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Influenza B Viruses Exhibit Lower Within-Host Diversity than Influenza A Viruses in Human Hosts. J Virol 2020; 94:JVI.01710-19. [PMID: 31801858 DOI: 10.1128/jvi.01710-19] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 11/29/2019] [Indexed: 12/11/2022] Open
Abstract
Influenza B virus (IBV) undergoes seasonal antigenic drift more slowly than influenza A virus, but the reasons for this difference are unclear. While the evolutionary dynamics of influenza viruses play out globally, they are fundamentally driven by mutation, reassortment, drift, and selection at the level of individual hosts. These processes have recently been described for influenza A virus, but little is known about the evolutionary dynamics of IBV during individual infections and transmission events. Here, we define the within-host evolutionary dynamics of IBV by sequencing virus populations from naturally infected individuals enrolled in a prospective, community-based cohort over 8,176 person-seasons of observation. Through analysis of high depth-of-coverage sequencing data from samples from 91 individuals with influenza B, we find that IBV accumulates lower genetic diversity than previously observed for influenza A virus during acute infections. Consistent with studies of influenza A viruses, the within-host evolution of IBVs is characterized by purifying selection and the general absence of widespread positive selection of within-host variants. Analysis of shared genetic diversity across 15 sequence-validated transmission pairs suggests that IBV experiences a tight transmission bottleneck similar to that of influenza A virus. These patterns of local-scale evolution are consistent with the lower global evolutionary rate of IBV.IMPORTANCE The evolution of influenza virus is a significant public health problem and necessitates the annual evaluation of influenza vaccine formulation to keep pace with viral escape from herd immunity. Influenza B virus is a serious health concern for children, in particular, yet remains understudied compared to influenza A virus. Influenza B virus evolves more slowly than influenza A virus, but the factors underlying this are not completely understood. We studied how the within-host diversity of influenza B virus relates to its global evolution by sequencing viruses from a community-based cohort. We found that influenza B virus populations have lower within-host genetic diversity than influenza A virus and experience a tight genetic bottleneck during transmission. Our work provides insights into the varying dynamics of influenza viruses in human infection.
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Divergent evolutionary trajectories of influenza B viruses underlie their contemporaneous epidemic activity. Proc Natl Acad Sci U S A 2019; 117:619-628. [PMID: 31843889 PMCID: PMC6955377 DOI: 10.1073/pnas.1916585116] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Two influenza B viruses (Victoria and Yamagata) cocirculate in humans and contribute to the estimated 290,000–650,000 annual influenza-attributed deaths. Here, we analysed influenza B genomic data to understand the causes of a recent surge in human influenza B infections. We found that evolution is acting differently on Yamagata and Victoria viruses and that this has led to the cocirculation of a diverse group of influenza B viruses. If this phenomenon continues, we could potentially witness the emergence of 3 or more distinct influenza B viruses that could require their own vaccine component, thereby complicating influenza vaccine formulation and highlighting the urgency of developing universal influenza vaccines. Influenza B viruses have circulated in humans for over 80 y, causing a significant disease burden. Two antigenically distinct lineages (“B/Victoria/2/87-like” and “B/Yamagata/16/88-like,” termed Victoria and Yamagata) emerged in the 1970s and have cocirculated since 2001. Since 2015 both lineages have shown unusually high levels of epidemic activity, the reasons for which are unclear. By analyzing over 12,000 influenza B virus genomes, we describe the processes enabling the long-term success and recent resurgence of epidemics due to influenza B virus. We show that following prolonged diversification, both lineages underwent selective sweeps across the genome and have subsequently taken alternate evolutionary trajectories to exhibit epidemic dominance, with no reassortment between lineages. Hemagglutinin deletion variants emerged concomitantly in multiple Victoria virus clades and persisted through epistatic mutations and interclade reassortment—a phenomenon previously only observed in the 1970s when Victoria and Yamagata lineages emerged. For Yamagata viruses, antigenic drift of neuraminidase was a major driver of epidemic activity, indicating that neuraminidase-based vaccines and cross-reactivity assays should be employed to monitor and develop robust protection against influenza B morbidity and mortality. Overall, we show that long-term diversification and infrequent selective sweeps, coupled with the reemergence of hemagglutinin deletion variants and antigenic drift of neuraminidase, are factors that contributed to successful circulation of diverse influenza B clades. Further divergence of hemagglutinin variants with poor cross-reactivity could potentially lead to circulation of 3 or more distinct influenza B viruses, further complicating influenza vaccine formulation and highlighting the urgent need for universal influenza vaccines.
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Puzelli S, Di Martino A, Facchini M, Fabiani C, Calzoletti L, Di Mario G, Palmieri A, Affanni P, Camilloni B, Chironna M, D'Agaro P, Giannecchini S, Pariani E, Serra C, Rizzo C, Bella A, Donatelli I, Castrucci MR. Co-circulation of the two influenza B lineages during 13 consecutive influenza surveillance seasons in Italy, 2004-2017. BMC Infect Dis 2019; 19:990. [PMID: 31752738 PMCID: PMC6873537 DOI: 10.1186/s12879-019-4621-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Since 1985, two antigenically distinct lineages of influenza B viruses (Victoria-like and Yamagata-like) have circulated globally. Trivalent seasonal influenza vaccines contain two circulating influenza A strains but a single B strain and thus provide limited immunity against circulating B strains of the lineage not included in the vaccine. In this study, we describe the characteristics of influenza B viruses that caused respiratory illness in the population in Italy over 13 consecutive seasons of virological surveillance, and the match between the predominant influenza B lineage and the vaccine B lineage, in each season. METHODS From 2004 to 2017, 26,886 laboratory-confirmed influenza cases were registered in Italy, of which 18.7% were type B. Among them, the lineage of 2465 strains (49%) was retrieved or characterized in this study by a real-time RT-PCR assay and/or sequencing of the hemagglutinin (HA) gene. RESULTS Co-circulation of both B lineages was observed each season, although in different proportions every year. Overall, viruses of B/Victoria and B/Yamagata lineages caused 53.3 and 46.7% of influenza B infections, respectively. A higher proportion of infections with both lineages was detected in children, and there was a declining frequency of B/Victoria detections with age. A mismatch between the vaccine and the predominant influenza B lineage occurred in eight out of thirteen influenza seasons under study. Considering the seasons when B accounted for > 20% of all laboratory-confirmed influenza cases, a mismatch was observed in four out of six seasons. Phylogenetic analysis of the HA1 domain confirmed the co-circulation of both lineages and revealed a mixed circulation of distinct evolutionary viral variants, with different levels of match to the vaccine strains. CONCLUSIONS This study contributes to the understanding of the circulation of influenza B viruses in Italy. We found a continuous co-circulation of both B lineages in the period 2004-2017, and determined that children were particularly vulnerable to Victoria-lineage influenza B virus infections. An influenza B lineage mismatch with the trivalent vaccine occurred in about two-thirds of cases.
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Affiliation(s)
- Simona Puzelli
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Viale Regina Elena 299, Rome, Italy.
| | - Angela Di Martino
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Viale Regina Elena 299, Rome, Italy
| | - Marzia Facchini
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Viale Regina Elena 299, Rome, Italy
| | - Concetta Fabiani
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Viale Regina Elena 299, Rome, Italy
| | - Laura Calzoletti
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Viale Regina Elena 299, Rome, Italy
| | - Giuseppina Di Mario
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Viale Regina Elena 299, Rome, Italy
| | - Annapina Palmieri
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Viale Regina Elena 299, Rome, Italy
| | | | | | - Maria Chironna
- Department of Biomedical Science and Human Oncology, University of Bari, Bari, Italy
| | | | | | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | | | - Caterina Rizzo
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Viale Regina Elena 299, Rome, Italy
| | - Antonino Bella
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Viale Regina Elena 299, Rome, Italy
| | - Isabella Donatelli
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Viale Regina Elena 299, Rome, Italy
| | - Maria Rita Castrucci
- Department of Infectious Diseases, Istituto Superiore di Sanità (ISS), Viale Regina Elena 299, Rome, Italy
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Spatial, Temporal and Genetic Dynamics Characteristics of Influenza B Viruses in China, 1973-2018. Virol Sin 2019; 35:14-20. [PMID: 31637629 DOI: 10.1007/s12250-019-00161-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 08/08/2019] [Indexed: 12/14/2022] Open
Abstract
Annual influenza B virus epidemics and outbreaks cause severe influenza diseases in humans and pose a threat to public health. China is an important epidemic area of influenza B viruses. However, the spatial, temporal transmission pathways and the demography history of influenza B viruses in China remain unknown. We collected the haemagglutinin gene sequences sampled of influenza B virus in China between 1973 and 2018. A Bayesian Markov chain Monte Carlo phylogeographic discrete approach was used to infer the spatial and temporal phylodynamics of influenza B virus. The Bayesian phylogeographic analysis of influenza B viruses showed that the North subtropical and South subtropical zones are the origins of the Victoria and Yamagata lineage viruses, respectively. Furthermore, the South temperate and North subtropical zones acted as transition nodes in the Victoria lineage virus dispersion network and that the North subtropical and Mid subtropical zones acted as transition nodes in the Yamagata lineage virus dispersion network. Our findings contribute to the knowledge regarding the spatial and temporal patterns of influenza B virus outbreaks in China.
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55
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The Development and Use of Reporter Influenza B Viruses. Viruses 2019; 11:v11080736. [PMID: 31404985 PMCID: PMC6723853 DOI: 10.3390/v11080736] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 12/15/2022] Open
Abstract
Influenza B viruses (IBVs) are major contributors to total human influenza disease, responsible for ~1/3 of all infections. These viruses, however, are relatively less studied than the related influenza A viruses (IAVs). While it has historically been assumed that the viral biology and mechanisms of pathogenesis for all influenza viruses were highly similar, studies have shown that IBVs possess unique characteristics. Relative to IAV, IBV encodes distinct viral proteins, displays a different mutational rate, has unique patterns of tropism, and elicits different immune responses. More work is therefore required to define the mechanisms of IBV pathogenesis. One valuable approach to characterize mechanisms of microbial disease is the use of genetically modified pathogens that harbor exogenous reporter genes. Over the last few years, IBV reporter viruses have been developed and used to provide new insights into the host response to infection, viral spread, and the testing of antiviral therapeutics. In this review, we will highlight the history and study of IBVs with particular emphasis on the use of genetically modified viruses and discuss some remaining gaps in knowledge that can be addressed using reporter expressing IBVs.
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Carlock MA, Ingram JG, Clutter EF, Cecil NC, Ramgopal M, Zimmerman RK, Warren W, Kleanthous H, Ross TM. Impact of age and pre-existing immunity on the induction of human antibody responses against influenza B viruses. Hum Vaccin Immunother 2019; 15:2030-2043. [PMID: 31291153 PMCID: PMC6773397 DOI: 10.1080/21645515.2019.1642056] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Pre-existing immunity to influenza is dependent on a number of factors and can vary greatly within and across influenza subtypes. In this study, volunteers (aged 18–85 years) were vaccinated with split, inactivated FluzoneTM in four consecutive influenza seasons from 2013 to 2016. The impact of repeat vaccination on breadth and durability of functional antibodies was assessed for total IgG and IgA anti-hemagglutinin (HA) binding antibodies and hemagglutination-inhibition (HAI) activity against both influenza B lineages. Many subjects were able to maintain high seroprotective titers to the vaccine strains in subsequent years, which resulted in low vaccine-induced seroconversion rates. This was especially evident in younger subjects who typically had higher titers and maintained these titers into the following season. In contrast, the HAI titers in elderly subjects were generally lower and more likely to decline prior to the start of the next influenza season. Immunological recall or ‘back-boosting’ to antigenically related viruses was associated with seroconversion. Overall, influenza vaccination in both younger and older people elicited broadly reactive immune responses within a lineage, as well as cross-reactive immune responses between lineages. This study exemplified the impact that age and influenza exposure history have on determining an individual’s ability to respond to future influenza infections.
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Affiliation(s)
- Michael A Carlock
- Center for Vaccines and Immunology, University of Georgia , Athens , GA , USA
| | - John G Ingram
- Center for Vaccines and Immunology, University of Georgia , Athens , GA , USA
| | - Emily F Clutter
- Center for Vaccines and Immunology, University of Georgia , Athens , GA , USA
| | - Noah C Cecil
- Center for Vaccines and Immunology, University of Georgia , Athens , GA , USA
| | - Moti Ramgopal
- Clinical Research Division, Martin Health System , Stuart , FL , USA
| | - Richard K Zimmerman
- Department of Family Medicine, University of Pittsburgh , Pittsburgh , PA , USA
| | | | | | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia , Athens , GA , USA.,Department of Infectious Diseases, University of Georgia , Athens , GA , USA
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Kuang X, Teng Z, Zhang X. Genotypic prevalence of norovirus GII in gastroenteritis outpatients in Shanghai from 2016 to 2018. Gut Pathog 2019; 11:40. [PMID: 31372183 PMCID: PMC6660925 DOI: 10.1186/s13099-019-0321-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/20/2019] [Indexed: 12/30/2022] Open
Abstract
Background With the help of an existing citywide comprehensive surveillance on gastroenteritis outpatients, although norovirus genogroup II (NoV GII) was tested routinely, its genotypes were never investigated systematically on a municipal level. This study aimed to understand the prevalence, major genotypes and evolutional trends of NoV GII in Shanghai during the period of 2016–2018, and to provide molecular bases for early warning for any potential NoV outbreaks. Methods 27 sentinel hospitals from all 16 districts were recruited by stratified probability proportional to size (PPS) method in Shanghai comprehensive diarrhea surveillance programme. Stool samples were collected and screened for NoV GII by real-time reverse transcription polymerase chain reaction (qRT-PCR). For samples that were positive in qRT-PCR, conventional RT-PCR was performed to amplify the ORF1-ORF2 junction of NoV GII gene. Generated sequences were typed by RIVM online genotyping tool, and then strains of interest were analyzed phylogenetically using MEGA 6.0. Results A total of 7883 stool samples were collected from diarrhea outpatients, among which 6474 were from adults and 1409 were from children. 13.66% (1077 cases) were screened positive in qRT-PCR for NoV GII, from which 71.96% (775 cases) were sequenced successfully. The top three genotypes were GII.Pe/GII.4 (37%), GII.P17/GII.17 (26%) and GII.P16/GII.2 (17%). While GII.Pe/GII.4 detection rate decreased significantly over the 3 years (from 48.4 to 20.9%); GII.P16/GII.2 appeared for the first time in October 2016 and rose rapidly to 27.0% in 2017, but fell back to 23.4% in 2018. Meanwhile there was a significant increase for both GII.P12/GII.3 and GII.P7/GII.6 recombinant genotypes detected in adult population in 2018. Phylogenic analysis revealed the existence of multiple gene clusters within both of these recombinant genotypes. Conclusion Unlike the alternating circulation of GII.4 and non-GII.4 NoV observed in 2016 or 2017, the genotype profile of NoV GII in 2018 was characterized by the co-prevalence of multiple recombinant genotypes. A recent increase in detection rate in less reported recombinant genotypes such as GII.P12/GII.3 and GII.P7/GII.6 among adult population calls for a continuing close monitoring on NoV GII genotypes in case of potential local outbreaks. Electronic supplementary material The online version of this article (10.1186/s13099-019-0321-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaozhou Kuang
- Shanghai Municipal Center for Disease Control and Prevention, 1380 Zhongshan Road (west), Shanghai, 200336 China
| | - Zheng Teng
- Shanghai Municipal Center for Disease Control and Prevention, 1380 Zhongshan Road (west), Shanghai, 200336 China
| | - Xi Zhang
- Shanghai Municipal Center for Disease Control and Prevention, 1380 Zhongshan Road (west), Shanghai, 200336 China
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AlIbrahim M, Assaf-Casals A, Massaad E, Shaker R, Soudani N, Fayad D, Chamseddine S, Lteif-Khoury M, Chmaisse A, Isaac I, Anan H, Sadaka C, Radwan N, Ghanem S, Naous A, Karam M, Andary R, Dbaibo G, Zaraket H. Molecular epidemiology and genetic characterization of influenza B virus in Lebanon during 2016-2018. INFECTION GENETICS AND EVOLUTION 2019; 75:103969. [PMID: 31325610 DOI: 10.1016/j.meegid.2019.103969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/24/2019] [Accepted: 07/16/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND Influenza B viruses are a major cause of serious acute respiratory infections in humans. METHODS Nasopharyngeal swabs were collected from subjects with influenza-like illness during October 2016-June 2018 and screened for influenza A and B. The hemagglutinin (HA) and neuraminidase (NA) genes of the Lebanese influenza B specimens were sequenced and phylogenetically compared with the vaccine strains and specimens from the Eastern Mediterranean Region and Europe. RESULTS Influenza A and B viruses co-circulated between October and May and peaked between January and March. During the 2016-2017 season, A/H3N2 (33.4%) and B/Yamagata (29.7%) were the predominantly circulating viruses followed by B/Victoria and A/H1N1pdm09 viruses. During the 2017-2018 season, A/H3N2 (31.5%) and A/H1Npdm09 (29.3%) were most prevalent with co-circulation of B/Yamagata and to a lesser extent B/Victoria viruses. The B/Yamagata specimens belonged to clade-3 while the B/Victoria belonged to clade-1A. None of the analyzed specimens had a mutation known to confer resistance to NA inhibitors (NAIs). CONCLUSION Multiple subtypes of influenza co-circulate each year in Lebanon with a peak between January and March. The trivalent vaccine included a B/Victoria strain which mismatched the B/Yamagata lineage that predominated during the study period, highlighting the importance of quadrivalent vaccines.
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Affiliation(s)
- Malak AlIbrahim
- Department of Experimental Pathology, Immunology & Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Aia Assaf-Casals
- Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Division of Pediatric Infectious Diseases, Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Elie Massaad
- Department of Experimental Pathology, Immunology & Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Rouba Shaker
- Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Division of Pediatric Infectious Diseases, Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Nadia Soudani
- Department of Experimental Pathology, Immunology & Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Department of Biology, Faculty of Sciences, EDST, Lebanese University, Hadath, Lebanon
| | - Danielle Fayad
- Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Division of Pediatric Infectious Diseases, Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Sarah Chamseddine
- Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Division of Pediatric Infectious Diseases, Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Mireille Lteif-Khoury
- Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Division of Pediatric Infectious Diseases, Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Ahmad Chmaisse
- Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Division of Pediatric Infectious Diseases, Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Imad Isaac
- Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Division of Pediatric Infectious Diseases, Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Hind Anan
- Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Division of Pediatric Infectious Diseases, Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Christian Sadaka
- Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Division of Pediatric Infectious Diseases, Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Najwa Radwan
- Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Division of Pediatric Infectious Diseases, Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Soha Ghanem
- Department of Pediatrics, Makassed General Hospital, Beirut, Lebanon
| | - Amal Naous
- Department of Pediatrics, Makassed General Hospital, Beirut, Lebanon
| | | | | | - Ghassan Dbaibo
- Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Division of Pediatric Infectious Diseases, Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Hassan Zaraket
- Department of Experimental Pathology, Immunology & Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.
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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.
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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.
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Influenza Virus Vaccination Elicits Poorly Adapted B Cell Responses in Elderly Individuals. Cell Host Microbe 2019; 25:357-366.e6. [PMID: 30795982 DOI: 10.1016/j.chom.2019.01.002] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/30/2018] [Accepted: 01/03/2019] [Indexed: 01/17/2023]
Abstract
Influenza is a leading cause of death in the elderly, and the vaccine protects only a fraction of this population. A key aspect of antibody-mediated anti-influenza virus immunity is adaptation to antigenically distinct epitopes on emerging strains. We examined factors contributing to reduced influenza vaccine efficacy in the elderly and uncovered a dramatic reduction in the accumulation of de novo immunoglobulin gene somatic mutations upon vaccination. This reduction is associated with a significant decrease in the capacity of antibodies to target the viral glycoprotein, hemagglutinin (HA), and critical protective epitopes surrounding the HA receptor-binding domain. Immune escape by antigenic drift, in which viruses generate mutations in key antigenic epitopes, becomes highly exaggerated. Because of this reduced adaptability, most B cells activated in the elderly cohort target highly conserved but less potent epitopes. Given these findings, vaccines driving immunoglobulin gene somatic hypermutation should be a priority to protect elderly individuals.
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61
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Gutierrez B, Escalera-Zamudio M, Pybus OG. Parallel molecular evolution and adaptation in viruses. Curr Opin Virol 2019; 34:90-96. [PMID: 30703578 PMCID: PMC7102768 DOI: 10.1016/j.coviro.2018.12.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/11/2018] [Indexed: 01/05/2023]
Abstract
Parallel molecular evolution is the independent evolution of the same genotype or phenotype from distinct ancestors. The simple genomes and rapid evolution of many viruses mean they are useful model systems for studying parallel evolution by natural selection. Parallel adaptation occurs in the context of several viral behaviours, including cross-species transmission, drug resistance, and host immune escape, and its existence suggests that at least some aspects of virus evolution and emergence are repeatable and predictable. We introduce examples of virus parallel evolution and summarise key concepts. We outline the difficulties in detecting parallel adaptation using virus genomes, with a particular focus on phylogenetic and structural approaches, and we discuss future approaches that may improve our understanding of the phenomenon.
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Affiliation(s)
| | | | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom.
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62
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Liu Y, Tan HX, Koutsakos M, Jegaskanda S, Esterbauer R, Tilmanis D, Aban M, Kedzierska K, Hurt AC, Kent SJ, Wheatley AK. Cross-lineage protection by human antibodies binding the influenza B hemagglutinin. Nat Commun 2019; 10:324. [PMID: 30659197 PMCID: PMC6338745 DOI: 10.1038/s41467-018-08165-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 12/20/2018] [Indexed: 11/10/2022] Open
Abstract
Influenza B viruses (IBV) drive a significant proportion of influenza-related hospitalisations yet are understudied compared to influenza A. Current vaccines target the head of the viral hemagglutinin (HA) which undergoes rapid mutation, significantly reducing vaccine effectiveness. Improved vaccines to control IBV are needed. Here we developed novel IBV HA probes to interrogate humoral responses to IBV in humans. A significant proportion of IBV HA-specific B cells recognise both B/Victoria/2/87-like and B/Yamagata/16/88-like lineages in a distinct pattern of cross-reactivity. Monoclonal antibodies (mAbs) were reconstituted from IBV HA-specific B cells, including mAbs providing broad protection in murine models of lethal IBV infection. Protection was mediated by neutralising antibodies targeting the receptor binding domain, or via Fc-mediated functions of non-neutralising antibodies binding alternative epitopes including the IBV HA stem. This work defines antigenic cross-recognition between IBV lineages and provides guidance for the rational design of improved IBV vaccines for broad and durable protection. Immune recognition of Influenza B virus (IBV) is poorly understood. Here, Liu et al. use flow cytometry to characterize IBV-specific memory B cell responses following seasonal vaccination and show that elicited cross-reactive antibodies can protect against infection, providing a platform for vaccine design.
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Affiliation(s)
- Yi Liu
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Sinthujan Jegaskanda
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Robyn Esterbauer
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Danielle Tilmanis
- World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Malet Aban
- World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Aeron C Hurt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia.,World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia. .,Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia. .,ARC Centre for Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Adam K Wheatley
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia.
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63
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Henritzi D, Hoffmann B, Wacheck S, Pesch S, Herrler G, Beer M, Harder TC. A newly developed tetraplex real-time RT-PCR for simultaneous screening of influenza virus types A, B, C and D. Influenza Other Respir Viruses 2019; 13:71-82. [PMID: 30264926 PMCID: PMC6304318 DOI: 10.1111/irv.12613] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 09/12/2018] [Accepted: 09/13/2018] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Human- or avian-to-swine transmissions have founded several autonomously circulating influenza A virus (IAV) lineages in swine populations that cause economically important respiratory disease. Little is known on other human influenza virus types, like B (IBV) and C (ICV) in European swine, and of the recently detected novel animal influenza virus type D (IDV). OBJECTIVES Development of a cost-effective diagnostic tool for large-scale surveillance programmes targeting all four influenza virus types. METHODS An influenza ABCD tetraplex real-time RT-PCR (RT-qPCR) was developed in the frame of this study. A selection of reference virus strains and more than 4000 porcine samples from a passive IAV surveillance programme in European swine with acute respiratory disease were examined. RESULTS Two IBV, a single IDV but no ICV infections were identified by tetraplex RT-qPCR. IBV and IDV results were confirmed by conventional RT-PCR and partial sequence analysis. CONCLUSIONS The tetraplex RT-qPCR proved fit for purpose as a sensitive, specific and high-throughput tool to study influenza virus transmission at the human-animal interface. Complementing close-meshed active virological and serological surveillance is required to better understand the true incidence and prevalence of influenza virus type B, C and D infections in swine.
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Affiliation(s)
- Dinah Henritzi
- Institute of Diagnostic VirologyFriedrich‐Loeffler‐Institut (FLI)Greifswald‐Insel RiemsGermany
| | - Bernd Hoffmann
- Institute of Diagnostic VirologyFriedrich‐Loeffler‐Institut (FLI)Greifswald‐Insel RiemsGermany
| | | | | | - Georg Herrler
- University of Veterinary Medicine Hannover, FoundationHannoverGermany
| | - Martin Beer
- Institute of Diagnostic VirologyFriedrich‐Loeffler‐Institut (FLI)Greifswald‐Insel RiemsGermany
| | - Timm C. Harder
- Institute of Diagnostic VirologyFriedrich‐Loeffler‐Institut (FLI)Greifswald‐Insel RiemsGermany
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64
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The Influenza B Virus Hemagglutinin Head Domain Is Less Tolerant to Transposon Mutagenesis than That of the Influenza A Virus. J Virol 2018; 92:JVI.00754-18. [PMID: 29899093 DOI: 10.1128/jvi.00754-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/04/2018] [Indexed: 11/20/2022] Open
Abstract
Influenza A and B viruses can continuously evade humoral immune responses by developing mutations in the globular head of the hemagglutinin (HA) that prevent antibody binding. However, the influenza B virus HA over time displays less antigenic variation despite being functionally and structurally similar to the influenza A virus HA. To determine if the influenza B virus HA is under constraints that limit its antigenic variation, we performed a transposon screen to compare the mutational tolerance of the currently circulating influenza A virus HAs (H1 and H3 subtypes) and influenza B virus HAs (B/Victoria87 and B/Yamagata88 antigenic lineages). A library of insertional mutants for each HA was generated and deep sequenced after passaging to determine where insertions were tolerated in replicating viruses. The head domains of both viruses tolerated transposon mutagenesis, but the influenza A virus head was more tolerant to insertions than the influenza B virus head domain. Furthermore, all five of the known antigenic sites of the influenza A virus HA were tolerant of 15 nucleotide insertions, while insertions were detected in only two of the four antigenic sites in the influenza B virus head domain. Our analysis demonstrated that the influenza B virus HA is inherently less tolerant of transposon-mediated insertions than the influenza A virus HA. The reduced insertional tolerance of the influenza B virus HA may reveal genetic restrictions resulting in a lower capacity for antigenic evolution.IMPORTANCE Influenza viruses cause seasonal epidemics and result in significant human morbidity and mortality. Influenza viruses persist in the human population through generating mutations in the hemagglutinin head domain that prevent antibody recognition. Despite the similar selective pressures on influenza A and B viruses, influenza A virus displays a higher rate and breadth of antigenic variability than influenza B virus. A transposon mutagenesis screen was used to examine if the reduced antigenic variability of influenza B virus was due to inherent differences in mutational tolerance. This study demonstrates that the influenza A virus head domain and the individual antigenic sites targeted by humoral responses are more tolerant to insertions than those of influenza B virus. This finding sheds light on the genetic factors controlling the antigenic evolution of influenza viruses.
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65
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Histamine contributes to severe pneumonia in pigs infected with 2009 pandemic H1N1 influenza virus. Arch Virol 2018; 163:3015-3022. [PMID: 30066270 DOI: 10.1007/s00705-018-3973-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 07/20/2018] [Indexed: 01/22/2023]
Abstract
Histamine is a biogenic amine that influences many immune cells. In this study, we investigated the effect of histamine on the pathogenesis of 2009 pandemic H1N1 influenza virus in pigs. Histamine was not detected in the tracheal tissues of infected pigs, and no difference was found in the pathological damage found in infected pigs with and without treatment with a histamine antagonist. Lung tissues from untreated infected pigs showed severe interstitial pneumonia with accumulation of histamine, in contrast to those from infected pigs that were treated with the histamine antagonist. The expression of inflammatory cytokines was much higher in the lungs of untreated infected pigs than in infected pigs treated with the histamine antagonist. These data suggest that histamine necessary for the development of the severe pneumonia in infected pigs.
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Chan MCW, Kwok K, Zhang LY, Mohammad KN, Lee N, Lui GCY, Nelson EAS, Lai RWM, Leung TF, Chan PKS. Bimodal Seasonality and Alternating Predominance of Norovirus GII.4 and Non-GII.4, Hong Kong, China, 2014-2017 1. Emerg Infect Dis 2018; 24:767-769. [PMID: 29369754 PMCID: PMC5875276 DOI: 10.3201/eid2404.171791] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We report emerging subtropical bimodal seasonality and alternating predominance of norovirus GII.4 and non-GII.4 genotypes in Hong Kong. GII.4 predominated in summer and autumn months and affected young children, whereas emergent non-GII.4 genotypes predominated in winter months and affected all age groups. This highly dynamic epidemiology should inform vaccination strategies.
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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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