The panorama of the diversity of H5 subtype influenza viruses

Cheng, Hong; Chen, Ji Ming; Chen, Ji Wang; Sun, Yingxian; Li, Jin Ming; Wang, Zhi Liang

doi:10.1007/s11262-006-0018-3

Cited by 7 publications

(8 citation statements)

References 23 publications

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“…Figure 7B summarises the genealogy in a circularised graph in which the arrowheads indicate the direction of transfer and the width of the arrow indicate the rate of transfer to different locations. The analyses reveal viruses from the Atlantic and Afro-Eurasian locations form largely separate clades, which is consistent with previous studies (44, 45). However, we do find instances of transmission across this divide, most notably to and from Asia and Europe.…”

Section: Resultssupporting

confidence: 92%

Avian influenza viruses in wild birds: virus evolution in a multi-host ecosystem

Venkatesh

Poen

Bestebroer

et al. 2018

Preprint

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Section: Resultssupporting

confidence: 92%

Avian influenza viruses in wild birds: virus evolution in a multi-host ecosystem

Venkatesh

Poen

Bestebroer

et al. 2018

Preprint

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“…Phylogenetic analyses of H5‐LPAI sequences of both years presented an unexpected heterogeneity, which so far has been demonstrated only when influenza viruses from large geographic areas were compared. The separation of the Eurasian isolates from African and North American strains had shown similar variations in the previous investigations (Röhm et al., 1995; Garcia et al., 1997; Duan et al., 2007; Ma et al., 2007). All Bavarian H5 sequences clearly belonged to the Eurasian lineage (Fig.…”

Section: Discussionsupporting

confidence: 79%

Avian Influenza A Virus Monitoring in Wild Birds in Bavaria: Occurrence and Heterogeneity of H5 and N1 Encoding Genes

Lang¹,

Rinder

Hafner‐Marx³

et al. 2010

Zoonoses and Public Health

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To define avian influenza virus prevalence in wild birds in Bavaria, 12,930 tracheal, cloacal swabs or tissue samples from various waterfowl species were screened between January 2006 and December 2007. In 291 (2.3%) birds, genomes of influenza A viruses were detected by reverse transcription real-time PCR (rRT-PCR) targeting the matrix protein genes. Furthermore, solitary H5 hemagglutinin or N1 neuraminidase encoding genes were identified in 35 (0.3%) apparently healthy birds; whereas highly pathogenic (HPAI) H5N1 virus genomes were only diagnosed in dead wild birds (n = 93; 0.7%) found across this federal state region. In this study, multiple import events for H5N1 viruses were confirmed during 2006 and 2007. In addition, our findings argue against an existing HPAI H5N1 reservoir in aquatic birds in Bavaria. By contrast, phylogenetic analyses of the H5 or N1 sequences of low pathogenic avian influenza (LPAI) viruses revealed a marked diversity and multiple genetic lineages. This diversity of LPAI H5 and N1 subtype components indicates the existence of LPAI HA and NA gene pools which differ from the Bavarian HPAI H5N1. Moreover, the hemagglutinin amino acid differences between LPAI H5 viruses of a western European genotypic lineage observed in wild birds suggest a continuous evolution of LPAI viruses in Bavaria.

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“…Some attempts have been made to analyze the phylogenetic diversity and distribution of type A influenza viruses [4]–[7]. Among them, Liu and colleagues published a “panorama phylogenetic analysis” of all the 16 HA and 9 NA subtypes and they divided them into 68 HA and 49 NA lineages and sublineages [6].…”

Section: Introductionmentioning

confidence: 99%

A Complete Analysis of HA and NA Genes of Influenza A Viruses

et al. 2010

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BackgroundMore and more nucleotide sequences of type A influenza virus are available in public databases. Although these sequences have been the focus of many molecular epidemiological and phylogenetic analyses, most studies only deal with a few representative sequences. In this paper, we present a complete analysis of all Haemagglutinin (HA) and Neuraminidase (NA) gene sequences available to allow large scale analyses of the evolution and epidemiology of type A influenza.Methodology/Principal FindingsThis paper describes an analysis and complete classification of all HA and NA gene sequences available in public databases using multivariate and phylogenetic methods.Conclusions/SignificanceWe analyzed 18975 HA sequences and divided them into 280 subgroups according to multivariate and phylogenetic analyses. Similarly, we divided 11362 NA sequences into 202 subgroups. Compared to previous analyses, this work is more detailed and comprehensive, especially for the bigger datasets. Therefore, it can be used to show the full and complex phylogenetic diversity and provides a framework for studying the molecular evolution and epidemiology of type A influenza virus. For more than 85% of type A influenza HA and NA sequences into GenBank, they are categorized in one unambiguous and unique group. Therefore, our results are a kind of genetic and phylogenetic annotation for influenza HA and NA sequences. In addition, sequences of swine influenza viruses come from 56 HA and 45 NA subgroups. Most of these subgroups also include viruses from other hosts indicating cross species transmission of the viruses between pigs and other hosts. Furthermore, the phylogenetic diversity of swine influenza viruses from Eurasia is greater than that of North American strains and both of them are becoming more diverse. Apart from viruses from human, pigs, birds and horses, viruses from other species show very low phylogenetic diversity. This might indicate that viruses have not become established in these species. Based on current evidence, there is no simple pattern of inter-hemisphere transmission of avian influenza viruses and it appears to happen sporadically. However, for H6 subtype avian influenza viruses, such transmissions might have happened very frequently and multiple and bidirectional transmission events might exist.

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The panorama of the diversity of H5 subtype influenza viruses

Cited by 7 publications

References 23 publications

Avian influenza viruses in wild birds: virus evolution in a multi-host ecosystem

Avian influenza viruses in wild birds: virus evolution in a multi-host ecosystem

Avian Influenza A Virus Monitoring in Wild Birds in Bavaria: Occurrence and Heterogeneity of H5 and N1 Encoding Genes

A Complete Analysis of HA and NA Genes of Influenza A Viruses

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