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Høiby N. Pandemics: past, present, future: That is like choosing between cholera and plague. APMIS 2021; 129:352-371. [PMID: 33244837 PMCID: PMC7753327 DOI: 10.1111/apm.13098] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/13/2020] [Indexed: 12/22/2022]
Abstract
The major epidemic and pandemic diseases that have bothered humans since the Neolithic Age and Bronze Age are surveyed. Many of these pandemics are zoonotic infections, and the mathematical modeling of such infections is illustrated. Plague, cholera, syphilis, influenza, SARS, MERS, COVID‐19, and new potential epidemic and pandemic infections and their consequences are described and the background for the spread of acute and chronic infections and the transition to endemic infections is discussed. The way we can prevent and fight pandemics is illustrated from the old and new well‐known pandemics. Surprisingly, the political reactions through different periods have not changed much during the centuries.
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Affiliation(s)
- Niels Høiby
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Institute of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
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2
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Pollett S, Nelson MI, Kasper M, Tinoco Y, Simons M, Romero C, Silva M, Lin X, Halpin RA, Fedorova N, Stockwell TB, Wentworth D, Holmes EC, Bausch DG. Phylogeography of Influenza A(H3N2) Virus in Peru, 2010-2012. Emerg Infect Dis 2016. [PMID: 26196599 PMCID: PMC4517729 DOI: 10.3201/eid2108.150084] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
It remains unclear whether lineages of influenza A(H3N2) virus can persist in the tropics and seed temperate areas. We used viral gene sequence data sampled from Peru to test this source-sink model for a Latin American country. Viruses were obtained during 2010-2012 from influenza surveillance cohorts in Cusco, Tumbes, Puerto Maldonado, and Lima. Specimens positive for influenza A(H3N2) virus were randomly selected and underwent hemagglutinin sequencing and phylogeographic analyses. Analysis of 389 hemagglutinin sequences from Peru and 2,192 global sequences demonstrated interseasonal extinction of Peruvian lineages. Extensive mixing occurred with global clades, but some spatial structure was observed at all sites; this structure was weakest in Lima and Puerto Maldonado, indicating that these locations may experience greater viral traffic. The broad diversity and co-circulation of many simultaneous lineages of H3N2 virus in Peru suggests that this country should not be overlooked as a potential source for novel pandemic strains.
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Yoshida Y, Tsuneki A, Itagaki A, Tsuchie H, Okada T, Narai S, Kasagi M, Tanaka K, Ito A, Ryoke K, Kageyama S. Frequent Isolations of Influenza A Viruses (H1N1)pdm09 with Identical Hemagglutinin Sequences for More Than Three Months in Japan. Yonago Acta Med 2015; 58:165-171. [PMID: 26740735 PMCID: PMC4701988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 10/21/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Although it has been suggested that antigenic drift does not occur in a single epidemic season in temperate countries, there is not enough evidence on the circulation period of influenza virus with identical nucleotide sequences. Therefore, strains of influenza virus were isolated sequentially during five consecutive epidemic seasons in Japan and their nucleotide sequences were determined. METHODS Nasal swabs or aspirated nasal discharges were collected from influenza A virus antigen-positive individuals living in Tottori Prefecture, Japan for five consecutive winters starting in 2009-2010, and subjected to viral isolation, determination of hemagglutinin nucleotide sequence and phylogenic analyses. The nucleotide sequences were compared with each other and also with those of foreign strains in the International Nucleotide Sequence Database. RESULTS Totally 288 A(H1N1)pdm09 strains were tested and those composed 38 clusters with identical ones displaying 100% nucleotide homology. One strain showed sequential infections more than three months without any detectable mutation, and a maximum interval of two detection timings of strains was 94 days. This implies that influenza viruses mutate rarely in an epidemic season in Japan if they can be hypothesized, mutation frequency of influenza viruses being mostly the same among strains. Among these identical strains, two strains were not only identical to other Japanese isolates, but also to those isolated in Mongolia and Thailand in the same epidemic season. CONCLUSION These results suggest that genetic drift has occurred infrequently in Japan as shown in some other countries. The drifted strains may have generated somewhere else and entered into Japan. These results support the proposed 'sink-source' model of viral ecology in which new lineages are seeded from a persistent influenza reservoir in tropical countries to 'sink' populations in temperate regions including Japan.
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Affiliation(s)
- Yu Yoshida
- Division of Virology, Department of Microbiology and Immunology, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8503, Japan; †Division of Oral and Maxillofacial Biopathological Surgery, Department of Medicine of Sensory and Motor Organs, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Akeno Tsuneki
- Division of Virology, Department of Microbiology and Immunology, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Asao Itagaki
- Division of Virology, Department of Microbiology and Immunology, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Hideaki Tsuchie
- ‡Tottori Infectious Diseases Forum, Tottori Prefecture, Japan; §Tsuchie Internal Medicine and Pediatric Clinic, Sakaiminato 684-0011, Japan
| | - Takayoshi Okada
- ‡Tottori Infectious Diseases Forum, Tottori Prefecture, Japan; ‖Department of Pediatrics, Tottori Prefectural Kousei Hospital, Kurayoshi 682-0804, Japan
| | - Sakae Narai
- ‡Tottori Infectious Diseases Forum, Tottori Prefecture, Japan; ‖Department of Pediatrics, Tottori Prefectural Kousei Hospital, Kurayoshi 682-0804, Japan
| | - Masaaki Kasagi
- ‡Tottori Infectious Diseases Forum, Tottori Prefecture, Japan; ¶Kasagi Children's Clinic for Health Service, Yonago 683-0822, Japan
| | - Kiyoshi Tanaka
- ‡Tottori Infectious Diseases Forum, Tottori Prefecture, Japan; *Tanaka Pediatric Clinic, Tottori 680-0844, Japan
| | - Akiko Ito
- Division of Virology, Department of Microbiology and Immunology, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8503, Japan; †Division of Oral and Maxillofacial Biopathological Surgery, Department of Medicine of Sensory and Motor Organs, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Kazuo Ryoke
- †Division of Oral and Maxillofacial Biopathological Surgery, Department of Medicine of Sensory and Motor Organs, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Seiji Kageyama
- Division of Virology, Department of Microbiology and Immunology, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8503, Japan; ‡Tottori Infectious Diseases Forum, Tottori Prefecture, Japan
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4
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Wagner A. A genotype network reveals homoplastic cycles of convergent evolution in influenza A (H3N2) haemagglutinin. Proc Biol Sci 2015; 281:rspb.2013.2763. [PMID: 24827434 DOI: 10.1098/rspb.2013.2763] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Networks of evolving genotypes can be constructed from the worldwide time-resolved genotyping of pathogens like influenza viruses. Such genotype networks are graphs where neighbouring vertices (viral strains) differ in a single nucleotide or amino acid. A rich trove of network analysis methods can help understand the evolutionary dynamics reflected in the structure of these networks. Here, I analyse a genotype network comprising hundreds of influenza A (H3N2) haemagglutinin genes. The network is rife with cycles that reflect non-random parallel or convergent (homoplastic) evolution. These cycles also show patterns of sequence change characteristic for strong and local evolutionary constraints, positive selection and mutation-limited evolution. Such cycles would not be visible on a phylogenetic tree, illustrating that genotype network analysis can complement phylogenetic analyses. The network also shows a distinct modular or community structure that reflects temporal more than spatial proximity of viral strains, where lowly connected bridge strains connect different modules. These and other organizational patterns illustrate that genotype networks can help us study evolution in action at an unprecedented level of resolution.
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Affiliation(s)
- Andreas Wagner
- Institute of Evolutionary Biology and Environmental Sciences, University of Zurich, Building Y27, Winterthurerstrasse 190, Zurich 8057, Switzerland The Swiss Institute of Bioinformatics, Quartier Sorge, Batiment Genopode, Lausanne 1015, Switzerland The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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5
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Tan Y, Lam TTY, Wu C, Lee SS, Viboud C, Zhang R, Weinberger DM. Increasing similarity in the dynamics of influenza in two adjacent subtropical Chinese cities following the relaxation of border restrictions. J Gen Virol 2013; 95:531-538. [PMID: 24310518 DOI: 10.1099/vir.0.059998-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The drivers of influenza seasonality remain heavily debated, especially in tropical/subtropical regions where influenza activity can peak in winter, during the rainy season, or remain constant throughout the year. We compared the epidemiological and evolutionary patterns of seasonal influenza epidemics in Hong Kong and Shenzhen, two adjacent cities in subtropical southern China. This comparison represents a unique natural experiment, as connectivity between these two cities has increased over the past decade. We found that, whilst summer influenza epidemics in Shenzhen used to peak 1-3 months later than those in Hong Kong, the difference decreased after 2005 (P<0.0001). Phylogenetic analysis revealed that influenza isolates from Shenzhen have become genetically closer to those circulating in Hong Kong over time (P = 0.045). Furthermore, although Shenzhen isolates used to be more distant from the global putative source of influenza viruses than isolates from Hong Kong (P<0.001), this difference has narrowed (P = 0.02). Overall, our study reveals that influenza activities show remarkably distinct epidemiological and evolutionary patterns in adjacent subtropical cities and suggests that human mobility patterns can play a major role in influenza dynamics in the subtropics.
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Affiliation(s)
- Yi Tan
- Stanley Ho Centre for Emerging Infectious Diseases, School of Public Health and Primary Care, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China.,Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Chunli Wu
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, Guangdong, China
| | - Shui-Shan Lee
- Stanley Ho Centre for Emerging Infectious Diseases, School of Public Health and Primary Care, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Renli Zhang
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, Guangdong, China
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA.,Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
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6
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Poletto C, Meloni S, Colizza V, Moreno Y, Vespignani A. Host mobility drives pathogen competition in spatially structured populations. PLoS Comput Biol 2013; 9:e1003169. [PMID: 23966843 PMCID: PMC3744403 DOI: 10.1371/journal.pcbi.1003169] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 06/21/2013] [Indexed: 11/26/2022] Open
Abstract
Interactions among multiple infectious agents are increasingly recognized as a fundamental issue in the understanding of key questions in public health regarding pathogen emergence, maintenance, and evolution. The full description of host-multipathogen systems is, however, challenged by the multiplicity of factors affecting the interaction dynamics and the resulting competition that may occur at different scales, from the within-host scale to the spatial structure and mobility of the host population. Here we study the dynamics of two competing pathogens in a structured host population and assess the impact of the mobility pattern of hosts on the pathogen competition. We model the spatial structure of the host population in terms of a metapopulation network and focus on two strains imported locally in the system and having the same transmission potential but different infectious periods. We find different scenarios leading to competitive success of either one of the strain or to the codominance of both strains in the system. The dominance of the strain characterized by the shorter or longer infectious period depends exclusively on the structure of the population and on the the mobility of hosts across patches. The proposed modeling framework allows the integration of other relevant epidemiological, environmental and demographic factors, opening the path to further mathematical and computational studies of the dynamics of multipathogen systems.
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Affiliation(s)
- Chiara Poletto
- Computational Epidemiology Laboratory, Institute for Scientific Interchange, Turin, Italy.
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7
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HUANG P, LIANG LJ, HOU NM, ZHANG X, SU WZ, YU SY, ZHANG YH, WU J, CHEN WQ. Phylogenetic, molecular and drug-sensitivity analysis of HA and NA genes of human H3N2 influenza A viruses in Guangdong, China, 2007-2011. Epidemiol Infect 2013; 141:1061-9. [PMID: 22827898 PMCID: PMC9151889 DOI: 10.1017/s0950268812001318] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 05/23/2012] [Accepted: 05/30/2012] [Indexed: 11/06/2022] Open
Abstract
Annual H3N2 subtype influenza outbreaks in Guangdong, China are a severe public health issue and require ongoing monitoring of emerging viral variants. The variation and evolution of haemagglutinin (HA) and neuraminidase (NA) genes of influenza isolates from Guangdong during 2007-2011 and others from GenBank were analysed using Lasergene 7.1 and MEGA 5.05, and serological analysis of antigens was determined by haemagglutination inhibition (HI). Susceptibility to antiviral drugs was correlated with genetic mutations. Phylogenetic analysis and alignment of HA and NA genes were performed on 18 Guangdong isolates and 26 global reference strains. The non-synonymous (dN) evolutionary rate of HA1 was 3.13 times that of HA2. Compared with the A/Perth/16/2009 vaccine HA gene, homologies of Guangdong isolates were between 98.8-99.7% and 98.0-98·4% in 2009 and 2010, respectively. Amino-acid substitutions were found in five epitopes of HA1 from Guangdong isolates between 2007 and 2011, especially in epitopes B (N160K) and D (K174R/N). The K189E/N/Q and T228A mutations in the receptor-binding site (RBS) occurred in the 2010 strains, which affected the antigenicity of HA1. The antigenicity of the epidemic H3N2 isolates in 2010 was somewhat different from that of A/Perth/16/2009. The Guangdong H3N2 isolates were determined to be oseltamivir-resistant with IC50 of 0.396 ± 0.085 nmol/l (n=17) and zanamivir-resistant with IC50 of 0.477 ± 0.149 nmol/l (n=18). Variations were present in epitopes B and D, two sites in the RBS and two glycosylation sites in the Guangdong H3N2 HA1 gene. The majority of the Guangdong H3N2 isolates were sensitive to oseltamivir and zanamivir. Compared to the World Health Organization 2012 vaccine strains, Guangdong H3N2 strains varied genetically and antigenically to some degree.
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MESH Headings
- Antibodies, Viral
- Antigens, Viral
- Antiviral Agents/pharmacology
- Biological Evolution
- China/epidemiology
- Disease Outbreaks
- Drug Resistance, Viral
- Gene Expression Regulation, Viral/physiology
- Genetic Variation
- Hemagglutinins, Viral/genetics
- Hemagglutinins, Viral/metabolism
- Humans
- Influenza A Virus, H3N2 Subtype/drug effects
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza, Human/epidemiology
- Influenza, Human/virology
- Neuraminidase/genetics
- Neuraminidase/metabolism
- Phylogeny
- RNA, Viral
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Affiliation(s)
- P. HUANG
- Key Laboratory for Emergency Pathogen Detection, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
- Department of Epidemiology, School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - L.-J. LIANG
- Key Laboratory for Emergency Pathogen Detection, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
- Department of Epidemiology, School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - N.-M. HOU
- Key Laboratory for Emergency Pathogen Detection, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - X. ZHANG
- Key Laboratory for Emergency Pathogen Detection, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - W.-Z. SU
- Key Laboratory for Emergency Pathogen Detection, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - S.-Y. YU
- Department of Epidemiology, School of Public Health and Tropic Medicine, Southern Medical University, Guangzhou, China
| | - Y.-H. ZHANG
- Key Laboratory for Emergency Pathogen Detection, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - J. WU
- Key Laboratory for Emergency Pathogen Detection, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - W. Q. CHEN
- Department of Epidemiology, School of Public Health, Sun Yat-Sen University, Guangzhou, China
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8
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Viboud C, Nelson MI, Tan Y, Holmes EC. Contrasting the epidemiological and evolutionary dynamics of influenza spatial transmission. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120199. [PMID: 23382422 DOI: 10.1098/rstb.2012.0199] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In the past decade, rapid increases in the availability of high-resolution molecular and epidemiological data, combined with developments in statistical and computational methods to simulate and infer migration patterns, have provided key insights into the spatial dynamics of influenza A viruses in humans. In this review, we contrast findings from epidemiological and molecular studies of influenza virus transmission at different spatial scales. We show that findings are broadly consistent in large-scale studies of inter-regional or inter-hemispheric spread in temperate regions, revealing intense epidemics associated with multiple viral introductions, followed by deep troughs driven by seasonal bottlenecks. However, aspects of the global transmission dynamics of influenza viruses are still debated, especially with respect to the existence of tropical source populations experiencing high levels of genetic diversity and the extent of prolonged viral persistence between epidemics. At the scale of a country or community, epidemiological studies have revealed spatially structured diffusion patterns in seasonal and pandemic outbreaks, which were not identified in molecular studies. We discuss the role of sampling issues in generating these conflicting results, and suggest strategies for future research that may help to fully integrate the epidemiological and evolutionary dynamics of influenza virus over space and time.
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Affiliation(s)
- Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA.
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9
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Kucharski AJ, Gog JR. The role of social contacts and original antigenic sin in shaping the age pattern of immunity to seasonal influenza. PLoS Comput Biol 2012; 8:e1002741. [PMID: 23133346 PMCID: PMC3486889 DOI: 10.1371/journal.pcbi.1002741] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 08/31/2012] [Indexed: 11/23/2022] Open
Abstract
Recent serological studies of seasonal influenza A in humans suggest a striking characteristic profile of immunity against age, which holds across different countries and against different subtypes of influenza. For both H1N1 and H3N2, the proportion of the population seropositive to recently circulated strains peaks in school-age children, reaches a minimum between ages 35–65, then rises again in the older ages. This pattern is little understood. Variable mixing between different age classes can have a profound effect on disease dynamics, and is hence the obvious candidate explanation for the profile, but using a mathematical model of multiple influenza strains, we see that age dependent transmission based on mixing data from social contact surveys cannot on its own explain the observed pattern. Instead, the number of seropositive individuals in a population may be a consequence of ‘original antigenic sin’; if the first infection of a lifetime dominates subsequent immune responses, we demonstrate that it is possible to reproduce the observed relationship between age and seroprevalence. We propose a candidate mechanism for this relationship, by which original antigenic sin, along with antigenic drift and vaccination, results in the age profile of immunity seen in empirical studies. The way in which a population builds immunity to influenza affects outbreak size and the emergence of new strains. However, although age-specific immunity has been widely discussed for the 2009 influenza pandemic, the age profile of immunity to seasonal influenza remains little understood. In contrast to many infections, the proportion of people immune to recent strains peaks in school-age children then reaches a minimum between ages 35–65, before rising again in older age groups. Our results suggest that rather than variable mixing between different age groups being solely responsible, the pattern may be shaped by an effect known as ‘original antigenic sin’, by which the first infection of a lifetime dictates subsequent immune responses: instead of developing antibodies to every new virus that is encountered, the immune system may reuse the response to a similar virus it has already seen. The framework we describe, which extends theoretical models to allow for comparison with data, also opens the possibility of investigating the mechanisms behind patterns of immunity to other evolving pathogens.
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Affiliation(s)
- Adam J Kucharski
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom.
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10
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Age profile of immunity to influenza: effect of original antigenic sin. Theor Popul Biol 2011; 81:102-12. [PMID: 22209755 DOI: 10.1016/j.tpb.2011.12.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 12/13/2011] [Accepted: 12/14/2011] [Indexed: 11/19/2022]
Abstract
When multiple infections are possible during an individual's lifetime, as with influenza, a host's history of infection and immunity will determine the result of future exposures. In turn, the suite of varying individual infection histories will shape the population level dynamics of the disease. Exploring the consequences of precisely how immunity is acquired using mathematical models has proven challenging though: if n strains have circulated previously, there are 2(n) combinations of past infection to consider. However, by using an age-structured mathematical model of a disease with multiple strains, we can examine the population immune profile without explicitly keeping track of all possible infection histories. This framework allows previously unknown consequences of assumptions about immune acquisition to be observed. In particular, we see that 'original antigenic sin' can reduce immunity in some age groups: these immune blind spots could be responsible for the unexpectedly high severity of certain past influenza epidemics.
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11
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Ito K, Igarashi M, Miyazaki Y, Murakami T, Iida S, Kida H, Takada A. Gnarled-trunk evolutionary model of influenza A virus hemagglutinin. PLoS One 2011; 6:e25953. [PMID: 22028800 PMCID: PMC3189952 DOI: 10.1371/journal.pone.0025953] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 09/13/2011] [Indexed: 01/08/2023] Open
Abstract
Human influenza A viruses undergo antigenic changes with gradual accumulation of amino acid substitutions on the hemagglutinin (HA) molecule. A strong antigenic mismatch between vaccine and epidemic strains often requires the replacement of influenza vaccines worldwide. To establish a practical model enabling us to predict the future direction of the influenza virus evolution, relative distances of amino acid sequences among past epidemic strains were analyzed by multidimensional scaling (MDS). We found that human influenza viruses have evolved along a gnarled evolutionary pathway with an approximately constant curvature in the MDS-constructed 3D space. The gnarled pathway indicated that evolution on the trunk favored multiple substitutions at the same amino acid positions on HA. The constant curvature was reasonably explained by assuming that the rate of amino acid substitutions varied from one position to another according to a gamma distribution. Furthermore, we utilized the estimated parameters of the gamma distribution to predict the amino acid substitutions on HA in subsequent years. Retrospective prediction tests for 12 years from 1997 to 2009 showed that 70% of actual amino acid substitutions were correctly predicted, and that 45% of predicted amino acid substitutions have been actually observed. Although it remains unsolved how to predict the exact timing of antigenic changes, the present results suggest that our model may have the potential to recognize emerging epidemic strains.
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Affiliation(s)
- Kimihito Ito
- Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
- PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Manabu Igarashi
- Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Yutaka Miyazaki
- Faculty of Liberal Arts and Sciences, Osaka University of Economics and Law, Yao, Japan
| | - Teiji Murakami
- Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Syaka Iida
- Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Hiroshi Kida
- Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
- Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- OIE Reference Laboratory for Highly Pathogenic Avian Influenza, Sapporo, Japan
- SORST, Japan Science and Technology Agency, Saitama, Japan
| | - Ayato Takada
- Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
- School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
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12
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[Bioinformatics technologies for the analysis of antigenic evolution of influenza viruses]. Uirusu 2011; 61:3-13. [PMID: 21972551 DOI: 10.2222/jsv.61.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Human influenza viruses mutate from time to time, causing annual epidemics worldwide. The strong immune pressure in the human population selects a new variant every year, and the antigenic change is one of the primary reasons why vaccination is not a perfect measure to control seasonal influenza. Thus prediction of antigenic change of influenza A virus has been one of the major public health goals. In this review bioinformatics technologies that have been developed to achieve this goal were summarized.
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13
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Martinez-Hernandez F, Jimenez-Gonzalez DE, Martinez-Flores A, Villalobos-Castillejos G, Vaughan G, Kawa-Karasik S, Flisser A, Maravilla P, Romero-Valdovinos M. What happened after the initial global spread of pandemic human influenza virus A (H1N1)? A population genetics approach. Virol J 2010; 7:196. [PMID: 20727188 PMCID: PMC2936310 DOI: 10.1186/1743-422x-7-196] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 08/20/2010] [Indexed: 11/21/2022] Open
Abstract
Viral population evolution dynamics of influenza A is crucial for surveillance and control. In this paper we analyzed viral genetic features during the recent pandemic caused by the new influenza human virus A H1N1, using a conventional population genetics approach based on 4689 hemagglutinin (HA) and neuraminidase (NA) sequences available in GenBank submitted between March and December of 2009. This analysis showed several relevant aspects: a) a scarce initial genetic variability within the viral isolates from some countries that increased along 2009 when influenza was dispersed around the world; b) a worldwide virus polarized behavior identified when comparing paired countries, low differentiation and high gene flow were found in some pairs and high differentiation and moderate or scarce gene flow in others, independently of their geographical closeness, c) lack of positive selection in HA and NA due to increase of the population size of virus variants, d) HA and NA variants spread in a few months all over the world being identified in the same countries in different months along 2009, and e) containment of viral variants in Mexico at the beginning of the outbreak, probably due to the control measures applied by the government.
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Affiliation(s)
- Fernando Martinez-Hernandez
- Departamento de Ecología de Agentes Patogenos, Hospital General Dr, Manuel Gea Gonzalez, Calzada de Tlalpan 4800, DF 14080, Mexico
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14
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Intraseasonal dynamics and dominant sequences in H3N2 influenza. PLoS One 2010; 5:e8544. [PMID: 20049091 PMCID: PMC2796395 DOI: 10.1371/journal.pone.0008544] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Accepted: 11/02/2009] [Indexed: 11/30/2022] Open
Abstract
Long-term influenza evolution has been well studied, but the patterns of sequence diversity within seasons are less clear. H3N2 influenza genomes sampled from New York State over ten years indicated intraseasonal changes in evolutionary dynamics. Using the mean Hamming distance of a set of amino acid or nucleotide sequences as an indicator of its diversity, we found that influenza sequence diversity was significantly higher during the early epidemic period than later in the influenza season. Diversity was lowest during the peak of the epidemic, most likely due to the high prevalence of a single dominant amino acid sequence or very few dominant sequences during the peak epidemic period, corresponding with rapid expansion of the viral population. The frequency and duration of dominant sequences varied by influenza protein, but all proteins had an abundance of one distinct sequence during the peak epidemic period. In New York State from 1995 to 2005, high sequence diversity during the early epidemic suggested that seasonal antigenic drift could have occurred primarily in this period, followed by a clonal expansion of typically one clade during the peak of the epidemic, possibly indicating a shift to neutral drift or purifying selection.
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15
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Evidence for persistence of and antiviral resistance and reassortment events in seasonal influenza virus strains circulating in Cambodia. J Clin Microbiol 2009; 48:295-7. [PMID: 19889906 DOI: 10.1128/jcm.01687-09] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The analysis of A/H1N1 and A/H3N2 influenza viruses collected between 2005 and 2008 in Cambodia detected strains resistant to oseltamivir and confirmed widespread resistance to adamantanes. Phylogenetic analyses revealed intrasubtype reassortment, probable reemergence of A/H3N2 viruses in two consecutive seasons, and cocirculation of different lineages in each subtype.
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Pariani E, Amendola A, Zappa A, Bianchi S, Colzani D, Anselmi G, Zanetti A, Tanzi E. Molecular characterization of influenza viruses circulating in Northern Italy during two seasons (2005/2006 and 2006/2007) of low influenza activity. J Med Virol 2008; 80:1984-91. [DOI: 10.1002/jmv.21323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Abstract
The relationship between influenza antigenic drift and vaccination lies at the intersection of evolutionary biology and public health, and it must be viewed and analyzed in both contexts simultaneously. In this paper, 1 review what is known about the effects of antigenic drift on vaccination and the effects of vaccination on antigenic drift, and I suggest some simple ways to detect the presence of antigenic drift in seasonal influenza data. If antigenic drift occurs on the time scale of a single influenza season, it may be associated with the presence of herd immunity at the beginning of the season and may indicate a need to monitor for vaccine updates at the end of the season. The relationship between antigenic drift and vaccination must also be viewed in the context of the global circulation of influenza strains and the seeding of local and regional epidemics. In the data sets I consider--from New Zealand, New York, and France--antigenic drift can be statistically detected during some seasons, and seeding of epidemics appears to be endogenous sometimes and exogenous at other times. Improved detection of short-term antigenic drift and epidemic seeding would significantly benefit influenza monitoring efforts and vaccine selection.
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Affiliation(s)
- Maciej F Boni
- Resources for the Future, Washington, DC 20036, USA.
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18
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Nelson MI, Edelman L, Spiro DJ, Boyne AR, Bera J, Halpin R, Ghedin E, Miller MA, Simonsen L, Viboud C, Holmes EC. Molecular epidemiology of A/H3N2 and A/H1N1 influenza virus during a single epidemic season in the United States. PLoS Pathog 2008; 4:e1000133. [PMID: 18725925 PMCID: PMC2495036 DOI: 10.1371/journal.ppat.1000133] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Accepted: 07/23/2008] [Indexed: 01/10/2023] Open
Abstract
To determine the spatial and temporal dynamics of influenza A virus during a single epidemic, we examined whole-genome sequences of 284 A/H1N1 and 69 A/H3N2 viruses collected across the continental United States during the 2006–2007 influenza season, representing the largest study of its kind undertaken to date. A phylogenetic analysis revealed that multiple clades of both A/H1N1 and A/H3N2 entered and co-circulated in the United States during this season, even in localities that are distant from major metropolitan areas, and with no clear pattern of spatial spread. In addition, co-circulating clades of the same subtype exchanged genome segments through reassortment, producing both a minor clade of A/H3N2 viruses that appears to have re-acquired sensitivity to the adamantane class of antiviral drugs, as well as a likely antigenically distinct A/H1N1 clade that became globally dominant following this season. Overall, the co-circulation of multiple viral clades during the 2006–2007 epidemic season revealed patterns of spatial spread that are far more complex than observed previously, and suggests a major role for both migration and reassortment in shaping the epidemiological dynamics of human influenza A virus. This study is the first of its kind to reconstruct the spread of an epidemic of influenza A virus across a single country, in this case the United States. In contrast to a single viral lineage spreading across this country, a phylogenetic analysis of the whole-genome sequences of more than 300 influenza A viruses of the A/H1N1 and A/H3N2 subtypes sampled from the 2006–2007 epidemic season reveals that multiple phenotypically and antigenically distinct viral lineages of entered and co-circulated in the US during this time. Furthermore, the widespread co-circulation of multiple lineages, even in geographically remote localities, allowed for frequent reassortment between influenza A viruses of the same subtype. Through reassortment, a minor lineage of A/H3N2 viruses surprisingly re-acquired sensitivity to the adamantane class of antiviral drugs, and a new A/H1N1 antigenic variant emerged that later became globally dominant. In sum, these results highlight the complexity of the spread of influenza A virus in time and space, and highlight the need for intensified global surveillance involving whole-genome sequence data.
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Affiliation(s)
- Martha I. Nelson
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Laurel Edelman
- Surveillance Data Inc., Plymouth Meeting, Pennsylvania, United States of America
| | - David J. Spiro
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Alex R. Boyne
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Jayati Bera
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Rebecca Halpin
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Elodie Ghedin
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mark A. Miller
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lone Simonsen
- Department of Global Health, School of Public Health and Health Services, The George Washington University, Washington, D.C., United States of America
| | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Edward C. Holmes
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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19
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Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, Holmes EC. The genomic and epidemiological dynamics of human influenza A virus. Nature 2008; 453:615-9. [PMID: 18418375 DOI: 10.1038/nature06945] [Citation(s) in RCA: 706] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Accepted: 03/19/2008] [Indexed: 11/09/2022]
Abstract
The evolutionary interaction between influenza A virus and the human immune system, manifest as 'antigenic drift' of the viral haemagglutinin, is one of the best described patterns in molecular evolution. However, little is known about the genome-scale evolutionary dynamics of this pathogen. Similarly, how genomic processes relate to global influenza epidemiology, in which the A/H3N2 and A/H1N1 subtypes co-circulate, is poorly understood. Here through an analysis of 1,302 complete viral genomes sampled from temperate populations in both hemispheres, we show that the genomic evolution of influenza A virus is characterized by a complex interplay between frequent reassortment and periodic selective sweeps. The A/H3N2 and A/H1N1 subtypes exhibit different evolutionary dynamics, with diverse lineages circulating in A/H1N1, indicative of weaker antigenic drift. These results suggest a sink-source model of viral ecology in which new lineages are seeded from a persistent influenza reservoir, which we hypothesize to be located in the tropics, to sink populations in temperate regions.
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Affiliation(s)
- Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3JT, UK.
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20
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Nelson MI, Simonsen L, Viboud C, Miller MA, Holmes EC. Phylogenetic analysis reveals the global migration of seasonal influenza A viruses. PLoS Pathog 2007; 3:1220-8. [PMID: 17941707 PMCID: PMC2323296 DOI: 10.1371/journal.ppat.0030131] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Accepted: 07/24/2007] [Indexed: 11/24/2022] Open
Abstract
The winter seasonality of influenza A virus in temperate climates is one of the most widely recognized, yet least understood, epidemiological patterns in infectious disease. Central to understanding what drives the seasonal emergence of this important human pathogen is determining what becomes of the virus during the non-epidemic summer months. Herein, we take a step towards elucidating the seasonal emergence of influenza virus by determining the evolutionary relationship between populations of influenza A virus sampled from opposite hemispheres. We conducted a phylogenetic analysis of 487 complete genomes of human influenza A/H3N2 viruses collected between 1999 and 2005 from Australia and New Zealand in the southern hemisphere, and a representative sub-sample of viral genome sequences from 413 isolates collected in New York state, United States, representing the northern hemisphere. We show that even in areas as relatively geographically isolated as New Zealand's South Island and Western Australia, global viral migration contributes significantly to the seasonal emergence of influenza A epidemics, and that this migration has no clear directional pattern. These observations run counter to suggestions that local epidemics are triggered by the climate-driven reactivation of influenza viruses that remain latent within hosts between seasons or transmit at low efficiency between seasons. However, a complete understanding of the seasonal movements of influenza A virus will require greatly expanded global surveillance, particularly of tropical regions where the virus circulates year-round, and during non-epidemic periods in temperate climate areas. The winter seasonality of influenza A virus in temperate climates is one of the most puzzling epidemiological patterns in infectious disease. To help resolve the issue of influenza seasonality, we studied, using viral genome sequence data, the patterns of global migration of influenza A virus, particularly between the northern and southern hemispheres. A phylogenetic analysis of approximately 900 complete genomes of the H3N2 subtype of human influenza A virus sampled from New Zealand and Australia (southern hemisphere), and New York state, United States (northern hemisphere), revealed that cross-hemisphere migration frequently occurs in both directions and involves multiple viral strains. Such global viral traffic therefore contributes significantly to the introduction of new influenza epidemics in both northern and southern hemispheres. These results also show that influenza A virus migrates afar during non-epidemic periods, rather than persisting locally at low levels during the influenza “off-season”. However, although this represents the largest and first bihemisphere study of its kind to our knowledge, the results highlight the need for sampling from tropical regions and during non-epidemic periods in temperate areas. Studies of this kind are critical to fully understand the geographical dispersal of influenza A virus and the role of climate in triggering seasonal epidemics.
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Affiliation(s)
- Martha I Nelson
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Lone Simonsen
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mark A Miller
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Edward C Holmes
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail:
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21
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Nelson MI, Simonsen L, Viboud C, Miller MA, Taylor J, George KS, Griesemer SB, Ghedin E, Sengamalay NA, Spiro DJ, Volkov I, Grenfell BT, Lipman DJ, Taubenberger JK, Holmes EC. Stochastic processes are key determinants of short-term evolution in influenza a virus. PLoS Pathog 2007; 2:e125. [PMID: 17140286 PMCID: PMC1665651 DOI: 10.1371/journal.ppat.0020125] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 10/20/2006] [Indexed: 11/18/2022] Open
Abstract
Understanding the evolutionary dynamics of influenza A virus is central to its surveillance and control. While immune-driven antigenic drift is a key determinant of viral evolution across epidemic seasons, the evolutionary processes shaping influenza virus diversity within seasons are less clear. Here we show with a phylogenetic analysis of 413 complete genomes of human H3N2 influenza A viruses collected between 1997 and 2005 from New York State, United States, that genetic diversity is both abundant and largely generated through the seasonal importation of multiple divergent clades of the same subtype. These clades cocirculated within New York State, allowing frequent reassortment and generating genome-wide diversity. However, relatively low levels of positive selection and genetic diversity were observed at amino acid sites considered important in antigenic drift. These results indicate that adaptive evolution occurs only sporadically in influenza A virus; rather, the stochastic processes of viral migration and clade reassortment play a vital role in shaping short-term evolutionary dynamics. Thus, predicting future patterns of influenza virus evolution for vaccine strain selection is inherently complex and requires intensive surveillance, whole-genome sequencing, and phenotypic analysis. A comparative analysis of 413 complete genomes of the H3N2 subtype of human influenza A virus sampled from New York State, United States, the largest and first population-based study of its kind, reveals that viral evolution within epidemic seasons is dominated by the random importation of genetically different viral strains from other geographic areas, rather than by natural selection favoring local strains able to escape the human immune response. Multiple clades of genetically distinct viral strains cocirculate across the entire state within any season and occasionally exchange genes through reassortment. Both genetic diversity and geographic viral “traffic” are extensive within epidemics. Therefore, the evolution of influenza A virus is strongly shaped by random migration and reassortment and is far harder to predict than previously realized. Consequently, intensive sampling and whole-genome sequencing are essential for selecting viral strains for future vaccine production.
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Affiliation(s)
- Martha I Nelson
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Lone Simonsen
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mark A Miller
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jill Taylor
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Kirsten St George
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Sara B Griesemer
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Elodie Ghedin
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Naomi A Sengamalay
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - David J Spiro
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Igor Volkov
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Bryan T Grenfell
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David J Lipman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jeffery K Taubenberger
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Edward C Holmes
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail:
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22
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Abstract
ABSTRACT
The purpose of this state‐of‐the‐science review was to identify strategies and household‐level interventions for public health nurses to help prevent the acquisition and spread of viral upper respiratory infections (URI) in the community. Even though viral URI are a major global economic and social problem, surprisingly little research has been conducted to attempt to prevent them or reduce their transmission, probably because URI (with the exception of epidemic influenza) are generally considered to be mild and self‐limited. Based on the research to date, public health nurses can use several promising strategies for prevention: (a) provide more tailored educational messages regarding preventive strategies such as vaccination, hand hygiene, spatial separation of infected household members, avoidance of antibiotics to treat viral URI, and environmental cleaning (e.g., for toys or other shared items), which are delivered personally rather than passively (e.g., pamphlets placed in a waiting room); (b) use each patient encounter in any setting to encourage influenza vaccination for relevant risk groups; (c) encourage use of alcohol hand sanitizers by household members during the cold and flu season; and (d) provide opportunities for skill development for adult and child household members (e.g., cover your cough, when to seek care or an antibiotic).
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Affiliation(s)
- Elaine L Larson
- School of Nursing and Mailman School of Public Health, Columbia University, New York, NY 10032, USA.
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23
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Abstract
Recent developments in complete-genome sequencing, antigenic mapping and epidemiological modelling are greatly improving our knowledge of the evolution of human influenza virus at the epidemiological scale. In particular, recent studies have revealed a more complex relationship between antigenic evolution, natural selection and reassortment than previously realized. Despite these advances, there is much that remains to be understood about the epidemiology of influenza virus, particularly the processes that determine the virus's strong seasonality. We argue that a complete understanding of the evolutionary biology of this important human pathogen will require a genomic view of genetic diversity, including the acquisition of polymorphism data from within individual hosts and from geographical regions, particularly the tropics, which have been poorly surveyed to date.
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Affiliation(s)
- Martha I Nelson
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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