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Journal of Virology, April 2008, p. 3405-3414, Vol. 82, No. 7
0022-538X/08/$08.00+0 doi:10.1128/JVI.02468-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

International Institute of Infection and Immunity, Shantou University, Shantou, Guangdong 515031, China,1 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, China,2 Virology Division, Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 380153
Received 16 November 2007/ Accepted 16 January 2008
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99%) with their corresponding descendant viruses in most gene segments. These results suggest a direct transmission link for H5N1 viruses between Yunnan and Vietnam and also between Hunan and Indonesia during 2002 and 2003. Poultry trade may be responsible for virus introduction to Vietnam, while the transmission route from Hunan to Indonesia remains unclear. |
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One of these novel reassortants (genotype Z) became dominant in southern China since early 2002 (5, 22) and was subsequently transmitted to neighboring countries in East and Southeast Asia in 2003 and 2004 (22). These H5N1 genotype Z viruses caused extensive outbreaks in poultry and were repeatedly introduced into humans, eventually becoming endemic in poultry in Vietnam and Indonesia (27). The persistent introduction of H5N1 virus into humans raises the possibility that it emerges as a human pandemic strain, either as a purely avian virus adapting to human-to-human transmission or through reassortment with current human influenza virus strains (32, 35). Although surveillance in market poultry was strengthened after outbreaks in these regions, the source and virus dissemination pathway in Southeast Asia remains uncertain due to the lack of convincing information prior to this spread.
The second major transmission wave of those HPAI H5N1 viruses occurred in 2005 after a major outbreak in migratory waterfowl at Qinghai Lake in northern China (2, 9). Systematic influenza surveillance in southern China provided sufficient information to understand the evolutionary pathway of these Qinghai-like viruses (clade 2.2) and to predict the development of this lineage (4, 5, 22). Similarly, the evolutionary pathway of the currently dominant H5N1 variant (clade 2.3.4 or Fujian-like) was also detected as early as March 2005 (26). These incidents highlight the importance of long-term surveillance to understand the development of H5N1 influenza viruses.
The lack of sufficient information prior to the outbreak of 2003 has led to controversy regarding the wave 1 transmission pathway in Southeast Asia. Previously, analysis based on the available sequence data concluded that all of the H5N1 viruses detected in Southeast Asia had originated from either Guangdong or Hong Kong (22, 27, 34). To clarify this question and further understand the genesis and evolutionary pathway of H5N1 viruses, we characterized 73 H5N1 influenza viruses isolated from our surveillance program in southern China from January 2001 to February 2004. During that period H5N1 viruses evolved rapidly and were genetically diversified; however, antigenic and genetic analyses clearly show that transmission of H5N1 viruses between Yunnan and Vietnam and also between Hunan and Indonesia in 2002 and 2003 initiated the wave 1 outbreaks. The phylogenetic relationships between the viruses from southern China and Southeast Asia, along with their geographic distribution, suggest that poultry trade may be responsible for virus introduction into Vietnam, while the transmission route from Hunan to Indonesia could be either via migratory birds or poultry movement. The present study also revealed that extensive genetic reassortment not only resulted in increased genetic diversity of those HPAI H5N1 viruses but also caused subsequent outbreaks that directly led to the dissemination of these viruses both within China and to neighboring countries.
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Antigenic analysis. Virus isolates were subtyped by standard hemagglutination inhibition (HI) tests using a panel of the World Health Organization reference antisera, while the antigenic characteristics of the H5N1 influenza viruses were compared by an HI assay with five ferret polyclonal antisera and five monoclonal antibodies (MAbs) as previously described (15). The MAbs 3C8, 1F1B8, 10DD2, and 14D4 to the hemagglutinin (HA) of Ck/HK/YU22/02 were produced in our laboratories, and MAb CP176/26 to the HA of Ck/Pennsylvania/1/83 and the five ferret antisera were produced by the Department of Infectious Diseases at St. Jude Children's Research Hospital, Memphis, TN. The HI assay started at 1:40 dilutions for ferret antisera and at 1:100 dilutions for all MAbs.
To visualize similarity between the antigenic reaction patterns of different viruses, numerical analysis of HI titers was conducted by using PRIMER version 5.2.9 (PRIMER-E, Plymouth, United Kingdom). Titers in the HI assay below the detection level and greater than 12,800 for MAbs were converted to 0 and 25,600 in this analysis, respectively. The data were standardized and square-root transformed, and the Bray-Curtis coefficient (3) was used to construct a similarity matrix. Hierarchical agglomerative clustering with group average linking (28) was conducted, and a dendrogram was produced. Nonmetric multidimensional scaling (19) was also used to produce two- and three-dimensional ordinations over 100 iterations. The two-dimensional configuration with lowest overall stress is presented.
Phylogenetic and molecular analysis. To identify the possible source and understand the evolutionary pathway of the established HPAI H5N1 influenza virus in this region, 73 representative H5N1 strains isolated from our surveillance program from January 2001 to February 2004, together with all publicly available sequence data, were phylogenetically analyzed. Virus isolates were selected to represent each of the sampling sites at different positive sampling occasions (Table 1).
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TABLE 1. H5N1 viruses isolated from poultry in southern Chinaa
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Sequence similarity. To confirm the interrelationship of viruses isolated in southern China in 2002 and 2003 and viruses that were isolated in Southeast Asia during 2003, the similarity of each gene segment was determined using MEGA 4.0 (20). To calculate their similarity (p distances), full-length amino acid alignments of each gene segments were used.
Nucleotide sequence accession numbers. The nucleotide sequences obtained in the present study are available from GenBank under accession numbers CY028924 to CY029507.
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Antigenic analysis. Antigenic analysis of representative strains with MAbs and ferret antisera against reference H5 viruses demonstrated a diversity of reaction patterns (Table 2). In all, six antigenic patterns or groups were recognized for the viruses characterized in the present study (Table 2 and Fig. 1). The antigenic reaction pattern of two viruses isolated from Shantou in 2001 and 2002 (Dk/ST/195/01 and Ck/ST/28/02) were similar to Ck/Pennsylvania/1/83 (antigenic group I), as noted in our previous study (8) that indicates establishment from early aquatic H5 subtype virus. Two viruses (Dk/ST/1101/01 and Dk/YN/971/02) were similar to those viruses isolated from Hong Kong from 2002 and 2003 (antigenic group II). Interestingly, two representative viruses isolated from Hunan (Ck/HN/23/02 and Dk/HN/795/02) had reaction patterns similar to those of early Indonesian viruses (e.g., Ck/IDN/BL/03) (antigenic group IV), while two representative viruses from Yunnan (Ck/YN/1083/03 and Ck/YN/1251/03) had reaction patterns similar to those of clade 1 viruses isolated from Vietnam (e.g., Ck/VNM/27/03) (antigenic group V). The close relationships between the viruses from southern China and Southeast Asia were confirmed in the phylogenetic analyses (see below).
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TABLE 2. HI titers from antigenic analyses of influenza A H5N1 virusesa
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FIG. 1. Numerical analysis of HI titers (see Table 2) by nonmetric multidimensional ordination in two dimensions (A) and using hierarchical agglomerative clustering (B). Each antigenic group (circled) has been labeled on the cluster (see also Table 2).
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FIG. 2. Phylogenetic relationships of the HA (A) and NA (B) genes of representative influenza A viruses. The numbers above and below the branch nodes indicate neighbor-joining bootstrap values of 50% and Bayesian posterior probabilities of >95, respectively. Analyses were based on nucleotides 22 to 1,032 of the HA gene and nucleotides 1 to 1,090 of the NA gene. The HA and NA gene trees were rooted to duck/Hokkaido/51/96 and chicken/Scotland/59, respectively. Colors indicate viruses isolated from southern China (blue), Vietnam (red), and Indonesia (red). Scale bar, 0.01 nucleotide substitutions per site. Abbreviations: BHGs, bar-headed goose; BHgull, brown-headed gull; Ck, chicken; Cu, chukkar; Dk, duck; FJ, Fujian; Gf, Guinea fowl; Gs, goose; GD, Guangdong; GX, Guangxi; GY, Guiyang; HK, Hong Kong; HN, Hunan; IDN, Indonesia; JX, Jiangxi; Mall, mallard; MDk, migratory duck; MYS, Malaysia; NGA, Nigeria; Pa, partridge; Ph, pheasant; Qa, quail; QH, Qinghai; SCk, silky chicken; ST, Shantou; THA, Thailand; VNM, Vietnam; WDk, wild duck; YN, Yunnan.
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Phylogenetic analysis of neuraminidase (NA) gene revealed two major lineages derived from the Gs/GD-like NA (Fig. 2B). The first lineage included 11 viruses detected in Shantou (Guangdong) in 2001 and 2002 and that did not have a deletion in the stalk region of the NA. It is noteworthy that the NA gene of Dk/ST/195/01 has the same 20-amino-acid (aa) deletion in its NA stalk region that is seen in all H5N1 genotype Z viruses. The majority of the viruses from the present study belonged to a second lineage in which the viruses had a 20-aa deletion in the NA stalk and were isolated in different regions since 2001 (Fig. 2B). The close phylogenetic relationship between viruses from Hunan (e.g., Dk/HN/795/02) and Indonesia and between viruses from Yunnan (e.g., Ck/YN/1215/02) and Vietnam were maintained for the NA gene (Fig. 2B).
Phylogenetic analyses of the internal genes. Phylogenetic relationships of the internal genes of representative viruses indicated that frequent reassortment between cocirculating viruses had resulted in a number of novel genotypes being detected in poultry from 2001 to 2003 (Fig. 3). The majority of the novel genotypes were detected in Shantou (Guangdong) live-poultry markets and clustered with other influenza subtype viruses (H9N1 and H9N2), confirming the frequent reassortment of cocirculating viruses, as detected in our previous studies of other subtypes (7, 12, 14, 15, 38). All internal genes of Dk/ST/195/01 consistently grouped with Gs/GD/1/96, providing the first record of a Gs/GD-like virus with the 20-aa NA stalk deletion (Fig. 2 and 3). The internal gene segments of those Hunan (clade 2.3.1) and Yunnan (clade 2.4) viruses maintained monophyletic groups, a finding consistent with their HA and NA phylogenies.
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FIG. 3. Phylogenetic relationships of the PB2 (A), PB1 (B), PA (C), NP (D), M (E), and NS (F) genes of representative influenza A viruses. The numbers above and below the branch nodes indicate neighbor-joining bootstrap values of 50% and Bayesian posterior probabilities of >95, respectively. Analyses were based on nucleotides 986 to 2288, 1 to 1480, 1404 to 2151, 1 to 990, 1 to 998, and 1 to 842, respectively. All gene trees were rooted to A/equine/Prague/1/56 except PB1 and PA, which were midpoint rooted. Colors indicate viruses isolated from southern China (blue), Vietnam (red), and Indonesia (red). Scale bar, 0.01 nucleotide substitutions per site. Abbreviations: BHGs, bar-headed goose; BHgull, brown-headed gull; Ck, chicken; Cu, chukkar; Dk, duck; FJ, Fujian; Gf, Guinea fowl; Gs, goose; GD, Guangdong; GX, Guangxi; GY, Guiyang; HK, Hong Kong; HN, Hunan; IDN, Indonesia; JX, Jiangxi; Mall, mallard; MDk, migratory duck; MYS, Malaysia; NGA, Nigeria; Pa, partridge; Ph, pheasant; Qa, quail; QH, Qinghai; SCk, silky chicken; ST, Shantou; THA, Thailand; VNM, Vietnam; WDk, wild duck; YN, Yunnan.
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Amino acid similarity.
In order to evaluate the genetic similarity of the Yunnan/Vietnam and Hunan/Indonesia viruses, we calculated the mean percent similarities of deduced amino acid sequence for each of the gene segments between these two groups of viruses (Table 3). The similarities of the HA and the NA genes were, respectively, 98.1 and 98.9% for Yunnan/Vietnam and 99.6 and 99.2% for Hunan/Indonesia. The mean percentage similarity for Yunnan/Vietnam was
99.5% for all internal genes, while for Hunan/Indonesia the mean percentage similarity also was
99.5% for all internal genes except for the NS gene (98.01%). The extremely high similarities between these two virus groups confirm that the viruses isolated from Yunnan and Hunan during 2002 are the likely direct progenitors of those clade 1 viruses in Vietnam and clade 2.2 viruses in Indonesia, respectively.
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TABLE 3. Amino acid similarity of viruses isolated in southern China and Southeast Asia
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-2,3-NeuAcGal receptors (16, 29, 40). Other amino acid residues relevant to receptor-binding sites were identical to those of HK/156/97 and Gs/GD-like viruses in most isolates, but with some notable differences. Most of the progenitor Yunnan viruses characterized had an HA Ser129Leu substitution, which had been previously observed in clade 1 viruses (27), while the Hunan and Indonesian isolates maintained 129-Ser (Table 4) . In the NA amino acid sequences, all isolates characterized had 274-His, indicating sensitivity to oseltamivir (33). All eight clade 1 progenitor viruses from Yunnan had both the Leu26Ile and the Ser31Asn substitutions in the M2 protein (Table 4). These mutations may confer resistance to the amantadines, and both are present in all Vietnam clade 1 viruses characterized to date. No amantadine resistance mutations were observed in the two Hunan viruses that are progenitors to Indonesian isolates. |
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TABLE 4. Genetic signature of viruses isolated from southern China and Southeast Asiaa
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In the present study, our findings clearly demonstrate a direct precursor-descendant relationship between Yunnan and Vietnam (clade 1) and Hunan and Indonesia (clade 2.1) H5N1 viruses. All of the viruses from Hunan and Yunnan were isolated from November 2002 to April 2003, just prior to the onset of the first major transmission and outbreak wave in Southeast Asia that was first reported in November 2003 (22). These results suggest a transmission of H5N1 viruses from Yunnan to Vietnam and from Hunan to Indonesia.
The results of the antigenic analysis strongly correlated with the phylogenetic relationships. Molecular characterization at the amino acid level showed that the precursor-descendant viruses had almost identical amino acid sequences and identified consistent residue signatures between Yunnan-Vietnam and Hunan-Indonesia H5N1 viruses. For example, the dual Leu26Ile and Ser31Asn amantadine resistance mutations in the M2 protein of all Vietnam clade 1 viruses is also present in the Yunnan precursors (6). This provides evidence that these amantadine resistance mutations were present as early as 2002 in the viruses that were introduced into Vietnam to form clade 1, rather than resistance developing in Vietnam.
Since Yunnan shares a 600-km border with Vietnam (Fig. 4), it is reasonable to suggest that the virus was introduced into Vietnam through the trade of poultry at the border region. However, similar virus movement from Guangxi to Vietnam was observed in 2001 and 2005 and, more recently, with the Fujian-like variant (clade 2.3.1) (5, 26). Since we did not begin influenza surveillance in Guangxi until 2004, which also shares a long border with Vietnam (Fig. 4), we cannot exclude the possibility that viruses from Guangxi may also be clade 1 precursors.
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FIG. 4. Map of southern China showing the provinces under influenza surveillance and wave 1 transmission pathway of H5N1 viruses from southern China to other Southeast Asian regions.
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The HPAI H5N1 viruses have been prevalent in poultry for 11 years in southern China (26, 39). At present, these viruses are endemic and panzootic in different types of poultry, especially in aquatic birds in many countries across Asia, Africa, and Europe (5, 9, 26). Historically, 24 HPAI H5 and H7 outbreaks have been recorded worldwide (1), but the prevalence of Gs/GD-like H5N1 variants is the first and only example of an HPAI virus that has persisted in poultry for an extended period and spread over such a huge geographical area. The Gs/GD-like H5N1 virus is also the only HPAI virus that has undergone such extensive reassortment to generate so many different variants (5, 13, 22). Interestingly, previous studies indicate that all of these reassortants have been generated in China (5, 13, 22). Since many H9N2 and H6N1 variants have also been simultaneously recognized from southern China, a reasonable explanation is that the cocirculation of different subtypes of influenza viruses has promoted reassortment events (7, 38). However, influenza viruses are broadly prevalent in their natural reservoirs, wild aquatic birds, in most of the H5N1-affected regions (1, 35). Therefore, why the current H5N1 viruses circulating in other affected regions have not undergone reassortment with "local" viruses remains a fascinating question.
The continuing endemicity of HPAI H5N1 virus in countries across three continents has given rise to a persistent and unprecedented pandemic threat. Our present study, together with previous reports, has repeatedly demonstrated that the only way to identify and understand the genesis and transmission pathways of this infectious agent is through systematic influenza surveillance (5, 8, 13, 15, 22, 26, 27). More importantly, systematic influenza surveillance can provide critical information in determining effective disease control measures. The successful intervention and control of HPAI H5N1 in Hong Kong in the last decade provides the best example of this.
Published ahead of print on 23 January 2008. ![]()
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