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Levin SA, Dushoff J, Plotkin JB. Evolution and persistence of influenza A and other diseases. Math Biosci 2004; 188:17-28. [PMID: 14766091 DOI: 10.1016/j.mbs.2003.08.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2002] [Revised: 08/13/2003] [Accepted: 08/13/2003] [Indexed: 10/26/2022]
Abstract
The evolution of the etiological agents of disease presents one of the greatest challenges for their control, and makes essential complementing standard epidemiological investigations with broader approaches that allow for evolutionary change. Given the stunning genetic diversity that is possible for many such agents, such as the influenza virus, it is impossible to represent all of the diversity manifest at the level of amino acid sequences. We show that drift-variant influenza strains naturally cluster into groups which are associated with functionally important epitopic regions. Dominant clusters typically replace each other every 2-5 years, and this feature is fundamental to the development of vaccination strategies. We furthermore show that stochastic fluctuations can greatly magnify small interference effects among strains, or even among subtypes, leading for example to competitive exclusion in situations where such effects would be unexpected based on the usual deterministic models. We suggest that this effect might be involved in the explanations of some persistent empirical anomalies.
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Affiliation(s)
- Simon A Levin
- Department of Ecology and Evolutionary Biology, Princeton University, 203 Eno Hall, Princeton, NJ 08544 1003, USA.
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Abstract
Sixty-one SARS coronavirus genomic sequences derived from the early, middle, and late phases of the severe acute respiratory syndrome (SARS) epidemic were analyzed together with two viral sequences from palm civets. Genotypes characteristic of each phase were discovered, and the earliest genotypes were similar to the animal SARS-like coronaviruses. Major deletions were observed in the Orf8 region of the genome, both at the start and the end of the epidemic. The neutral mutation rate of the viral genome was constant but the amino acid substitution rate of the coding sequences slowed during the course of the epidemic. The spike protein showed the strongest initial responses to positive selection pressures, followed by subsequent purifying selection and eventual stabilization.
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Nakajima K, Nobusawa E, Tonegawa K, Nakajima S. Restriction of amino acid change in influenza A virus H3HA: comparison of amino acid changes observed in nature and in vitro. J Virol 2003; 77:10088-98. [PMID: 12941919 PMCID: PMC224596 DOI: 10.1128/jvi.77.18.10088-10098.2003] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We introduced 248 single-point amino acid changes into hemagglutinin (HA) protein of the A/Aichi/2/68 (H3N2) strain by a PCR random mutation method. These changes were classified as positive or negative according to their effect on hemadsorption activity. We observed following results. (i) The percentage of surviving amino acid changes on the HA1 domain that did not abrogate hemadsorption activity was calculated to be ca. 44%. In nature, it is estimated to be ca. 39.6%. This difference in surviving amino acid changes on the HA protein between natural isolates and in vitro mutants might be due to the immune pressure against the former. (ii) A total of 26 amino acid changes in the in vitro mutants matched those at which mainstream amino acid changes had occurred in the H3HA1 polypeptide from 1968 to 2000. Of these, 25 were positive. We suggest that the majority of amino acid changes on the HA protein during evolution might be restricted to those that were positive on the HA of A/Aichi/2/68. (iii) We constructed two-point amino acid changes on the HA protein by using positive mutants. These two-point amino acid changes with a random combination did not inhibit hemadsorption activity. It is possible that an accumulation of amino acid change might occur without order. (iv) From the analysis of amino acids participating in mainstream amino acid change, each antigenic site could be further divided into smaller sites. The amino acid substitutions in the gaps between these smaller sites resulted in mostly hemadsorption-negative changes. These gap positions may play an important role in maintaining the function of the HA protein, and therefore amino acid changes are restricted at these locations.
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Affiliation(s)
- Katsuhisa Nakajima
- Department of Virology, Nagoya City University, 1 Kawasumi, Mizuho-chou, Mizuho-ku, Nagoya 467-8601, Japan.
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Ruan Y, Wei CL, Ling AE, Vega VB, Thoreau H, Se Thoe SY, Chia JM, Ng P, Chiu KP, Lim L, Zhang T, Chan KP, Lin Ean LO, Ng ML, Leo SY, Ng LFP, Ren EC, Stanton LW, Long PM, Liu ET. Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection. Lancet 2003; 361:1779-85. [PMID: 12781537 PMCID: PMC7140172 DOI: 10.1016/s0140-6736(03)13414-9] [Citation(s) in RCA: 331] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The cause of severe acute respiratory syndrome (SARS) has been identified as a new coronavirus. Whole genome sequence analysis of various isolates might provide an indication of potential strain differences of this new virus. Moreover, mutation analysis will help to develop effective vaccines. METHODS We sequenced the entire SARS viral genome of cultured isolates from the index case (SIN2500) presenting in Singapore, from three primary contacts (SIN2774, SIN2748, and SIN2677), and one secondary contact (SIN2679). These sequences were compared with the isolates from Canada (TOR2), Hong Kong (CUHK-W1 and HKU39849), Hanoi (URBANI), Guangzhou (GZ01), and Beijing (BJ01, BJ02, BJ03, BJ04). FINDINGS We identified 129 sequence variations among the 14 isolates, with 16 recurrent variant sequences. Common variant sequences at four loci define two distinct genotypes of the SARS virus. One genotype was linked with infections originating in Hotel M in Hong Kong, the second contained isolates from Hong Kong, Guangzhou, and Beijing with no association with Hotel M (p<0.0001). Moreover, other common sequence variants further distinguished the geographical origins of the isolates, especially between Singapore and Beijing. INTERPRETATION Despite the recent onset of the SARS epidemic, genetic signatures are emerging that partition the worldwide SARS viral isolates into groups on the basis of contact source history and geography. These signatures can be used to trace sources of infection. In addition, a common variant associated with a non-conservative aminoacid change in the S1 region of the spike protein, suggests that immunological pressures might be starting to influence the evolution of the SARS virus in human populations.
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Affiliation(s)
- Yijun Ruan
- Genome Institute of Singapore, Singapore
| | | | - Ai Ee Ling
- Virology Section, Department of Pathology, Singapore General Hospital, Singapore
| | | | | | - Su Yun Se Thoe
- Virology Section, Department of Pathology, Singapore General Hospital, Singapore
| | | | - Patrick Ng
- Genome Institute of Singapore, Singapore
| | | | - Landri Lim
- Genome Institute of Singapore, Singapore
| | - Tao Zhang
- Genome Institute of Singapore, Singapore
| | - Kwai Peng Chan
- Virology Section, Department of Pathology, Singapore General Hospital, Singapore
| | - Lynette Oon Lin Ean
- Virology Section, Department of Pathology, Singapore General Hospital, Singapore
| | - Mah Lee Ng
- Department of Microbiology and Electron Microscopy Unit, National University of Singapore
| | | | - Lisa FP Ng
- Genome Institute of Singapore, Singapore
| | | | | | | | - Edison T Liu
- Genome Institute of Singapore, Singapore
- Correspondence to: Dr Edison T Liu, 1 Science Park Road 05–01, Singapore Science Park II, Singapore, 117528
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Qi Z, Hu Y, Li W, Chen Y, Zhang Z, Sun S, Lu H, Zhang J, Bu D, Ling L, Chen R. Phylogeny of SARS-CoV as inferred from complete genome comparison. CHINESE SCIENCE BULLETIN-CHINESE 2003; 48:1175-1178. [PMID: 32214702 PMCID: PMC7089017 DOI: 10.1007/bf03183930] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2003] [Accepted: 06/06/2003] [Indexed: 11/18/2022]
Abstract
SARS-CoV, as the pathogeny of severe acute respiratory syndrome (SARS), is a mystery that the origin of the virus is still unknown even a few isolates of the virus were completely sequenced. To explore the genesis of SARS-CoV, the FDOD method previously developed by us was applied to comparing complete genomes from 12 SARS-CoV isolates to those from 12 previously identified coronaviruses and an unrooted phylogenetic tree was constructed. Our results show that all SARS-CoV isolates were clustered into a clique and previously identified coronaviruses formed the other clique. Meanwhile, the three groups of coronaviruses depart from each other clearly in our tree that is consistent with the results of prevenient papers. Differently, from the topology of the phylogenetic tree we found that SARS-CoV is more close to group 1 within genus coronavirus. The topology map also shows that the 12 SARS-CoV isolates may be divided into two groups determined by the association with the SARS-CoV from the Hotel M in Hong Kong that may give some information about the infectious relationship of the SARS.
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Affiliation(s)
- Zhen Qi
- Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yu Hu
- Institute of Computing Technology, Chinese Academy of Sciences, 100080 Beijing, China
| | - Wei Li
- Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing, China
| | - Yanjun Chen
- Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Zhihua Zhang
- Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Shiwei Sun
- Institute of Computing Technology, Chinese Academy of Sciences, 100080 Beijing, China
| | - Hongchao Lu
- Institute of Computing Technology, Chinese Academy of Sciences, 100080 Beijing, China
| | - Jingfen Zhang
- Institute of Computing Technology, Chinese Academy of Sciences, 100080 Beijing, China
| | - Dongbo Bu
- Institute of Computing Technology, Chinese Academy of Sciences, 100080 Beijing, China
| | - Lunjiang Ling
- Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Runsheng Chen
- Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- Institute of Computing Technology, Chinese Academy of Sciences, 100080 Beijing, China
- Beijing Genomics Institute, Chinese Academy of Sciences, 101300 Beijing, China
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McCormack GP, Clewley JP. The application of molecular phylogenetics to the analysis of viral genome diversity and evolution. Rev Med Virol 2002; 12:221-38. [PMID: 12125014 DOI: 10.1002/rmv.355] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
DNA sequencing and molecular phylogenetics are increasingly being used in virology laboratories to study the transmission of viruses. By reconstructing the evolutionary history of viral genomes the behaviour of viral populations can be modelled, and the future of epidemics may be forecast. The manner in which such viral DNA sequences are analysed is the focus of this review. Many researchers resort to the often-quoted 'black box' approach because phylogenetics theory can be daunting, and phylogenetics software packages can appear to be difficult to use. However, because phylogenetic analyses are often used in important and sensitive arenas, for example to provide evidence indicating transmission between persons, it is vital that appropriate care is taken to estimate reliably true relationships. In this review, we discuss how a molecular phylogenetics study should be approached, give an overview of the methods and programs for analysing DNA sequence data, and point readers to appropriate texts for further details. The aim of this review, therefore, is to provide researchers with an easy to understand guide to molecular phylogenetics, with special reference to viral genomes.
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Affiliation(s)
- Grace P McCormack
- Biology Department, National University of Ireland, Maynooth, County Kildare, Ireland
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Plotkin JB, Dushoff J, Levin SA. Hemagglutinin sequence clusters and the antigenic evolution of influenza A virus. Proc Natl Acad Sci U S A 2002; 99:6263-8. [PMID: 11972025 PMCID: PMC122937 DOI: 10.1073/pnas.082110799] [Citation(s) in RCA: 181] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2002] [Indexed: 11/18/2022] Open
Abstract
Continual mutations to the hemagglutinin (HA) gene of influenza A virus generate novel antigenic strains that cause annual epidemics. Using a database of 560 viral RNA sequences, we study the structure and tempo of HA evolution over the past two decades. We detect a critical length scale, in amino acid space, at which HA sequences aggregate into clusters, or swarms. We investigate the spatio-temporal distribution of viral swarms and compare it to the time series of the influenza vaccines recommended by the World Health Organization. We introduce a method for predicting future dominant HA amino acid sequences and discuss its potential relevance to vaccine choice. We also investigate the relationship between cluster structure and the primary antibody-combining regions of the HA protein.
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Affiliation(s)
- Joshua B Plotkin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA.
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Bush RM, Fitch WM, Smith CB, Cox NJ. Predicting influenza evolution: the impact of terminal and egg-adapted mutations. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0531-5131(01)00643-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
Phylogenetic trees reconstruct past evolution and can provide evidence of past evolutionary pressure on genes and on individual codons. In addition to tracing past evolutionary events, molecular phylogenetics might also be used to predict future evolution. Our ability to verify adaptive hypotheses using phylogenetics has broad implications for vaccine design, genomics and structural biology.
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Ayala FJ, Fitch WM, Clegg MT. Variation and evolution in plants and microorganisms: toward a new synthesis 50 years after Stebbins. Proc Natl Acad Sci U S A 2000; 97:6941-4. [PMID: 10860953 PMCID: PMC34366 DOI: 10.1073/pnas.97.13.6941] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- F J Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697-2525, USA.
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