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1 Department of Infectious, Parasitic and Immune-Mediated Diseases and Department of Food Safety and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
2 State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR
3 Department of Veterinary Public Health and Animal Pathology, Faculty of Veterinary Medicine, University of Bologna, Ozzano Emilia (BO), Italy
4 Istituto Zooprofilattico Sperimentale of Lombardia and Emilia, Parma, Italy
5 Istituto Zooprofilattico Sperimentale of Lombardia and Emilia, Brescia, Italy
Correspondence
Laura Campitelli
laura.campitelli{at}iss.it
| ABSTRACT |
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Published online ahead of print on 24 October 2007 as DOI 10.1099/vir.0.83111-0.
The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are EU158100–EU158178.
Supplementary material is available with the online version of this paper.
| INTRODUCTION |
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| METHODS |
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Antigenic characterization.
Subtype identification of influenza viruses was performed by using haemagglutination-inhibition (HI) and neuraminidase-inhibition (NI) assays with a panel of reference antigens and antisera, as described previously (WHO, 2002
). A more detailed analysis of HA antigenic reactivity was carried out by the HI test using a panel of hyperimmune rabbit and chicken sera to A/Ruddy turnstone/New Jersey/65/85 (H7N3), A/Turkey/Italy/2676/99 (H7N1) (the index case strain isolated during the 1999–2000 H7N1 Italian poultry outbreak) and A/Turkey/Italy/214845/02 (H7N3) virus. In addition, a panel of post-infection ferret sera against A/Chicken/Italy/13474/99 (H7N1) virus, also isolated during the 1999–2000 H7N1 outbreak, and a monoclonal antibody to A/Turkey/Italy/2676/99 were used. The HI test was performed using horse red blood cells (HRBCs) according to standard procedures with minor modifications (Stephenson et al., 2003
). Basically, a 1 % suspension of HRBCs in 0.5 % BSA/PBS was used throughout the procedure and HI titres were read after 60 min.
Gene sequencing.
Viral RNA was extracted from infected allantoic fluids as described earlier and reverse-transcribed using a 12 bp oligonucleotide primer (5'-AGCAAAAGCAGG-3') and Superscript II reverse transcriptase (Invitrogen) as described previously (Campitelli et al., 2002
). We PCR-amplified the coding region of the viral gene segments with gene-specific primers using the Expand High-Fidelity PCR system (Roche) according to the manufacturer's protocol. Amplified products of the expected size were purified with the QIAquick PCR purification kit (Qiagen), sequenced using the BigDye Terminator Cycle-Sequencing Ready Reaction (Applied Biosystems) and analysed on ABI Prism 310 DNA sequencer (Applied Biosystems).
Sequence and phylogenetic analysis.
Sequence assembly was performed with the Lasergene package (version 4.0; DNASTAR). Sequences obtained in this study were aligned with selected sequences available from GenBank, using the CLUSTAL_X program (Thompson et al., 1997
), and edited with BioEdit 7.05 (Hall, 1999
). Phylogenetic analysis was carried out in two steps: first, substitution models for each gene segment analysed were determined using MODELTEST 3.06 (Posada & Crandall, 1998
); subsequently, maximum-likelihood (ML) phylogenetic trees were inferred using PAUP* 4.0 (Swofford, 2002
), according to the selected models. Statistical analyses included bootstrap analyses (1000 bootstrap replicates) and the zero-branch-length test (Swofford & Sullivan, 2003
), also performed with PAUP*. Identification of potential glycosylation sites was done with the PPSearch program, available at www.ebi.ac.uk/ppsearch.
Virus genotyping.
Genotypes were defined by gene phylogeny. Gene segments were assigned to a given phylogenetic grouping, or sublineage, according to their position on each segment-specific tree, when the identified cluster complied with the following criteria: (i) starting from the tip of a phylogeny, a monophyletic clade is identified when it is supported by a bootstrap support of >80 % and/or by P values
0.001. Moreover, all taxa in the proposed clade must have 95 % or greater identity with each other; (ii) when the bootstrap score or the P value at the node supporting the proposed segment-specific clade is less than the arbitrary cut-off value, all the taxa in the clade must have at least 95 % or greater sequence identity with each other and less than 94.9 % identity with the gene segments of viruses belonging to other phylogenetic groups.
| RESULTS |
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Serological comparison of the H7 viruses circulating in Italy and China between 1999 and 2005 in different species revealed no significant differences in their antigenic pattern, except for the index case of the 1999 AI epidemic caused by H7N1 virus, A/Turkey/Italy/2676/99, that showed a fourfold higher titre against its homologous antiserum and monoclonal antibody compared with most of the other strains tested. Thus, only a limited antigenic drift was observed among these Eurasian viruses (Table 2
).
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Phylogenetic relationships were inferred for each of the eight gene segments after selecting the best-fitting nucleotide substitution models (see Supplementary Table S1 available in JGV Online). All virus genes belonged to the main Eurasian avian lineage, as no evidence of reassortment with genes belonging to the North American avian gene pool was found. HA genes, including the Chinese strains, fell within the same subgroup with a high statistical support. They were clearly distinct from both an H7N3 virus isolated in Taiwan in 1998 and several H7 strains circulating in Europe from 1989 to 1996 (Fig. 1a
). The monophyletic group observed for the HA gene contrasts with the situation observed in most other gene segments. Three different NA subtypes (N1, N3 or N7) were associated with the H7 viruses. In particular, A/Mallard/Italy/199/01 and A/Mallard/Italy/250/02, which were isolated 1 month apart in the same area, possessed an almost identical HA gene (99.8 % identity) but their NA genes belonged to the N3 and N1 subtypes, respectively. Noteworthy is the fact that A/Mallard/Italy/250/02 shares a very recent common ancestor with the N1 genes of the H7N1/99 Italian viruses responsible for the 1999–2000 epidemics in poultry, whose direct precursor in the wild bird reservoir had not been identified previously. Within each NA subtype, the viruses clustered in the same branches (Supplementary Fig. S1 available in JGV Online).
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Virus genotyping
To illustrate better the diverse gene constellations within the H7 avian strains under study, each one of the phylogenetic lineages identified for every gene was assigned a different colour and a visual representation of the virus genotype of each representative virus isolate was obtained, as described by other authors (Hatchette et al., 2004
) (Fig. 4
). These lineages are also represented on the phylogenetic trees (Figs 1
–3
). Throughout the period 1999–2005, six different genotype combinations were observed within the H7 subtype viruses identified in Eurasian countries. In each of the years of isolation a different genotype emerged, although in some years more than one genotype was detected. In 2002, H7N3 and H7N1 viruses were isolated in Italy; in 2003, two H7N7 subtype viruses with different genotypes circulated in the Netherlands and in China, and an H7N3 virus in Italy. The H7N3 genotype was identified in Italy for three consecutive years, in different avian species (wild waterfowl in 2001 and domestic poultry in 2002–2003), as a consequence of a likely interspecies transmission event from wild to domestic birds followed by a long-lasting epizootic in commercial poultry (Campitelli et al., 2004
).
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Molecular characterization
HA gene.
The H7 HAs of Eurasian viruses differed mainly because of the presence or absence of an insertion of multibasic amino acids at the cleavage site, known to confer an HP phenotype to H5 and H7 subtype viruses. This motif was found only in Italian H7N1 viruses isolated between December 1999 and March 2000 (represented by A/Guinea fowl/Italy/155/00 strain) and in all the H7N7 Dutch strains (Banks et al., 2001
; Fouchier et al., 2004
). We then looked at the amino acids that define the receptor-binding pocket, usually highly conserved throughout all avian subtypes (Nobusawa et al., 1991
). As expected, most of the H7 strains retained the avian consensus sequence of the receptor-binding site (RBS), known to confer the ability to bind preferentially to Neu5Ac
2, 3-Gal receptor determinants. However, A/Mallard/Italy/250/02 (H7N1) showed an amino acid substitution (A
S) at position 128 (138, according to H3 numbering), which is part of the right edge of the RBS.
The HA glycosylation pattern indicated that all wild and domestic duck viruses possessed five potential glycosylation (CHO) sites throughout the molecule (HA1+HA2). This pattern was also retained by the H7N3 turkey and chicken strains, regardless of the species and time of isolation, and by the H7N7 Dutch strains, except for A/Netherlands/219/03, which displayed an additional CHO site at residue 123 (Fouchier et al., 2003
). On the other hand, almost all H7N1 viruses isolated in Italy in 1999–2000 had one of two extra CHO sites at positions 123 and 149 (Banks et al., 2001
).
NA gene.
The sialidase active site (Colman et al., 1993
) was conserved in all the analysed viruses. The most remarkable feature, when comparing H7 virus NAs, was the presence or absence of a fairly long deletion in the NA stalk region. Both H7N1 and H7N3 subtype viruses from wild waterfowl had a full-length NA gene, whereas viruses of the same subtypes isolated from domestic poultry had a deletion of 22 and 23 aa, respectively, as already reported (Banks et al., 2001
; Campitelli et al., 2004
), even though they shared a high level of nucleotide similarity along the rest of the molecule (98.6–99.0 % among H7N3 viruses and 97.7 % between A/Mallard/Italy/250/02 and A/Turkey/Italy/4169/99). An NA deletion was not observed in any of the H7N7 viruses analysed, irrespective of their species of origin, of additional CHO sites in the HA, and of their pathogenic phenotype. For the N1 and N3 NA proteins, the number of glycosylation sites varied depending on the stalk deletion: wild bird viruses had six CHO sites, three of which, located within the stalk region, were lost in domestic poultry viruses. All N7 NA genes had nine glycosylation sites.
Internal protein genes.
Several amino acid positions within the internal protein sequences have been associated with features such as virulence, host range and interspecies transmission, and resistance to antivirals. The NS1 genes of the H7 viruses coded for full-length proteins; thus, no deletions were observed either in the C-terminal region or within the protein. Amino acid changes at positions 92 (D92E) and 149 (V149A) have been associated with increased virulence of H5N1 influenza viruses in man and chickens, respectively (Seo et al., 2002
; Li et al., 2006
). All the H7 viruses in our study had 92D and 149A. The four C-terminal amino acids, recently shown to bind to protein interaction domains of intracellular scaffold proteins (Obenauer et al., 2006
) were represented by the motif ESEV, typical of AIVs.
Two changes in the virus polymerase complex that have been frequently associated with adaptation of an AIV to growth in a mammalian host are E627K and D701N of PB2 (Hatta et al., 2001
; Li et al., 2005
). The former had already been reported in the H7 Dutch virus that caused lethal viral pneumonia in man, A/Netherlands/219/03 (Fouchier et al., 2004
) but no other H7 virus in our study, either from poultry or from wild birds, possessed it. The latter change was not detected in any of the H7 strains.
Finally, we checked the M2 genes for the presence of mutations known to code for resistance to amantadine, an anti-influenza drug commonly used in swine and humans (Gubareva & Hayden, 2006
). Interestingly, one of the wild waterfowl isolates, A/Mallard/Italy/250/02, showed the change S31N, considered sufficient to induce full resistance to amantadine.
| DISCUSSION |
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All the viruses analysed in our study are from Eurasia, an extremely wide geographical region within which multiple migratory flyways can be identified. Phylogenetic evidence that a number of genes of H7 viruses isolated in Italy are most closely related to viruses from southern China indicates that these major flyways overlap, allowing different bird populations to come in contact with each other (Olsen et al., 2006
), and further supports the hypothesis of a continuous evolution of the influenza gene pool through reassortment. Analogous patterns have also been identified for LP H5 viruses (Duan et al., 2007
).
Previous findings suggested that the number of potential reassortants arising from coinfection of ducks with two or more viruses is limited, possibly because of non-viability of defined gene constellations (Sharp et al., 1997
). In the present study, gene exchange appeared to occur randomly, without constraints among different gene sublineages of avian viruses: as an example, we found no correlation between the H7 HA genes and a specific sublineage of any of the remaining genome segments, in agreement with recent studies carried out on the feral Canadian duck gene pool and the AI polymerase gene complex (Widjaja et al., 2004
; Macken et al., 2006
).
Most genes of H7 poultry viruses (H7N1/IT/99 and H7N7/NL/03) share recent common ancestors with those of wild birds, and the Italian H7N3 poultry viruses have been shown to be the result of a direct introduction of a wild bird virus in toto in domestic poultry (Campitelli et al., 2004
). These data indicate that AIVs in poultry species do not constitute separate evolutionary cycles; rather, a continuous virus exchange between wild aquatic birds and domestic species seems likely, as also confirmed by studies on H6N2 viruses in chickens in California and by the ability shown by the HP H5N1 virus in Asia to move back from domestic to wild aquatic birds (Webby et al., 2002
; Guan et al., 2002
).
H7N1 and H7N3 strains isolated from poultry species possess a deleted NA protein in the stalk region, a feature considered a marker of adaptation of a virus from wild birds to poultry hosts, which is frequently accompanied by additional carbohydrate groups at the tip of the HA molecule (Matrosovich et al., 1999
). In this way, the virus is thought to compensate the impairment of sialidase activity by reducing binding affinity to sialylglycoconjugates, as evidenced by in vitro studies (Baigent & McCauley, 2001
; Wagner et al., 2002
). However, only the H7N1 viruses have additional glycosylation groups on the HA globular head. On the other hand, the NA stalk of both chicken and human H7N7 viruses from The Netherlands is not deleted, although an additional CHO site was present on the HA protein of at least one strain, A/Netherlands/219/03 (Fouchier et al., 2004
). All of these data indicate that co-mutation of these two genes, aimed at balancing HA and NA activities, does not constitute an absolute requirement for an avian virus from aquatic birds to adapt to terrestrial species, under natural conditions.
Differences in receptor-binding specificity between human and avian viruses represent a major barrier to efficient transmission of an AIV among mammals (Matrosovich et al., 2006
). Moreover, as little as two amino acid substitutions may be sufficient to cause a change in receptor-binding preference from the avian
-2,3 to the human
-2,6 sialic acid receptor, as shown for the H5N1 and H1N1 subtype viruses (Yamada et al., 2006
; Tumpey et al., 2007
). Our study shows that a duck virus, A/Mallard/Italy/250/02, possesses an amino acid change (A138S, H3 numbering) on the right edge of the RBS, while not showing any additional glycosylation site on its globular head. As reported by other authors, A138 is a highly conserved position in avian viruses of all subtypes, whereas in several human H1 strains A138S substitution seems to increase their ability to bind to
-2,6 sialic acid receptors, specific for human viruses (Matrosovich et al., 1997
). Thus, virus variants circulating in wild waterfowl and bearing amino acid changes that might favour a partial or complete switch towards a human-type receptor specificity could facilitate transmission and adaptation to a mammalian host.
We also detected a mutation in the M2 gene of A/Mallard/Italy/250/02 virus (S31N) known to confer resistance to amantadine, an anti-influenza drug effective on both human and animal influenza A viruses (Scholtissek et al., 1998
). Amantadine resistant viruses have been detected among avian strains of poultry origin, and have been associated, at least in South East Asia, with the use of amantadine against the H5N1 viruses in commercial poultry (Ilyushina et al., 2005
; Cheung et al., 2006
), whereas no data are available on wild waterfowl viruses. Due to the high frequency generation of random point mutations by the viral transcriptase, it is very likely that this substitution, as well as the one in the HA RBS, is the result of random selection of variants bearing these changes.
Our study highlights once again the close relationship between AIV in poultry and wild birds. Moreover, in order to understand the mechanisms and ecological interactions that favour the emergence of potentially dangerous influenza A viruses, it supports the idea that more extensive and long-term AI surveillance programmes, as well as a thorough genetic characterization of AIVs isolated all over the world, must be implemented. In this regard, attention should be placed not only on H5 and H7 subtype viruses that represent a more immediate threat for poultry industry but also on other subtypes of relevance for public health, such as H1, H2, H3 and H9.
| ACKNOWLEDGEMENTS |
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Received 24 April 2007;
accepted 3 October 2007.
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