Human/Swine H1N1 Influenza

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    HistoryEdited Jun 7, 2009 11:19 AM by Andrew Rambaut…

    Phylogenetics (all segments) with additional swine isolates

    Preliminary modeled NJ trees showing relationship to HK swine viruses. The new Hong Kong swine viruses were isolated through the HKU swine surveillance program supervised by Prof. Yi Guan and Prof. Malik Peiris.


    Genotype_2May09.png
    Download file "Genotype_2May09.pdf"

    To identify the evolutionary history of each of gene segments, multiple sequence alignments of each of the gene segments first using all available data to identify relationships between the swine/human influena A (H1N1) viruses and all other sequences and also to determine appropriate rooting. We then compiled datasets using representative virus isolates from each of the major lineages identified. MrModeltest 2.2 (Nylander, 2004) was used to determine the appropriate DNA substitution model and γ-rate heterogeneity, and the generated models (GTR+I+G in all cases) were used in all subsequent analyses. Neighbor-joining (NJ) trees were constructed using PAUP* 4.0 (Swofford, 2001). Phylogenies generated were used to infer the reassortment pathway of the swine/human influena A (H1N1) viruses.
    Sw_H1_nj.tre.pdf
    Sw_N1_nj.tre.pdf
    Sw_PB2_nj.tre.pdfSw_PB1_nj.tre.pdfSw_PA_nj.tre.pdfSw_NP_nj.tre.pdfSw_M_nj.tre.pdfSw_NS_nj.tre.pdfDownload file "Sw_H1_nj.tre.pdf"
    Download file "Sw_N1_nj.tre.pdf"
    Download file "Sw_PB2_nj.tre.pdf"
    Download file "Sw_PB1_nj.tre.pdf"
    Download file "Sw_PA_nj.tre.pdf"
    Download file "Sw_NP_nj.tre.pdf"
    Download file "Sw_M_nj.tre.pdf"
    Download file "Sw_NS_nj.tre.pdf"

    Comments

    Gavin Smith
    May 2, 2009

    The isolate SW/HK/NS857/01 (H1N2) is in an odd position in the PB1 tree. We need to look at the traces again as it looks like a contigging error.

    /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