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Influenza

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+#REDIRECT [[Influenza]]
-{{flu}}
-{{evolutionary biology}}
-{{Lead rewrite|date=April 2010}}
-The virus causing [[influenza]] is one of the best known pathogens found in various [[species]]. In particular, the virus is found in birds as well as [[mammal]]s including horses, pigs, and humans.<ref name=six>{{cite journal |doi=10.1371/journal.pone.0005022 |pmid=19325912 |pmc=2658884 |last1=Liu |first1=S |last2=Kang |first2=J |last3=Chen |first3= J |last4=Tai |first4=D |last5=Jiang |first5=W |last6=Hou |first6=G |last7=Chen |first7=J |last8=Li |first8=J |last9=Huang |first9=B |year=2009 |title=Panorama phylogenetic diversity and distribution of type A influenza virus |journal=PLoS ONE |volume=4 |pages=1–20 |editor1-last=Field |editor1-first=Dawn |issue=3 }}</ref> The [[phylogeny]], or the evolutionary history of a particular species, is an important component when analyzing the '''evolution of influenza'''. [[Phylogenetic tree]]s are graphical models of the relationships between various species. They can be used to trace the virus back to particular species and show how organisms that look so different may be so closely related.<ref name=six/>
-==Mechanisms of evolution==
-Two common mechanisms by which viruses evolve are [[reassortment]] and [[genetic drift]].<ref name=nine>{{cite journal |doi=10.1007/BF01728660 |last1=Scholtissek |first1=C |year=1995 |title=Molecular evolution of influenza viruses|journal=Virus Genes |volume=11 |issue=2–3 |pages=209–215 |url=http://springerlink.metapress.com/content/v5747t6n11622627/fulltext.pdf |pmid=8828147 }}</ref>
-===Reassortment===
-Reassortment, also known as [[antigenic shift]], allows new viruses to evolve under both natural conditions and in artificial cultures.<ref name=nine/> Reassortment occurs in similar fashion as chromosome crossover events, as two different viral strains may come in contact and transfer some of their genetic information. This crossing-over event creates a mixture of the two viral strains, which may replicate as one hybrid virus that expresses traits from both original viruses.<ref name = twelve>{{cite journal |doi=10.1371/journal.pone.0093094 |last1=Peng |first1=J |last2=Yang |first2=H |last3=Jiang |first3=H |last4=Lin |first4=YX |last5=Lu |first5=CD |last6=Xu |first6=YW |last7=Zeng |first7=J |year=2014 |title=The origin of novel avian influenza A (H7N9) and mutation dynamics for its human-to-human transmissible capacity |journal=PLoS ONE |volume=9 |issue=3 |pages=e93094 |pmid=24671138 |pmc=3966860}}</ref> The mechanism of the evolutionary force of antigenic shift allows influenza viruses to exchange genes with strains that infect different species. Under this mechanism, a human influenza virus could exchange genes with an avian strain, and that is how pandemic strains arise. There have been three occurrences of pandemics caused by antigenic shift since 1900, and it could just as easily happen again.<ref name=thirteen>{{cite journal |last1=Clancy |first1=S |year=2008 |title=Genetics of the influenza virus |journal=Nature Education |volume=1 |issue=1 |url=http://www.nature.com/wls/topicpage/genetics-of-the-influenza-virus-716 }}</ref> In fact, the 1957 evolution of the H2N2 virus is thought to be a result of reassortment.<ref name=nine/> In this case, human H1N1 strains and avian influenza A [[genes]] were mixed.<ref name=nine/> Infecting tissue cultures can demonstrate how [[pathogenic]] qualities can evolve for a particular species even though the reassorted virus may be nonpathogenic for another species.<ref name=nine/> A prime example of evolution under natural conditions is the reassortment of two avian influenza strains that were discovered in dead seals back in 1979.<ref name=nine/>
-===Drift===
-New viruses can also emerge by drift. Drift can refer to [[genetic drift]] or [[antigenic]] drift.<ref name=nine/> [[Mutation]] and [[Selection (biology)|selection]] for the most advantageous variation of the virus takes place during this form of evolution.<ref name=nine/> Antigenic mutants can evolve quickly due to the high mutation rate in viruses. The cause of the antigenic drift lies in the mechanisms of RNA synthesis itself. Mutations arise very easily simply due to the error prone [[RNA polymerase]] and its lack of proofreading mechanisms. These mutations lead to subtle changes in the HA and NA genes which completely changes the infectious capabilities of the virus. These changes allow for almost endless possibilities for new viral strains to arise<ref name=twelve/> and it is the antigenic drift of the HA and NA genes that allow for the virus to infect humans that receive vaccines for other strains of the virus.<ref name=eleven>{{cite journal |doi=10.1038/nrmicro3248 |last1=Hofer |first1=U |year=2014 |title=Viral evolution: Past, present, and future of influenza viruses |journal=Nature Reviews Microbiology |volume=12 |issue=4 |pages=237 |pmid=24608335 }}</ref> This evolution occurs under the pressure of [[antibodies]] or immune system responses.<ref name=nine/>
-==Transmission==
-===Species and barriers===
-The transmission, or how the influenza virus is passed from one species to another, varies. There are barriers that prevent the flow of the virus between some species ranging from high to low transmission. For example, there is no direct pathway between humans and birds.<ref name=nine/> Pigs however, serve as an open pathway. There is a limited barrier for them to spread the virus.<ref name=nine/> Therefore, pigs act as a donator of the virus relatively easily.
-===Geographic differences===
-Phylogenetic maps are a graphical representation of the geographic relationships among species. They indicate that the human influenza virus is minimally impacted by geographic differences.<ref name=six/> However, both swine and avian influenza does appear to be geographically dependent.<ref name=six/> All three groups (avian, swine, and human) show chronological differences. The human influenza virus is retained in humans only, meaning it does not spread to other species.<ref name=six/> Some [[Lineage (evolution)|lineages]] and sublineages of the virus emerge and may be more prevalent in certain locations. For instance, many human influenza outbreaks begin in Southeast Asia.<ref name=nine/>
-==Phylogenetic analysis==
-Phylogenetic analysis can help determine past viruses and their patterns as well as determining a [[common ancestor]] of the virus. Past studies reveal that an avian virus spread to pigs and then to humans approximately 100 years ago.<ref name=nine/> This resulted in human lineages further evolving and becoming more prominent and stable.<ref name=nine/>
-Analysis can also feature relationships between species. The 1918 Spanish influenza virus demonstrates this. The [[hemagglutinin]] (HA) gene of the 1918 pandemic virus was closer in sequence to avian strains than other mammalian ones. Despite this genetic similarity, it is obviously a mammalian virus.<ref name=two>{{cite journal |doi=10.1073/pnas.96.4.1651 |last1=Reid |first1=A |last2=Fanning |first2=T |last3=Hultin |first3=J |last4= Taubenberger |first4= J |year=1999 |title=Origin and evolution of the 1918 "Spanish" influenza virus hemagglutinin gene|journal=Proceedings of the National Academy of Sciences USA |volume=96 |pages=1651–1656 |issue=4 |pmid=9990079 |pmc=15547}}</ref> The gene may have been adapting in humans even prior to 1918.<ref name=two/> Breaking down the phylogenetic history of the influenza virus shows that there is a common ancestor that reaches back before the 1918 outbreak that links the current human virus to the swine virus.<ref name=three>{{cite journal |last1=Gorman |first1=O |last2=Donis |first2=R |last3=Kawaoka |first3=Y |last4=Webster |first4=R |year=1990 |title=Evolution of influenza A virus PB2 genes: implications for evolution of the ribonucleoprotein complex and origin of human influenza A virus|journal=Journal of Virology |volume=64 |issue=10 |pages=4893–4902 |url=http://jvi.asm.org/cgi/content/abstract/64/10/4893 |pmid=2398532 |pmc=247979 }}</ref> The ancestor was derived from an avian host.<ref name=nine/>
-==Future impact and prediction strategies==
-===Phylogenetics===
-Looking at the past phylogenetic relationships of the influenza virus can help lead to information regarding treatment, resistance, vaccine strain selection, and of future possible influenza strains. By looking at how previous strains have evolved and gained new traits, the information can be applied to predict how current strains can evolve and even how novel strains might come about.<ref name=fourteen>{{cite journal |last1=Luksza |first1=M |last2=Lassig |first2=M |year=2014 |title=A predictive fitness model for influenza |journal=Nature |volume=507 |issue=7490 |pages=57–61 |doi=10.1038/nature13087|pmid=24572367 }}</ref> Another use of phylogeny for predicting future viral dangers would be through using [[phylogeography]]. Various lineages may continue their presence and reassort indicating the importance of a complete-genome approach to determine new influenza strains and future epidemics.<ref name=eight>{{cite journal |doi=10.1371/journal.pbio.0030300 |last1=Holmes |first1=E |last2=Ghedin |first2=E |last3=Miller |first3=N |last4=Taylor |first4=J |last5=Bao |first5=Y |last6=St George |first6=K |last7=Grenfell |first7=B |last8=Salzberg |first8=S |last9=Fraser |first9=C |last10=Lipman|first10=D |last11=Taubenberger |first11=J |year=2005 |title=Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses |journal=PLoS Biology |volume=3 |pages=1579–1589 |pmid=16026181 |pmc=1180517 |issue=9 }}</ref><ref name=ten>{{cite journal |last1=Vana |first1=G |last2=Westover |first2=K |year=2008 |title=Origin of the 1918 Spanish influenza virus: A comparative genomic analysis |journal=Molecular Phylogenetics and Evolution |volume=47 |pages=1100–1110 |doi=10.1016/j.ympev.2008.02.003 |issue=3 |pmid=18353690}}</ref> By studying how past strains have evolved while spreading to different geographic regions can allow scientists to predict how a strain might accumulate new mutations through its geographic distribution and the information could be used to protect different populations.<ref name=fifteen>{{cite journal |last1=Viboud |first1=C |last2=Boelle |first2=PY |last3=Carrat |first3=F |last4=Valleron |first4=AJ |last5=Flahault |first5=A |year=2003 |title=Prediction of the spread of influenza epidemics by the method of analogues |journal=American Journal of Epidemiology |volume=158 |issue=10 |pages=996–1006 |url=http://aje.oxfordjournals.org/content/158/10/996.short |doi=10.1093/aje/kwg239|pmid=14607808 }}</ref>
-All of these methods using historical data can help to diminish the effects of new influenza virus strains each flu season. By attempting to predict future mutations in HA and NA genes, scientists can choose vaccination strains that are likely to match future viruses, so antibodies can quickly recognize and mount an immune response against the virus. The one setback in this approach is that it is not useful against strains that evolve through antigenic shift (reassortment). It is impossible to predict when and with which strains these events will occur, and the fact that it could happen with strains from different species makes it all the more difficult.<ref name=thirteen/> Until a method is found to accurately predict what mutations will arise and when they come about, vaccines will continue to be created purely on guesswork with no guarantee that they will provide total protection from influenza.
-===Antiviral Resistance===
-More recently, there has been a huge increase in the amount of resistance to certain drugs, including the antiviral compound [[adamantane]].<ref name=seven>{{cite journal |doi=10.1093/molbev/msm103 |last1=Simonsen |first1=L |last2=Viboud |first2=C |last3=Grenfell |first3=B |last4=Dushoff |first4=J |last5=Jennings |first5=L |last6=Smit |first6=M |last7=Macken |first7=C |last8=Hata |first8=M |last9=Gog |first9=J |last10=Miller |first10=M. A. |last11=Holmes |first11=E. C. |year=2007 |title=The genesis and spread of reassortment human influenza A/H3N2 viruses conferring adamantane resistance |journal=Molecular Biology and Evolution |volume=24 |issue=8 |pages=1811–20 |url=http://mbe.oxfordjournals.org/cgi/content/full/24/8/1811#SEC4 |pmid=17522084 |display-authors=8 }}</ref> In fact, its resistance has recently climbed from 2 percent to nearly 90 percent.<ref name=seven/> These records of built up resistance infer that drugs, such as adamantine, will not be useful against the influenza virus in the future.
-==References==
-{{Reflist}}
-{{Evolution}}
 [[Category:Influenza]]