Human/Swine H1N1 Influenza
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Estimates of the date of origin of the outbreak
We hope to accurately estimate the time of the most recent common ancestor (TMRCA) of the outbreak. This provides a conservative estimate of the epidemic's origin (the outbreak may be older than the TMRCA, but not younger).
- UPDATED: Origin of outbreak (HA gene) 3 May 2009 - Oliver Pybus
- Origin of outbreak (HA gene) 30 Apr 2009 - Andrew Rambaut - a slightly different approach.
- UPDATED: Origin of outbreak (NA gene) 6 May 2009 - Oliver Pybus
- Complete genome pairwise comparisons 30 Apr 2009 - Mike Worobey
- Origin of outbreak (MP gene) 1 May 2009 - Gavin Smith and group
- Origin of outbreak (HA gene - with additional swine) 2 May 2009 - Gavin and group
- Origin of outbreak (NA gene - with additional swine) 2 May 2009 - Gavin and group
- Origin of outbreak (MP gene) 2 May 2009 - Oliver Pybus
- Origin of the outbreak (NP, NS, PA, PB1, PB2) 4th May 2009 - Gavin, Vijay, Justin
- Origin of the outbreak (PB2) 5th May 2009 - Gavin Smith, Vijay Dhanasekaren, Justin Bahl
- TMRCA all genes (GTR+G model) 4 May 2009 - Marco Salemi, Becca Gray
Graphical Summary:
Genetic structure of the outbreak
Analyses posted here aim to reconstruct the epidemic and transmission history of the outbreak from sampled gene sequences. Current estimates are understandably uncertain, as limited time has elapsed since sampling of this epidemic began. As the epidemic proceeds, these analyses will become progressively more certain.
Current sampling of gene segments and distribution of differences from the consensus:
Estimates of evolutionary rate
These analyses aim to estimate rates of evolution of different flu genes, by analysis of previously sampled swine or human flu sequences. These rate estimates are important because the sampling times between sequences in the current epidemic are not yet sufficient to estimate an outbreak-specific evolutionary rate.
- HA gene molecular clock rate 29 Apr 2009 - Oliver Pybus
- NA gene molecular clock rate 30 Apr 2009 - Oliver Pybus
- MP gene molecular clock rate 1 May 2009 - Oliver Pybus
- HA gene clock rate (human seasonal H1N1) 30 Apr 2009 - Mike Worobey
- MP molecular clock test 2 May 2009 - Gavin and group
- Molecular clock tests of the NP, NS, PA, PB1 genes 4 May 2009 - Gavin, Vijay and Justin
- Molecular clock test of the PB2 gene. Cinco de Mayo - Gavin Smith, Vijaykrishna Dhanasekaran, Justin Bahl
- Molecular clock analysis of all genes 4 May 2009 - Marco Salemi, Becca Gray & Group
Estimates of the basic reproductive number (R0)
/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
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