Human/Swine H1N1 Influenza
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Analyses of the phylogenetic origin of the outbreak and its reassortment history
There has been confusion about the origin of the virus and whether it should be called swine flu. Obviously it is now a human flu in that it is spreading from person to person but it is clear from the analyses here and elsewhere that it has its immediate origins in swine flu. More specifically it is the product of a reassortment event between at least 2 swine flu variants. One of these variants (the 'Triple reassortant') has some genes with their own unique histories including links to avian strains and human H3N2 (one of the circulating season forms). The problem is that these genes entered pig flu at least 20 years ago (first isolation) but probably longer (Zhou et al. 1999). Given such a long time (at flu's evolution rate) it seems unlikely that this has a direct bearing on the emergence of the current outbreak.
By far the most parsimonious explanation for the phylogenetic results here is that the final reassortment between classic swine flu and Eurasian swine flu occurred in a pig infected with both variants.
A paper describing the phylogenetic origin and dating the common ancestors with swine flu has just been published.
Reconstruction of the sequence of reassortment events leading up to the emergence of S-OIV. Shaded boxes represent host species, avian (green), swine (red), and human (grey). Coloured lines represent interspecies transmission pathways of influenza genes. The 8 genomic segments are represented as parallel lines in descending order of size. Dates marked with dashed vertical lines on “elbows” indicate the mean time of divergence of the S-OIV genes from corresponding virus lineages. Reassortment events not involved with the emergence of human disease are omitted. Fort Dix refers to the last major outbreak of S-OIV in humans.
Figure from Smith et al. 2009 Nature. In press: doi:10.1038/nature08182. Copyright S.J.Lycett and A.Rambaut. Published under the creative commons licence.
- Phylogenetics of all segments - Andrew Rambaut 25 Apr 2009
- Phylogenetics (all segments) with additional swine isolates - Gavin Smith, Vijaykrishna Dhanasekaran, Justin Bahl 02 May 2009
- Phylogenetics of H1N1 with an even wider sampling of avian, swine and human isolates - Work in progress, Brian Foley
- Phylogenetics of Polymerase in HXNX (avian, swine, human) - work in progress, Sam Lycett
- Evolutionary history of H1N1 genes (Marco Salemi, Becca Gray)- updated 5 May 2009
/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
Comments
Vijay Dhanasekaran
May 5, 2009
Hi Marco, The PB1 gene is not derived from an avian-like virus, but is derived from swine H3N2 viruses, that in turn got this gene from human H3N2 viruses.
Marco Salemi
May 5, 2009
Hi Vijay, you're right, thanks for the correction! I will post an amended figure later today. It's difficult to come up with a single cartoon tree representing all the major lineages, any suggestion?
Vijay Dhanasekaran
May 5, 2009
Hi Marco, the PB1 gene tree would be good to make the cartoon fig. It also contains a human (H3N2) derived swine lineage
in addition to the above lineages.