Human/Swine H1N1 Influenza
HistoryEdited Apr 30, 2009 5:43 PM by Andrew Rambaut…

Phylogenetics of all segments

Phylogenetic position of A/California/04/2009 for each genomic segment.

Analysis by Andrew Rambaut 26 Apr 2009

Preliminary Neighbor-Joining trees using the HKY distance metric.




Blue and green shading denote clades of related strains although extensive reassortment and heterogenous sampling means that these clades contain different sets of strains.

See below for PDF versions of all these trees.
HA SegmentNA gene

MP

NP

NS

PA

PB1

PB2
PDF versions of these trees:
  • HA genomic segment: Download file "HA.NJ.pdf"
  • MP genomic segment: Download file "MP.NJ.pdf"
  • NA genomic segment: Download file "NA.NJ.pdf"
  • NP genomic segment: Download file "NP.NJ.pdf"
  • NS genomic segment: Download file "NS.NJ.pdf"
  • PA genomic segment: Download file "PA.NJ.pdf"
  • PB1 genomic segment: Download file "PB1.NJ.pdf"
  • PB2 genomic segment: Download file "PB2.NJ.pdf"



Comments

Philippe Lemey
Apr 30, 2009

Can't really read the location data from the taxa names, but maybe it would be nice to do a discrete phylogeographic analysis on all segments, and making a single GE visualization of them?

Oliver Pybus
Apr 30, 2009

Andrew - you could attach the pdf files, rather than importing images, which would enable the taxa names to be read,

Andrew Rambaut
Apr 30, 2009

Done.

/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/HotListrambaut2009-07-08 14:53:06+00:002009-07-08 14:53:06updated10Updated links to final versionlycett2009-07-01 05:34:14+00:002009-07-01 05:34:14updated9rambaut2009-06-12 07:40:19+00:002009-06-12 07:40:19updated8Added tag - hotrambaut2009-06-12 07:40:17+00:002009-06-12 07:40:17addTag7rambaut2009-06-12 07:40:08+00:002009-06-12 07:40:08updated6rambaut2009-06-12 07:27:06+00:002009-06-12 07:27:06updated5rambaut2009-06-12 07:17:50+00:002009-06-12 07:17:50updated4rambaut2009-06-12 07:15:25+00:002009-06-12 07:15:25updated3rambaut2009-06-12 07:15:17+00:002009-06-12 07:15:17updated2First additionrambaut2009-06-12 07:13:50+00:002009-06-12 07:13:50created1wiki2009-07-08T14:53:06+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 Rambaut10 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 Vijaykris...Falserambaut2009-07-08T14:53:06+00:00Shanghai/71T/09 does not have PB2-627Klycett2009-06-28 16:11:04+00:002009-06-28 16:11:04updated7lycett2009-06-28 16:06:53+00:002009-06-28 16:06:53updated6lycett2009-06-19 07:03:23+00:002009-06-19 07:03:23updated5Added tag - hotlycett2009-06-19 07:03:22+00:002009-06-19 07:03:22addTag4A/Shanghai/71T/2009 & PB2-627Klycett2009-06-18 22:40:51+00:002009-06-18 22:40:51updated3PB2-627K on A/Shanghai/71T/2009lycett2009-06-18 22:34:10+00:002009-06-18 22:34:10updated2First additionlycett2009-06-18 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+00:00comas2009-05-10 21:28:29+00:002009-05-10 21:28:29updated6comas2009-05-10 21:27:07+00:002009-05-10 21:27:07updated5comas2009-05-10 21:26:45+00:002009-05-10 21:26:45updated4Added tag - hotcomas2009-05-10 21:26:43+00:002009-05-10 21:26:43addTag3comas2009-05-10 21:26:25+00:002009-05-10 21:26:25updated2First additioncomas2009-05-10 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+00:00pybus2009-05-08 15:45:54+00:002009-05-08 15:45:54updated6pybus2009-05-06 19:32:17+00:002009-05-06 19:32:17updated5Added tag - selectionpybus2009-05-06 18:30:11+00:002009-05-06 18:30:11addTag4Added tag - hotpybus2009-05-06 18:29:59+00:002009-05-06 18:29:59addTag3pybus2009-05-06 18:29:25+00:002009-05-06 18:29:25updated2First additionpybus2009-05-06 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+00:00comas2009-05-08 12:59:46+00:002009-05-08 12:59:46updated7rambaut2009-05-08 11:40:12+00:002009-05-08 11:40:12updated6Added tag - genetic structurecomas2009-05-08 10:49:11+00:002009-05-08 10:49:11addTag5Added tag - transmissioncomas2009-05-08 10:48:52+00:002009-05-08 10:48:52addTag4comas2009-05-08 10:45:56+00:002009-05-08 10:45:56updated3Added tag - hotcomas2009-05-08 10:44:35+00:002009-05-08 10:44:35addTag2First additioncomas2009-05-08 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