Abstract
Since November 2016, Europe witnesses another wave of incursion of highly pathogenic avian influenza (HPAI) A(H5) viruses of the Asian origin goose/Guangdong (gs/GD) lineage. Infections with H5 viruses of clade 2.3.4.4b affect wild bird and poultry populations. H5 viruses of clades 2.2, 2.3.1.2c and 2.3.4.4a were detected previously in Europe in 2006, 2010 and 2014. Clades 2.2.1.2 and 2.3.2.1.c are endemic in Egypt and Western Africa, respectively and have caused human fatalities. Evidence exists of their co-circulation in the Middle East. Subtype H5 viruses of low pathogenicity (LPAI) are endemic in migratory wild bird populations. They potentially mutate into highly pathogenic phenotypes following transmission into poultry holdings. However, to date only the gs/GD H5 lineage had an impact on human health. Rapid and specific diagnosis marks the cornerstone for control and eradication of HPAI virus incursions. We present the development and validation of five real-time RT-PCR assays (RT-qPCR) that allow sequencing-independent pathotype and clade-specific distinction of major gs/GD HPAI H5 virus clades and of Eurasian LPAI viruses currently circulating. Together with an influenza A virus-generic RT-qPCR, the assays significantly speed up time-to-diagnosis and reduce reaction times in a OneHealth approach of curbing the spread of gs/GD HPAI viruses.
Highlights
Influenza A viruses constitute a virus species in the family Orthomyxoviridae
We developed rapid diagnostic solutions on the basis of quantitative reverse transcription real-time PCR assays (RT-qPCR), to pathotype, without sequencing, goose/ Guangdong (gs/GD) lineage highly pathogenic avian influenza (HPAI) and Eurasian low pathogenicity (LPAI) H5 subtype viruses, and to distinguish HPAI gs/GD viruses of clades 2.2.1.2, 2.3.2.1 and 2.3.4.4, including viruses of the ongoing 2016 epizootic in Europe
The assays reported here are primarily intended for screening purposes of avian samples; confirmatory assays, including nt sequence analyses and antigenic characterisation, are still required for new incursions and outbreak scenarios that feature an expansion of the geographic area and/or the range of affected species or poultry sectors
Summary
Influenza A viruses constitute a virus species in the family Orthomyxoviridae They harbour single-stranded negative-sense RNA arranged into eight genomic segments. The intrinsically error-prone influenza virus genome replication machinery promotes the generation of quasi-species that can be shaped by directional selection pressures, e.g. following host species switches or by specific herd immunity. In the latter case, antigenic drift variants are selected that may escape immunity by very few amino acid substitutions in the HA [2]
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