tag:blogger.com,1999:blog-1871542942842750523.post460636967199191513..comments2023-07-24T10:40:57.739-04:00Comments on dechronization: Swine Flu: Info-epidemiologyGlorhttp://www.blogger.com/profile/17707197225963721646noreply@blogger.comBlogger15125tag:blogger.com,1999:blog-1871542942842750523.post-27680749585423657882009-08-24T12:53:19.332-04:002009-08-24T12:53:19.332-04:00I can't fall into the entire "swine flu&q...I can't fall into the entire "swine flu" craze because I think it's a wee melodramatic. Most people that come in contact with it have zero symptoms, or just sleep it off. Why we Americans have lost our minds over the swine flu is beyond me. How many deaths in the U.S. have been attributed to it??Digital Scaleshttp://www.digitalscalesaz.comnoreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-74806313617175057772009-08-13T12:41:14.199-04:002009-08-13T12:41:14.199-04:00People with regular exposure to pigs are at increa...People with regular exposure to pigs are at increased risk of swine flu. More than 1100 people worldwide have died from swine flu since it emerged in Mexico and the US in April, according to the latest figures from the World.Sujan Patriciahttp://www.asiarooms.com/noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-7014449193796160042009-06-15T14:53:02.236-04:002009-06-15T14:53:02.236-04:00thanks for the information..really gr8 help for no...thanks for the information..really gr8 help for not-so-tech savy bloggers :)..keep us updated.Good Health Bloghttps://www.blogger.com/profile/01518857049400884588noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-23102266971976635292009-05-28T21:52:44.013-04:002009-05-28T21:52:44.013-04:00Good research Susan, Thanks for link.Good research Susan, Thanks for link.Natural Remedieshttp://www.healthremedies.comnoreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-53387095752247902112009-05-02T13:05:00.000-04:002009-05-02T13:05:00.000-04:00It clearly is a more complicated history that that...It clearly is a more complicated history that that. A new analysis out today, provides a hypothesis of how reassortment has likely produced the new H1N1 "swine flu" viruses we're seeing. A nice schematic is available <A HREF="http://tree.bio.ed.ac.uk/groups/influenza/wiki/aea97/Phylogenetic_analysis_and_reassortment.html" REL="nofollow">here.</A>Susan Perkinshttps://www.blogger.com/profile/05944116263349266952noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-86368537988069478962009-05-02T11:35:00.000-04:002009-05-02T11:35:00.000-04:00I think it's ironic that Taubenberger et al were a...<EM>I think it's ironic that Taubenberger et al were arguing that the 1918 virus came from avians, when their chart shows that it unambiguously is close to classical swine flu.</EM>You've got it backwards. The 1918 flu didn't come from swine flu. Swine flu came from the 1918 flu. That's why it looks like classic swine flu -- because it's the parent of swine flu. The order is avian -> 1918 human -> swine.<br /><br />This has been known since the 1930s.iayorkhttp://www.iayork.com/MysteryRays/noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-25052123153485768532009-05-01T09:39:00.000-04:002009-05-01T09:39:00.000-04:00A quick link to the great website of phylogenetic,...A <A HREF="http://tree.bio.ed.ac.uk/groups/influenza/" REL="nofollow">quick link</A> to the great website of phylogenetic, phylogeographic, and demographic analyses of H1N1 by Holmes, Pybus, Rambaut et al.Susan Perkinshttps://www.blogger.com/profile/05944116263349266952noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-39591084996978124542009-04-30T15:45:00.000-04:002009-04-30T15:45:00.000-04:00Hi,
As a first pass, I tried doing a similar ana...Hi, <br /><br />As a <A HREF="http://koppology.blogspot.com/2009/04/swine-flu-phylogeny-part-ii.html" REL="nofollow">first pass</A>, I tried doing a similar analysis, using the first 100 BLAST hits for each gene and a ML methodology. I'd definitely appreciate any feedback, especially from you guys. <br /><br />For a second attempt I'm going to try rooting the tree and will also add the genes that <A HREF="http://www.ncbi.nlm.nih.gov/pubmed/16208372?ordinalpos=53&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum" REL="nofollow"><br />Taubenberger et al.</A> used to characterize the 1918 influenza virus. By the way, I think it's ironic that Taubenberger et al were arguing that the 1918 virus came from avians, when their chart shows that it unambiguously is close to classical swine flu. <br /><br />I agree though, I think this is best left up to the experts -- I am mostly doing this for fun. <br /><br />Specifically, <A HREF="http://www.wired.com/wiredscience/2009/04/swinefluupdate/" REL="nofollow">Steve Salzberg et al.</A> seem to know what they're doing. <br /><br />Best, <br />DavidDavidhttps://www.blogger.com/profile/14326089794226622680noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-68328600841488439962009-04-30T15:44:00.000-04:002009-04-30T15:44:00.000-04:00The importance of vaccine and preparedness has bec...The importance of vaccine and preparedness has become more obvious in wake of the "swine flu virus". The CDC has developed a healthcare hand book to help combat a variety of Vaccine Preventable Diseases. <br /><br />The CDC’s Epidemiology and Prevention of Vaccine-Preventable Diseases, 11th Edition (The Pink Book) – Just Released!<br /> <br /><br />The new, 11th edition of the Centers for Disease Control and Prevention’s (CDC) Epidemiology and Prevention of Vaccine Preventable Diseases (The Pink Book) is now available from the Public Health Foundation (PHF). “The Pink Book” provides physicians, nurses, nurse practitioners, physician assistants, pharmacists, and others with comprehensive information on vaccine-preventable diseases. The new 11th edition contains the latest information and updates on immunization, including:<br /><br />Revised principles of vaccination <br />Updated recommendations on immunization <br />New immunization strategies for healthcare practices and providers <br />Guidelines on vaccine safety <br />This essential resource is now available for ordering online by visiting the PHF online store at http://bookstore.phf.org. Ordering via mail, phone, fax, and purchase order is also available by calling PHF toll-free at (877)252-1200 for full instructions.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-73428710255597994272009-04-29T15:06:00.000-04:002009-04-29T15:06:00.000-04:00I might even happen to know someone...someone clos...I might even happen to know someone...someone close...who is working on this very problem as we speak.Susan Perkinshttps://www.blogger.com/profile/05944116263349266952noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-6357742231704284992009-04-29T15:03:00.000-04:002009-04-29T15:03:00.000-04:00I think this other blogger had a good idea, but sh...I think this other blogger had a good idea, but she definitely should have been a little more circumspect before publicizing her results. Even if the neighbor-joining tree can be trusted it seems clear that sampling is an issue with her trees. I assumed there would be people doing this job with the appropriate methods, seems like a great opportunity for someone with training in phylogenetics to make a difference.Glorhttps://www.blogger.com/profile/17707197225963721646noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-34626743268055386032009-04-29T14:27:00.000-04:002009-04-29T14:27:00.000-04:00Wow! This swine flu outbreak has the bloggers goi...Wow! This swine flu outbreak has the bloggers going crazy. Just received an alert from <A HREF="http://www.genomeweb.com/node/915761?emc=el&m=374599&l=2&v=e6ae0fd5bb" REL="nofollow">Genome web</A>, which pointed me to <A HREF="http://scienceblogs.com/digitalbio/2009/04/did_the_california_h1n1_swine.php" REL="nofollow">this blog</A> by Sandra Porter. Porter apparently downloaded some sequences off GenBank and used their tree-building methods (NJ only of course) to come to the conclusion that the new strains are related to those from an outbreak at a county fair in Ohio in 2007. Many people commented on that post, pointing out the multitude of problems with this analysis and cautioning that this relationship is not upheld so rushing off to publicize this is not a good idea. The moral of the story is probably: let trained systematists make trees. Just because a web application will let you do it doesn't mean you should.Susan Perkinshttps://www.blogger.com/profile/05944116263349266952noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-79829715229888852702009-04-27T18:07:00.000-04:002009-04-27T18:07:00.000-04:00Correction 1: I meant that this could potentially ...Correction 1: I meant that this could potentially be a case of intra-subtype reassortment – a combination of U.S. H1 and Eurasian N1. This is only what I consider to be a logical interpretation of the CDC's MMWR article (see above) on the 2 SoCal cases. I have no molecular subtyping information on any other case, therefore it would be irresponsible to generalize.<br /><br />Correction 2: I meant to write "<A HREF="http://www3.niaid.nih.gov/topics/Flu/Research/basic/AntigenicShiftIllustration.htm" REL="nofollow">antigenic shift</A>", not "drift".<br /><br />Sorry about that. I can't seem to edit my own comment on Blogger. Let's hope the data becomes available soon.sergios-orestis kolokotronishttps://www.blogger.com/profile/05492639186814501804noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-68446502523525211682009-04-26T21:51:00.000-04:002009-04-26T21:51:00.000-04:00Get on it, Sergios!Get on it, Sergios!Susan Perkinshttps://www.blogger.com/profile/05944116263349266952noreply@blogger.comtag:blogger.com,1999:blog-1871542942842750523.post-35828791004552744302009-04-26T20:48:00.000-04:002009-04-26T20:48:00.000-04:00Maybe a reassorting strain? The CDC's journal Morb...Maybe a reassorting strain? The CDC's journal <I>Morbidity and Mortality Weekly Report</I> (MMWR) <A HREF="http://www.cdc.gov/mmwr/preview/mmwrhtml/mm5815a5.htm" REL="nofollow">reported on April 24</A> on the two SoCal cases that they are indeed swine influenzavirus A (H1N1). It is notable that these two cases appear to be epidemiologically unlinked yet genetically similar. Their "<A HREF="http://en.wikipedia.org/wiki/Influenza_hemagglutinin" REL="nofollow">hemagglutinin (HA)</A> gene sequences are similar to those of swine influenzaviruses that have circulated among U.S. pigs since ~1999; however, two genes coding for the <A HREF="http://en.wikipedia.org/wiki/Neuraminidase" REL="nofollow">neuraminidase (NA)</A> and <A HREF="" REL="nofollow">matrix (M)</A> proteins are similar to corresponding genes of swine influenzaviruses of the Eurasian lineage" [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/19081490" REL="nofollow">Ref</A>]. It's possible this is evidence of <A HREF="http://www3.niaid.nih.gov/topics/Flu/Research/basic/AntigenicDriftIllustration.htm" REL="nofollow">antigenic drift</A> (<A HREF="http://www.hhmi.org/biointeractive/animations/subunit/sub_frames.htm" REL="nofollow">video</A>). Although since there is no formal national surveillance program for swine influenzaviruses to inform us on which strains are actually present in the North American pig population.<br /><br />I don't know if I am missing this outbreak's sequences on public databases, but it'd be good for public health if independent groups of scientists could analyze sequences as they get produced to estimate mutation rates, the evolution of resistance/susceptibility to antiviral drugs, etc.<br /><br />There is -yet- no apparent link between humans and contact with pigs, so maybe the sequences can help tease apart patterns.sergios-orestis kolokotronishttps://www.blogger.com/profile/05492639186814501804noreply@blogger.com