDS Research Center, National Institute of Infectious Diseases, Toyama, Shinjuku-ku, Tokyo, Japan
| | - Adeeba Kamarulzaman
- Department of Medicine, 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. .,School of Medical and Life Sciences, Sunway University, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
| |
Collapse
|
5
|
Lei N, Wang HB, Zhang YS, Zhao JH, Zhong Y, Wang YJ, Huang LY, Ma JX, Sun Q, Yang L, Shu YL, Li SM, Sun LL. Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. Sci Rep 2019; 9:2432. [PMID: 30792414 PMCID: PMC6384887 DOI: 10.1038/s41598-018-38105-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 12/10/2018] [Indexed: 11/15/2022] Open
Abstract
Two influenza B virus lineages, B/Victoria and B/Yamagata, are co-circulating in human population. While the two lineages are serologically distinct and TIV only contain one lineage. It is important to investigate the epidemiological and evolutionary dynamics of two influenza B virus lineages in Beijing after the free influenza vaccine policy from 2007. Here, we collected the nasopharyngeal swabs of 12657 outpatients of influenza-like illness and subtyped by real-time RT-PCR during 2011–2017. The HA and NA genes of influenza B were fully sequenced. The prevalence is the highest in the 6–17 years old group among people infected with influenza B. Yamagata-lineage virus evolved to two inter-clade from 2011–2014 to 2014–2017. The amino acids substitutions of HA1 region were R279K in strains of 2011–2014 and L173Q, M252V in strains of 2014–2017. Substitutions L58P, I146V were observed in HA1 region of Victoria-lineage virus in 2011–2012 and I117V, N129D were showed in 2015–2017. Phylogenetic analysis of NA showed Yamagata-Victoria inter-lineage reassortant occurred in 2013–2014. Influenza B mainly infect the school-aged children in Beijing and the free influenza vaccine inoculation does not seem to block school-age children from infection with influenza B. The antigen characteristics of circulating influenza B were different to the recommended vaccine strains. We concluded that the Victoria-lineage vaccine strain should been changed and the free influenza vaccine should be revalued.
Collapse
Affiliation(s)
- Na Lei
- Chaoyang District Center for Disease Prevention and Control, Beijing, 100021, China.,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, 102206, China
| | - Hai-Bin Wang
- Chaoyang District Center for Disease Prevention and Control, Beijing, 100021, China
| | - Yu-Song Zhang
- Chaoyang District Center for Disease Prevention and Control, Beijing, 100021, China
| | - Jian-Hong Zhao
- Chaoyang District Center for Disease Prevention and Control, Beijing, 100021, China
| | - Yi Zhong
- Chaoyang District Center for Disease Prevention and Control, Beijing, 100021, China
| | - Yuan-Jie Wang
- Chaoyang District Center for Disease Prevention and Control, Beijing, 100021, China
| | - Li-Yong Huang
- Chaoyang District Center for Disease Prevention and Control, Beijing, 100021, China
| | - Jian-Xin Ma
- Chaoyang District Center for Disease Prevention and Control, Beijing, 100021, China
| | - Qiang Sun
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, 102206, China.,School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, 510275, China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, 102206, China
| | - Yue-Long Shu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing, 102206, China.,School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, 510275, China
| | - Shu-Ming Li
- Chaoyang District Center for Disease Prevention and Control, Beijing, 100021, China.
| | - Ling-Li Sun
- Chaoyang District Center for Disease Prevention and Control, Beijing, 100021, China.
| |
Collapse
|
6
|
Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses. J Virol Methods 2019; 266:30-33. [PMID: 30677464 DOI: 10.1016/j.jviromet.2019.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/04/2019] [Accepted: 01/17/2019] [Indexed: 12/20/2022]
Abstract
We compared two sample preparation protocols for whole genome sequencing of influenza A viruses. Each protocol was assessed using cDNA quantity and quality and the resulting mean genome coverage after sequencing. Both protocols produced acceptable result for samples with high viral load, whereas one protocol performed slightly better with limited virus count.
Collapse
|
7
|
Korsun NS, Angelova SG, Trifonova IT, Georgieva IL, Tzotcheva IS, Mileva SD, Voleva SE, Kurchatova AM, Perenovska PI. Predominance of influenza B/Yamagata lineage viruses in Bulgaria during the 2017/2018 season. Epidemiol Infect 2019; 147:e76. [PMID: 30869003 PMCID: PMC6518837 DOI: 10.1017/s0950268818003588] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/18/2018] [Accepted: 12/12/2018] [Indexed: 12/14/2022] Open
Abstract
In this study, we investigated the antigenic and genetic characteristics of influenza viruses circulating in Bulgaria during the 2017/2018 season. The detection and typing/subtyping of influenza viruses were performed using real-time RT-PCR. Results of antigenic characterisation, phylogenetic and amino acid sequence analyses of representative influenza strains are presented. The season was characterised by the predominance of B/Yamagata viruses, accounting for 77% of detected influenza viruses, followed by A(H1N1)pdm09 (17%), B/Victoria (3.7%) and A(H3N2) (2.4%). The sequenced B/Yamagata, B/Victoria, A(H1N1)pdm09 and A(H3N2) viruses belonged to the genetic groups 3, 1A, 6B.1 and 3C.2a1, respectively. Amino acid analysis of B/Yamagata isolates revealed the presence of three changes in haemagglutinin (HA), eight changes in neuraminidase (NA) and a number of substitutions in internal proteins compared with the B/Phucket/3073/2013 vaccine virus. Despite the amino acid changes, B/Yamagata viruses remained antigenically related to the vaccine strain. B/Victoria isolates fell into a group of viruses with double deletion (Δ162-163) in HA1. Substitutions in HA and NA sequences of B/Victoria, A(H1N1)pdm09 and A(H3N2) viruses were also identified compared with the vaccine strains, including in antigenic sites. The results of this study confirm the genetic variability of circulating influenza viruses and the need for continual antigenic and molecular surveillance.
Collapse
Affiliation(s)
- N. S. Korsun
- Department of Virology, National Centre of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - S. G. Angelova
- Department of Virology, National Centre of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - I. T. Trifonova
- Department of Virology, National Centre of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - I. L. Georgieva
- Department of Virology, National Centre of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - I. S. Tzotcheva
- Paediatric Clinic, University Hospital Alexandrovska, Sofia Medical University, Sofia, Bulgaria
| | - S. D. Mileva
- Paediatric Clinic, University Hospital Alexandrovska, Sofia Medical University, Sofia, Bulgaria
| | - S. E. Voleva
- Department of Virology, National Centre of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - A. M. Kurchatova
- Department of Epidemiology, National Centre of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - P. I. Perenovska
- Paediatric Clinic, University Hospital Alexandrovska, Sofia Medical University, Sofia, Bulgaria
| |
Collapse
|
8
|
Ye F, Chen XJ, Guan WD, Pan SH, Yang ZF, Chen RC. Analysis of influenza B virus lineages and the HA1 domain of its hemagglutinin gene in Guangzhou, southern China, during 2016. Virol J 2018; 15:175. [PMID: 30428893 PMCID: PMC6236879 DOI: 10.1186/s12985-018-1085-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 10/21/2018] [Indexed: 02/05/2023] Open
Abstract
Background Few studies have analyzed influenza B virus lineages based on hemagglutinin A (HA) gene sequences in southern China. The present study analyzed the HA gene and the lineages of influenza B virus isolates from Guangzhou during 2016, and compared our results with the WHO-recommended vaccine strain. Methods Ninety patients with influenza B were recruited from the First Hospital of Guangzhou Medical University. Throat swab specimens of 72 patients had high viral loads. Among these 72 isolates, the HA1 domain of the HA gene in 43 randomly selected isolates was sequenced using reverse transcription-polymerase chain reaction (RT-PCR), and analyzed using MEGA 5.05. Results Eight of the 90 patients (8.9%) also had influenza A virus infections. Analysis of the 43 influenza B virus isolates indicated that 34 (79.1%) were from the Victoria lineage and 9 (20.9%) were from the Yamagata lineage. A comparison isolates in our Victoria lineage with the B/Brisbane/60/2008 strain indicated 12 mutation sites in the HA1 domain, 4 of which (I132V, N144D, C196S, and E198D) were in antigenic epitopes. A comparison of isolates in our Yamagata lineage with the B/Phuket/3073/2013 stain indicated 5 mutation sites in the HA1 domain, none of which was in an antigenic epitope. None of the isolates had a mutation in regions of the neuraminidase gene (NA) that are known to confer resistance to NA inhibitors. Conclusion In Guangzhou during 2016, most influenza B virus isolates were from the Victoria lineage, in contrast to the vaccine strain recommended by the WHO for this period. Electronic supplementary material The online version of this article (10.1186/s12985-018-1085-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Feng Ye
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease; Guangzhou Institute of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 151 Yan Jiang Road, Guangzhou, Guangdong, 510120, People's Republic of China.
| | - Xiao-Juan Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease; Guangzhou Institute of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 151 Yan Jiang Road, Guangzhou, Guangdong, 510120, People's Republic of China
| | - Wen-da Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease; Guangzhou Institute of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 151 Yan Jiang Road, Guangzhou, Guangdong, 510120, People's Republic of China
| | - Si-Hua Pan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease; Guangzhou Institute of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 151 Yan Jiang Road, Guangzhou, Guangdong, 510120, People's Republic of China
| | - Zi-Feng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease; Guangzhou Institute of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 151 Yan Jiang Road, Guangzhou, Guangdong, 510120, People's Republic of China
| | - Rong-Chang Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease; Guangzhou Institute of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 151 Yan Jiang Road, Guangzhou, Guangdong, 510120, People's Republic of China
| |
Collapse
|
9
|
Monamele CG, Vernet MA, Njankouo MR, Kenmoe S, Schoenhals M, Yahaya AA, Anong DN, Akoachere JF, Njouom R. Genetic characterization of influenza B virus in Cameroon and high frequency of reassortant strains. J Med Virol 2018; 90:1848-1855. [PMID: 30036447 DOI: 10.1002/jmv.25273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/05/2018] [Indexed: 11/06/2022]
Abstract
Influenza B is broadly divided into B/Victoria and B/Yamagata lineages based on its genetic and antigenic properties. We describe in this study the first report on genome characterization of type B influenza virus in the Cameroon National Influenza Center (NIC) between 2014 and 2017. Respiratory samples were collected as part of the influenza surveillance activity in the NIC. RNA products were tested for the presence of influenza using the CDC Influenza A/B typing panel. Thirty-five samples positive for influenza B were selected for sequencing three gene segments (HA, NA, and M) and phylogenetic trees were generated by MEGA version 6.0. Nucleotide phylogenetic analysis of the HA gene revealed the presence of three major clades among Cameroonian strains. All Victoria lineages grouped into B/Victoria clade 1A, while, Yamagata lineages grouped into Yamagata clade 2 (2014 strains) and Yamagata clade 3 (2015-2017). We observed a high frequency of reassortant viruses with Yamagata-like HA gene and Victoria-like NA gene (27.4%; 23/84). The results from this study confirm variations in the genome composition of type B influenza virus and emphasize on the relevance of molecular surveillance for spotting peculiar genetic variants of public health and clinical significance.
Collapse
Affiliation(s)
- Chavely Gwladys Monamele
- Virology Department, Centre Pasteur of Cameroon, Institute Pasteur International Network, Yaounde, Cameroon.,Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
| | - Marie-Astrid Vernet
- Virology Department, Centre Pasteur of Cameroon, Institute Pasteur International Network, Yaounde, Cameroon
| | - Mohamadou Ripa Njankouo
- Virology Department, Centre Pasteur of Cameroon, Institute Pasteur International Network, Yaounde, Cameroon
| | - Sebastien Kenmoe
- Virology Department, Centre Pasteur of Cameroon, Institute Pasteur International Network, Yaounde, Cameroon
| | - Matthieu Schoenhals
- Virology Department, Centre Pasteur of Cameroon, Institute Pasteur International Network, Yaounde, Cameroon
| | - Ali Ahmed Yahaya
- World Health Organization, Regional Office for Africa, Brazzaville, Congo
| | - Damian Nota Anong
- Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon.,Department of Biological Sciences, University of Bamenda, Bamenda, Cameroon
| | | | - Richard Njouom
- Virology Department, Centre Pasteur of Cameroon, Institute Pasteur International Network, Yaounde, Cameroon
| |
Collapse
|
10
|
Hibino A, Massaad E, Kondo H, Saito R, Odagiri T, Takemae N, Tsunekuni R, Saito T, Kyaw Y, Lin N, Myint YY, Tin HH, Le Khanh Hang N, Mai LQ, Yagami R, Shobugawa Y, Lam T, Zaraket H. Neuraminidase inhibitor susceptibility and evolutionary analysis of human influenza B isolates from three Asian countries during 2012-2015. INFECTION GENETICS AND EVOLUTION 2018; 62:27-33. [PMID: 29665435 DOI: 10.1016/j.meegid.2018.04.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 03/26/2018] [Accepted: 04/11/2018] [Indexed: 11/16/2022]
Abstract
Influenza B viruses of both the Yamagata and the Victoria lineages are implicated in a large proportion of the morbidity and mortality associated with influenza outbreaks. In this study, we characterized the full genomes of 53 influenza B viruses isolated during 2012-2015 in three Asian countries: Japan, Myanmar, and Vietnam. Analysis of the hemagglutinin (HA) genes revealed co-circulation of both the Yamagata and Victoria lineages within the same season in these countries. Our analysis revealed, that a large proportion of viruses circulating during 2013-2014 in Japan and Vietnam were mismatched to the vaccine supporting the rationale for using quadrivalent vaccines. Molecular analysis of the neuraminidase (NA) genes did not reveal any of the previously reported substitutions associated with reduced susceptibility to neuraminidase inhibitors (NAIs). However, one isolate from Nagasaki displayed reduced inhibition by NAIs, associated with an NA-M426I substitution (N2-numbering). Phylogenetic analysis of the eight genome segments identified a 6 + 2 reassortant strain belonging to the Victoria lineage that circulated in Japan during the 2013-2014 season. This strain appears to have evolved from a descendent of a B/Brisbane/60/2008-like strain in an intra-lineage reassortment event involving the nucleoprotein (NP) and nonstructural (NS) genes. Therefore, influenza B strains circulating worldwide continue to evolve via complex reassortment events, which contribute to their survival and the emergence of new strains. These findings highlight the need for ongoing genome-wide studies of circulating viruses and assessing the implications of these evolutionary events on the vaccines.
Collapse
Affiliation(s)
- Akinobu Hibino
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Japan; Department of Pathology, Immunology, and Microbiology, Faculty of Medicine American University of Beirut, Lebanon
| | - Elie Massaad
- Department of Pathology, Immunology, and Microbiology, Faculty of Medicine American University of Beirut, Lebanon; Center for Infectious Disease Research, Faculty of Medicine American University of Beirut, Beirut, Lebanon
| | - Hiroki Kondo
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Japan
| | - Reiko Saito
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Japan.
| | - Takashi Odagiri
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Japan
| | - Nobuhiro Takemae
- Influenza and Prion Disease Research Center, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Ryota Tsunekuni
- Influenza and Prion Disease Research Center, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Takehiko Saito
- Influenza and Prion Disease Research Center, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | | | - Yadanar Kyaw
- Respiratory Medicine Department, Sanpya Hospital, Kyaikkasan Pagoda Road, Yangon, Myanmar
| | - Nay Lin
- Clinical Laboratory, Microbiology Section, Pyinmana Township Hospital, Naw Pyi Taw, Myanmar
| | - Yi Yi Myint
- Ministry of Health and Sports, Department traditional Medicine, Naw Pyi Taw, Myanmar
| | - Htay Htay Tin
- Ministry of Health and Sports, Department traditional Medicine, Naw Pyi Taw, Myanmar; National Health Laboratory, Ministry of Health and Sports, Yangon, Myanmar
| | | | - Le Quynh Mai
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Ren Yagami
- Center for Infectious Disease Research, Faculty of Medicine American University of Beirut, Beirut, Lebanon
| | - Yugo Shobugawa
- Center for Infectious Disease Research, Faculty of Medicine American University of Beirut, Beirut, Lebanon
| | - Tommy Lam
- School of Public Health, the University of Hong Kong, Hong Kong, China
| | - Hassan Zaraket
- Department of Pathology, Immunology, and Microbiology, Faculty of Medicine American University of Beirut, Lebanon; Center for Infectious Disease Research, Faculty of Medicine American University of Beirut, Beirut, Lebanon.
| |
Collapse
|