Re: articles
http://www.ncbi.nlm.nih.gov/pubmed/8407243
Intervirology. 1993;35(1-4):16-25.
Influenza--a model of an emerging virus disease.
Webster RG, Wright SM, Castrucci MR, Bean WJ, Kawaoka Y.
Department of Virology/Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tenn. 38101.
Influenza A viruses continue to emerge from the aquatic avian reservoir and cause pandemics. Phylogenetic analysis of the nucleotide sequence of all eight influenza A virus RNA segments indicate that all of the influenza viruses in mammalian hosts originate from the avian gene pool. In contrast to the rapid progressive changes in both the nucleotide and amino acid sequences of mammalian virus gene lineages, avian virus genes show far less variation and, in most cases, appear to be in evolutionary stasis. There are periodic exchanges of influenza virus genes or whole viruses between species giving rise to pandemics of diseases in humans, lower animals and birds. The periodic emergence of influenza viruses in mammalian species has been illustrated by the appearance of a new influenza virus in horses in northern China in 1989. Phylogenetic analysis of classical H1N1, avian-like H1N1 and human H3N2 viruses circulating in Italian pigs reveals that genetic reassortment is taking place between avian- and human-like viruses in the European pig population. These studies provide evidence supporting the possibility that pigs serve as a mixing vessel for reassortment between influenza viruses in mammalian and avian hosts and raise the question of whether the next pandemic of influenza will emerge in Europe!
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http://www.ncbi.nlm.nih.gov/pubmed/9391654
Acta Virol. 1997 Aug;41(4):231-9.
Evolutionary stasis of M1 gene of human influenza A viruses and the possibility of their subtyping by restriction analysis of M1 gene polymerase chain reaction product.
Park KY, Lee MG, Ryu JC, Park YK.
WHO National Influenza Center, NIH Korea, Seoul, South Korea.
Erratum in: Acta Virol 1997 Oct;41(5):302.
Nucleotide (nt) and amino acid (aa) sequences of the M1 protein in 36 human influenza A viruses were analyzed. The neighbor joining tree of the nt sequences revealed several lineages associated with past epidemics of human influenza. However, the tree of aa sequences revealed only few specific lineages. This discrepancy in phylogeny between nt and aa sequences indicates that the M1 protein of human influenza A virus nearly reached an evolutionary stasis. A simple subtyping method of human influenza A viruses by restriction fragment length polymorphism (RFLP) analysis of M1 gene polymerase chain reaction (PCR) products is discussed.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088557
(full article here:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088557/pdf/TB011817.pdf )
Philos Trans R Soc Lond B Biol Sci. 2001,Dec.29;356(1416):1817-28.
Emergence of influenza A viruses.
R J Webby and R G Webster
Department of Virology and Molecular Biology, St Jude Children's Research Hospital, 332 North Lauderdale, Memphis, TN 38105, USA.
This article has been cited by other articles in PMC.
Abstract
Pandemic influenza in humans is a zoonotic disease caused by the transfer of influenza A viruses or virus gene segments from animal reservoirs. Influenza A viruses have been isolated from avian and mammalian hosts, although the primary reservoirs are the aquatic bird populations of the world. In the aquatic birds, influenza is asymptomatic, and the viruses are in evolutionary stasis. The aquatic bird viruses do not replicate well in humans, and these viruses need to reassort or adapt in an intermediate host before they emerge in human populations. Pigs can serve as a host for avian and human viruses and are logical candidates for the role of intermediate host. The transmission of avian H5N1 and H9N2 viruses directly to humans during the late 1990s showed that land-based poultry also can serve between aquatic birds and humans as intermediate hosts of influenza viruses. That these transmission events took place in Hong Kong and China adds further support to the hypothesis that Asia is an epicentre for influenza and stresses the importance of surveillance of pigs and live-bird markets in this area.
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http://www.ncbi.nlm.nih.gov/pubmed/15269374
(fulll article here:
http://vir.sgmjournals.org/cgi/content/full/85/8/2327 )
J Gen Virol. 2004 Aug;85(Pt 8):2327-37.
Influenza A viruses in feral Canadian ducks: extensive reassortment in nature.
Hatchette TF, Walker D, Johnson C, Baker A, Pryor SP, Webster RG.
The current dogma of influenza accepts that feral aquatic birds are the reservoir for influenza A viruses. Although the genomic information of human influenza A viruses is increasing, little of this type of data is available for viruses circulating in feral waterfowl. This study presents the genetic characterization of 35 viruses isolated from wild Canadian ducks from 1983 to 2000, as the first attempt at a comprehensive genotypic analysis of influenza viruses isolated from feral ducks. This study demonstrates that influenza virus genes circulating in Canadian ducks have achieved evolutionary stasis. The majority of these duck virus genes are clustered in distinct North American clades; however, some H6 and H9 genes are clustered with those from Eurasian viruses. Genes appeared to reassort in a random fashion. None of the genotypes identified remained present throughout all of the years examined and most PA and PB2 genes that crossed over into swine were clustered in one phylogenetic grouping. Additionally, matrix genes were identified that branch very early in the evolutionary tree. These findings demonstrate the diversity of the influenza virus gene pool in Canadian ducks, and suggest that genes which cluster in specific phylogenetic groupings in the PB2 and PA genes can be used for markers of viruses with the potential for crossing the species barrier. A more comprehensive study of this important reservoir is needed to provide further insight into the genomic composition of viruses that crossover the species barrier, which would be a useful component to pandemic planning.
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http://www.ncbi.nlm.nih.gov/pubmed/16945980
(full article here:
http://mbe.oxfordjournals.org/cgi/content/full/23/12/2336 )
Mol Biol Evol. 2006 Dec;23(12):2336-41. Epub 2006 Aug 31.
Avian influenza virus exhibits rapid evolutionary dynamics.
Chen R, Holmes EC.
Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, PA, USA.
Influenza A viruses from wild aquatic birds, their natural reservoir species, are thought to have reached a form of stasis, characterized by low rates of evolutionary change. We tested this hypothesis by estimating rates of nucleotide substitution in a diverse array of avian influenza viruses (AIV) and allowing for rate variation among lineages. The rates observed were extremely high, at >10(-3) substitutions per site, per year, with little difference among wild and domestic host species or viral subtypes and were similar to those seen in mammalian influenza A viruses. Influenza A virus therefore exhibits rapid evolutionary dynamics across its host range, consistent with a high background mutation rate and rapid replication. Using the same approach, we also estimated that the common ancestors of the hemagglutinin and neuraminidase sequences of AIV arose within the last 3,000 years, with most intrasubtype diversity emerging within the last 100 years and suggestive of a continual selective turnover.
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http://www.ncbi.nlm.nih.gov/pubmed/16447493
Dev Biol (Basel). 2006;124:45-50.
Recent epidemiology and ecology of influenza A viruses in avian species in Europe and the Middle East.
Brown IH, Banks J, Manvell RJ, Essen SC, Shell W, Slomka M, Londt B, Alexander DJ.
Veterinary Laboratories Agency (Weybridge), Addlestone, Surrey, United Kingdom.
i.h.brown@vla.defra.gsi.gov.uk
There have been at least ten distinct outbreaks of LPAI or HPAI in poultry caused by H5 or H7 viruses in the last eight years in Europe and the Middle East. There appears to be an increased occurrence of such episodes consistent with global trends. As a result, surveillance systems have been enhanced to facilitate early detection of infection in poultry, together with active surveillance of wild bird populations. These complementary activities have resulted in the detection of a number of viruses in wild bird populations, including some with high genetic similarity to newly detected viruses in poultry, for example, H7N3 in Italy and H7N7 in the Netherlands. Furthermore, there is evidence for continued circulation of H5 and H7 viruses in wild Anseriformes, thereby presenting a real and current threat for the introduction of viruses to domestic poultry, especially those reared in outdoor production systems. Viruses of H9N2 subtype continue to circulate widely in the Middle East and are associated with significant disease problems in poultry. The epidemiology has the potential to be complicated further by introduction of novel viruses through illegal importation of captive birds, such as was detected with H5N1 in Belgium in 2004. Continual genetic exchange in the avian virus gene pool and independent evolution of all gene segments either within an individual host species or among wild bird hosts suggests that these viruses are not in evolutionary stasis in the natural reservoir.
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http://www.ncbi.nlm.nih.gov/pubmed/18234791
( full article here:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2268457 )
J Virol. 2008 Apr;82(7):3769-74. Epub 2008 Jan 30.
Phylogenetic evidence against evolutionary stasis and natural abiotic reservoirs of influenza A virus.
Worobey M.
Zhang et al. (G. Zhang, D. Shoham, D. Gilichinsky, S. Davydov, J. D. Castello, and S. O. Rogers, J. Virol. 80:12229-12235, 2006) have claimed to have recovered influenza A virus RNA from Siberian lake ice, postulating that ice might represent an important abiotic reservoir for the persistence and reemergence of this medically important pathogen. A rigorous phylogenetic analysis of these influenza A virus hemagglutinin gene sequences, however, indicates that they originated from a laboratory reference strain derived from the earliest human influenza A virus isolate, WS/33. Contrary to Zhang et al.'s assertions that the Siberian "ice viruses" are most closely related either to avian influenza virus or to human influenza virus strains from Asia from the 1960s (Zhang et al., J. Virol. 81:2538 [erratum], 2007), they are clearly contaminants from the WS/33 positive control used in their laboratory. There is thus no credible evidence that environmental ice acts as a biologically relevant reservoir for influenza viruses. Several additional cases with findings that seem at odds with the biology of influenza virus, including modern-looking avian influenza virus RNA sequences from an archival goose specimen collected in 1917 (T. G. Fanning, R. D. Slemons, A. H. Reid, T. A. Janczewski, J. Dean, and J. K. Taubenberger, J. Virol. 76:7860-7862, 2002), can also be explained by laboratory contamination or other experimental errors. Many putative examples of evolutionary stasis in influenza A virus appear to be due to laboratory artifacts.
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comment: while avian flu in wild birds (i.e. mallards,pintails,turnstones,)
usually acquires nucleotide-mutations
at a normal rate (like poultry or mammals) , [exceptions seen in
China , Alaska - see this thread:
http://www.flutrackers.com/forum/showthread.php?t=136122 ]
the "stasis" does occur wrt. amino-acid mutations.
Here they cluster around the index,
with only few amino-acid mutations difference.
This presumably happens since centuries.
Recent H5N1 in Asia looks like an exception, a virus rather distant from the index
in wild birds. The reason seems to be evolution in poultry, half-domestic ducks
and special species of wild birds like swans, geese, birds of prey. (not the classical mallards)
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Duck and human pandemic influenza A viruses retain sialidase activity under low pH conditions.
The majority of influenza A viruses isolated from wild birds, but not humans,
can replicate in the duck intestinal tract. Here we demonstrate that all duck isolates
tested universally retain sialidase activities under low pH conditions independent
of their neuraminidase (NA) subtypes. In contrast, the sialidase activities of most
isolates from humans and pigs practically disappear below pH 4.5, with the exception
of four human pandemic viruses isolated in 1957 and 1968.
Sequence comparisons among duck, human, and swine N2 NA subtypes indicate
that amino acids at positions 153, 253, 307, 329, 344, 347, 356, 368, 390, and 431
may be associated with the low pH stability of duck and human pandemic N2 NAs.
This finding suggests that the low pH stability of duck influenza A virus NA may be a
critical factor for replication in the intestinal tract through the digestive tract of ducks,
and that the properties of NAs are important for understanding the epidemiology
of the influenza virus.
(2001)
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http://www.ncbi.nlm.nih.gov/pubmed/...med_ResultsPanel.Pubmed_RVDocSum&ordinalpos=7
Catalonia, 2006-2009, 1374 birds,16 families, 62 viruses,
10 HAs,7 NAs, 13 subtypes. H4N6 (22.2%) ,H1N1 (18.5%).
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http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.0030061
(May 2007) 36809 birds from Northern Europe, 1999-2005, 332 flu-viruses
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lethal mutagenesis:
http://www.nytimes.com/2010/01/05/science/05lethal.html
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phylogenetic analyses of amino acid changes suggested that avian influenza viruses,
unlike mammalian strains, show low evolutionary rates (Gorman et al. 1990);
http://jvi.asm.org/cgi/content/abst...1119b48981ee39708a05c3f1&keytype2=tf_ipsecsha
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http://www.ncbi.nlm.nih.gov/pubmed/20059316
Influenza A Viruses in Wild Birds of the Pacific Flyway, 2005-2008.
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good list of links here:
http://www.apeiresearch.net/smenupage.php?menuid=7
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Virol. 2010 Jan 20. [Epub ahead of print]
Virus Shedding and Potential for Interspecies Waterborne Transmission of Highly Pathogenic
H5N1 in Sparrows and Chickens. Forrest HL, Kim JK, Webster RG.
A/duck/Laos/25/06 in sparrows and chickens. Inoculated birds shed virus at high titers from
the oropharynx and cloaca, and infection was fatal.
Waterborne transmission from inoculated sparrows to contact chickens was absent,
while 25% of sparrows were infected via waterborne transmission from chickens.
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