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1.
Infect Genet Evol ; 61: 208-214, 2018 07.
Article in English | MEDLINE | ID: mdl-29649578

ABSTRACT

From November 2015 to August 2016, 81 outbreaks of highly pathogenic (HP) H5 avian influenza virus were detected in poultry farms from South-Western France. These viruses were mainly detected in farms raising waterfowl, but also in chicken or guinea fowl flocks, and did not induce severe signs in waterfowl although they did meet the HP criteria. Three different types of neuraminidases (N1, N2 and N9) were associated with the HP H5 gene. Full genomes sequences of 24 H5HP and 6 LP viruses that circulated in the same period were obtained by next generation sequencing, from direct field samples or after virus isolation in SPF embryonated eggs. Phylogenetic analyses of the eight viral segments confirmed that they were all related to the avian Eurasian lineage. In addition, analyses of the "Time of the Most Recent Common Ancestor" showed that the common ancestor of the H5HP sequences from South-Western France could date back to early 2014 (±1 year). This pre-dated the first detection of H5 HP in poultry farms and was consistent with a silent circulation of these viruses for several months. Finally, the phylogenetic study of the different segments showed that several phylogenetic groups could be established. Twelve genotypes of H5HP were detected implying that at least eleven reassortment events did occur after the H5HP cleavage site emerged. This indicates that a large number of co-infections with both highly pathogenic H5 and other avian influenza viruses must have occurred, a finding that lends further support to prolonged silent circulation.


Subject(s)
Hemagglutinin Glycoproteins, Influenza Virus/genetics , Influenza A Virus, H5N1 Subtype , Influenza A Virus, H5N2 Subtype , Influenza in Birds/virology , Reassortant Viruses , Animals , France , Influenza A Virus, H5N1 Subtype/genetics , Influenza A Virus, H5N1 Subtype/pathogenicity , Influenza A Virus, H5N2 Subtype/genetics , Influenza A Virus, H5N2 Subtype/pathogenicity , Neuraminidase/genetics , Phylogeny , Poultry/virology , Poultry Diseases/virology , Reassortant Viruses/genetics , Reassortant Viruses/pathogenicity , Viral Proteins/genetics
2.
J Virol Methods ; 170(1-2): 86-9, 2010 Dec.
Article in English | MEDLINE | ID: mdl-20837066

ABSTRACT

The real-time polymerase chain reaction (PCR) is considered to be a suitable tool for nucleic acid quantitation because it is accurate, rapid and reliable. The reference protocol for quantitation of ostreid herpesvirus 1 in Pacific oysters Crassostrea gigas is based on a Sybr(®) Green real-time PCR developed by the IFREMER laboratory. The Frank Duncombe Departmental Laboratory has developed an alternative protocol based on TaqMan(®) chemistry (alternative technique). The quantitation limits were 1000 and 18UG/mg of tissues for the reference method and alternative protocols, respectively, and the latter protocol has a detection limit of 6UG/mg of tissues. The aim of this study was to compare the two protocols using DNA samples obtained from 210 spat. The kappa index (0.41) indicated a moderate concordance between the protocols, according to the measures of Landis and Koch. All samples that were positive by the reference protocol were also positive by the alternative protocol. Of the 76 samples that were negative by the reference protocol, 49 were positives by the alternative protocol. In conclusion, the alternative protocol is an improvement of the reference protocol in terms of sensitivity, specificity and rapidity (<3h).


Subject(s)
Crassostrea/virology , DNA Viruses/isolation & purification , Polymerase Chain Reaction/methods , Animals , Benzothiazoles , DNA Primers , DNA Viruses/genetics , Diamines , False Negative Reactions , Gene Expression Profiling , Organic Chemicals , Quinolines , Sensitivity and Specificity
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