Human/Swine H1N1 Influenza

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    HistoryEdited May 8, 2009 12:42 PM by Sam Lycett…

    Useful References

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    References relating to influenza evolution

    Dunham EJ, Dugan VG, Kaser EK, Perkins SE, Brown IH et al. (2009) Different evolutionary trajectories of European avian-like and classical swine H1N1 influenza A viruses. J Virol: JVI.02565-02508.http://jvi.asm.org/cgi/content/abstract/JVI.02565-08v1

    Lessler J, Cummings DAT, Fishman S, Vora A & Burke DS (2007) Transmissibility of swine flu at Fort Dix, 1976. J. R. Soc. Interface 4:755-762.http://rsif.royalsocietypublishing.org/content/4/15/755.long

    Nelson MI, Viboud C, Simonsen L, Bennett RT et al. (2008) Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918. PLoS Pathog 4: e1000012.http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1000012

    Newman AP, Reisdorf E, Beinemann J et al. (2008) Human case of swine influenza A (H1N1) triple reassortant virus infection, Wisconsin. Emerg Infect Dis 14:1470-1472. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18760023

    Kiso M, Mitamura K, Sakai-Tagawa Y, Shiraishi K, Kawakami C et al. (2004) Resistant influenza A viruses in children treated with oseltamivir: descriptive study. The Lancet 364: 759-765. http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(04)16934-1/fulltext


    Tsan-Yuk Lam, Chung-Chau Hon, Zhenggang Wang, Raymond Kin-Hi Hui, Fanya Zengand Frederick Chi-Ching Leung (2007) Evolutionary analyses of European H1N2 swine influenza A virus by placing timestamps on the multiple reassortment events. Virus Research131, 271-278. doi:10.1016/j.virusres.2007.08.012


    Abstract: A novel H1N2 swine influenza A virus emerged in Europe since 1994. Previous phylogenetic analyses revealed that its genome segments were derived from H1N1 human virus, H3N2 human virus and avian-like H1N1/H3N2 swine virus, indicating the possibility of multiple reassortments events. However, dates of these reassortment events have not been investigated systematically. In this study, we used both global and local molecular clock concepts in a maximum likelihood framework to extrapolate the times of origins of the genome segments in European H1N2 swine viruses, and deduced that novel neuraminidase, hemagglutinin and other internal protein genes were introduced to the European H1N2 lineage at the 1970s, early 1980s and late 1980s, respectively through reassortments. Furthermore, in light of the evolutionary timescale reconstructed for the H1N2 viruses, we argue that further reassortments, in addition to those responsible for the introductions of novel genome segments, might have also occurred among the viruses prior to the outbreaks arose in United Kingdom at 1994. Our results confirm that the viral genes of various origins have stably maintained in swine population for many years before the multiple genetic reassortant was detected. Our evolutionary analyses also suggested that the HA and NA genes evolved in a significantly higher rate of synonymous substitutions after they were introduced from human to swine and established the European H1N2 swine lineage.


    References relating to analysis methods used

    Drummond A, Pybus OG, Rambaut A (2003) Inference of viral evolutionary rates from molecular sequences. Adv. Parasitol. 54:331-58 [Review]

    Drummond AJ, Ho SY, Phillips MJ, Rambaut A. (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol. 4:e88

    Drummond AJ, Pybus OG, Rambaut A, Forsberg R, Rodrigo A (2003) Measurably evolving populations. Trends in Ecology & Evolution 18:481-8 [Review]

    Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214.

    Zwickl DJ. (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation, The University of Texas at Austin.

    Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology & Evolution 22:1185-92

    References to this outbreak

    Novel Swine-Origin Influenza AVIT (2009) Emergence of a Novel Swine-Origin Influenza A (H1N1) Virus in Humans. N Engl J Med: NEJMoa0903810.


    Comments

    /groups/influenza/search/index.rss?sort=modifiedDate&sortDirection=reverse&tag=sectionlist/groups/influenza/search/?sort=modifiedDate&sortDirection=reverse&tag=sectionSectionsCustomTagSidebarCustomTagSidebar?sort=modifiedDate&sortDirection=reverse&tag=section0/groups/influenza/sidebar/CustomTagSidebarmodifiedDate5CustomTagSidebarreversesectionSectionscustom/groups/influenza/search/index.rss?tag=hotlist/groups/influenza/search/?tag=hotWhat’s HotHotListHot!?tag=hot20/groups/influenza/sidebar/HotListrambautAndrew Rambaut2010-04-22 13:35:38+00:002010-04-22 13:35:38updated12rambautAndrew Rambaut2010-04-22 13:34:53+00:002010-04-22 13:34:53updated11rambautAndrew Rambaut2009-07-08 14:53:06+00:002009-07-08 14:53:06updated10Updated links to final versionlycettSam Lycett2009-07-01 05:34:14+00:002009-07-01 05:34:14updated9rambautAndrew Rambaut2009-06-12 07:40:19+00:002009-06-12 07:40:19updated8Added tag - hotrambautAndrew Rambaut2009-06-12 07:40:17+00:002009-06-12 07:40:17addTag7rambautAndrew Rambaut2009-06-12 07:40:08+00:002009-06-12 07:40:08updated6rambautAndrew Rambaut2009-06-12 07:27:06+00:002009-06-12 07:27:06updated5rambautAndrew Rambaut2009-06-12 07:17:50+00:002009-06-12 07:17:50updated4rambautAndrew Rambaut2009-06-12 07:15:25+00:002009-06-12 07:15:25updated3rambautAndrew Rambaut2009-06-12 07:15:17+00:002009-06-12 07:15:17updated2First additionrambautAndrew Rambaut2009-06-12 07:13:50+00:002009-06-12 07:13:50created1wiki2010-04-22T13:35:38+00:00groups/influenza/wiki/1b2c3FalseH1N1: Origins and evolution of the current epidemic/groups/influenza/wiki/1b2c3/H1N1_Origins_and_evolution_of_the_current_epidemic.htmlAndrew Rambaut12 updatesH1N1: Origins and evolution of the current epidemic Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic Gavin J. D. Smith1, Dhanasekaran Vijaykrishna1...Falserambaut2010-04-22T13:35:38+00:00Shanghai/71T/09 does not have PB2-627KlycettSam Lycett2009-06-28 16:11:04+00:002009-06-28 16:11:04updated7lycettSam Lycett2009-06-28 16:06:53+00:002009-06-28 16:06:53updated6lycettSam Lycett2009-06-19 07:03:23+00:002009-06-19 07:03:23updated5Added tag - hotlycettSam Lycett2009-06-19 07:03:22+00:002009-06-19 07:03:22addTag4A/Shanghai/71T/2009 & PB2-627KlycettSam Lycett2009-06-18 22:40:51+00:002009-06-18 22:40:51updated3PB2-627K on A/Shanghai/71T/2009lycettSam Lycett2009-06-18 22:34:10+00:002009-06-18 22:34:10updated2First additionlycettSam Lycett2009-06-18 22:12:59+00:002009-06-18 22:12:59created1wiki2009-06-28T16:11:04+00:00groups/influenza/wiki/8bc58FalsePB2-627K & PB2-701N in A/Shanghai/71T/2009/groups/influenza/wiki/8bc58/PB2627K__PB2701N_in_AShanghai71T2009.htmlSam Lycett7 updatesPB2-627K & PB2-701N in A/Shanghai/71T/2009 Notes on A/Shanghai/71T/2009 by Sam Lycett Update 28 June 09 The sequences A/Shanghai/71T/2009 were updated on 24...Falselycett2009-06-28T16:11:04+00:00comasIñaki Comas2009-05-10 21:28:29+00:002009-05-10 21:28:29updated6comasIñaki Comas2009-05-10 21:27:07+00:002009-05-10 21:27:07updated5comasIñaki Comas2009-05-10 21:26:45+00:002009-05-10 21:26:45updated4Added tag - hotcomasIñaki Comas2009-05-10 21:26:43+00:002009-05-10 21:26:43addTag3comasIñaki Comas2009-05-10 21:26:25+00:002009-05-10 21:26:25updated2First additioncomasIñaki Comas2009-05-10 21:13:16+00:002009-05-10 21:13:16created1wiki2009-05-10T21:28:29+00:00groups/influenza/wiki/aba06FalseUpdated Median Joining network (HA genes) - 8 May 2009 - Iñaki Comas/groups/influenza/wiki/aba06/Updated_Median_Joining_network_HA_genes__8_May_2009__Iaki_Comas.htmlIñaki Comas6 updatesUpdated Median Joining network (HA genes) - 8 May 2009 - Iñaki Comas Here is an update of the median joining network with all swine samples available at GISAID as of 8 of May. The alignment was provided by Oliver Pyb...Falsecomas2009-05-10T21:28:29+00:00pybusOliver Pybus2009-05-08 15:45:54+00:002009-05-08 15:45:54updated6pybusOliver Pybus2009-05-06 19:32:17+00:002009-05-06 19:32:17updated5Added tag - selectionpybusOliver Pybus2009-05-06 18:30:11+00:002009-05-06 18:30:11addTag4Added tag - hotpybusOliver Pybus2009-05-06 18:29:59+00:002009-05-06 18:29:59addTag3pybusOliver Pybus2009-05-06 18:29:25+00:002009-05-06 18:29:25updated2First additionpybusOliver Pybus2009-05-06 18:18:26+00:002009-05-06 18:18:26created1wiki2009-05-08T15:45:54+00:00groups/influenza/wiki/87337FalseAmino acid changes in HA, NA & MP leading to outbreak 6 May 2009 - Oliver Pybus and Samir Bhatt/groups/influenza/wiki/87337/Amino_acid_changes_in_HA_NA__MP_leading_to_outbreak_6_May_2009__Oliver_Pybus_and_Samir_Bhatt.htmlOliver Pybus6 updatesAmino acid changes in HA, NA & MP leading to outbreak 6 May 2009 - Oliver Pybus and Samir Bhatt So, I hear you ask, what amino acid changes have occurred along those long branches leading to the outbreak strain? Right, we've gone and ...Falsepybus2009-05-08T15:45:54+00:00comasIñaki Comas2009-05-08 12:59:46+00:002009-05-08 12:59:46updated7rambautAndrew Rambaut2009-05-08 11:40:12+00:002009-05-08 11:40:12updated6Added tag - genetic structurecomasIñaki Comas2009-05-08 10:49:11+00:002009-05-08 10:49:11addTag5Added tag - transmissioncomasIñaki Comas2009-05-08 10:48:52+00:002009-05-08 10:48:52addTag4comasIñaki Comas2009-05-08 10:45:56+00:002009-05-08 10:45:56updated3Added tag - hotcomasIñaki Comas2009-05-08 10:44:35+00:002009-05-08 10:44:35addTag2First additioncomasIñaki Comas2009-05-08 10:37:39+00:002009-05-08 10:37:39created1wiki2009-05-08T12:59:46+00:00groups/influenza/wiki/8e6d0FalseMedian joining network (HA gene) - 7May2009 - Iñaki Comas/groups/influenza/wiki/8e6d0/Median_joining_network_HA_gene__7May2009__Iaki_Comas.htmlIñaki Comas7 updatesMedian joining network (HA gene) - 7May2009 - Iñaki Comas I have created a median joining network with the HA sequences present in the NCBI as of 7May2009. This includes 49 isolates from different locat...Falsecomas2009-05-08T12:59:46+00:00hot/groups/influenza/search/index.rss?sort=modifiedDate&kind=all&sortDirection=reverse&excludePages=wiki/welcomelist/groups/influenza/search/?sort=modifiedDate&kind=all&sortDirection=reverse&excludePages=wiki/welcomeRecent ChangesRecentChangesListUpdates?sort=modifiedDate&kind=all&sortDirection=reverse&excludePages=wiki/welcome0/groups/influenza/sidebar/RecentChangesListmodifiedDateallRecent ChangesRecentChangesListUpdateswiki/welcomeNo recent changes.reverse5search