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A new piece in the puzzle of the novel avian-origin influenza A (H7N9) virus.

Lee RT, Gunalan V, Van TD, Le LT, Eisenhaber F, Maurer-Stroh S - Biol. Direct (2013)

Bottom Line: Using phylogenetic analysis on newly available sequences, we characterize A/chicken/Jiangsu/RD5/2013(H10N9) as currently closest precursor strain for the NA segment in the novel avian-origin H7N9 virus responsible for an outbreak in China.We also show that the internal segments of this precursor strain are closely related to those of the presumed precursor for the HA segment, A/duck/Zhejiang/12/2011(H7N3), which indicates that the sources of both HA and NA donors for the reassortant virus are of regional and not migratory-bird origin and highlights the role of chicken already in the early reassortment events.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Institute (BII), Agency for Science Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix Building, 138671 Singapore, Singapore. sebastianms@bii.a-star.edu.sg.

ABSTRACT
Using phylogenetic analysis on newly available sequences, we characterize A/chicken/Jiangsu/RD5/2013(H10N9) as currently closest precursor strain for the NA segment in the novel avian-origin H7N9 virus responsible for an outbreak in China. We also show that the internal segments of this precursor strain are closely related to those of the presumed precursor for the HA segment, A/duck/Zhejiang/12/2011(H7N3), which indicates that the sources of both HA and NA donors for the reassortant virus are of regional and not migratory-bird origin and highlights the role of chicken already in the early reassortment events.

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A new JS5-like(H10N9) precursor is the closest NA segment relative to the 2013 H7N9 and its internal genes are closely related to the HA donor ZJ12-like(H7N3). (A) Maximum likelihood phylogenetic tree of NA gene segments shows the NA from the novel avian-origin H7N9 virus (green) is more closely related to JS5-like (H10N9, red) than KO14-like (H7N9, blue) and precursors proposed by Lam et al. (pink). Methods: The H7N9 outbreak sequences were downloaded from GISAID’s EpiFlu™ database on June 13th 2013 (detailed acknowledgment in additional file 3) and complemented with best BLAST hits from Genbank as well as selected older representative strains as outgroup. The sequences were aligned with MAFFT using the L-INS-I parameters, the alignment was checked in Jalview and a nonredundant subset with less than 100% identity was retained. The phylogenetic tree was generated in PhyML with a gamma-distributed HKY85 substitution model. Positions with gaps and missing data were completely deleted, and 1000-replicate bootstrapping was performed; an average of these replicates is shown. (B), (C) Phylogenetic analysis of internal segments amongst H7N9 strains and other closely related strains shows close identity between the ZJ12-like(H7N3, dark blue) HA donor and JS5-like(H10N9, red) NA donor. Maximum-likelihood trees using nucleotide sequences of (B) NP and (C) PB2 gene segments were generated as described before. Reassortant H7N9 strains (green), presumed BJ16-like internal segment donor (purple), previously postulated KO14-like (H7N9) NA donor (blue), newly proposed N9 relative from Lam et al. (pink) and internal gene relatives from Wu et al. (dark red) are also indicated. (D) The NA gene segment of the reassortant H7N9 virus derives from JS5-like (H10N9, red), the HA gene segment from ZJ12-like (H7N3, blue) and the internal segments derive from BJ16-like or ZJ04-like (H9N2, orange) strains.
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Figure 1: A new JS5-like(H10N9) precursor is the closest NA segment relative to the 2013 H7N9 and its internal genes are closely related to the HA donor ZJ12-like(H7N3). (A) Maximum likelihood phylogenetic tree of NA gene segments shows the NA from the novel avian-origin H7N9 virus (green) is more closely related to JS5-like (H10N9, red) than KO14-like (H7N9, blue) and precursors proposed by Lam et al. (pink). Methods: The H7N9 outbreak sequences were downloaded from GISAID’s EpiFlu™ database on June 13th 2013 (detailed acknowledgment in additional file 3) and complemented with best BLAST hits from Genbank as well as selected older representative strains as outgroup. The sequences were aligned with MAFFT using the L-INS-I parameters, the alignment was checked in Jalview and a nonredundant subset with less than 100% identity was retained. The phylogenetic tree was generated in PhyML with a gamma-distributed HKY85 substitution model. Positions with gaps and missing data were completely deleted, and 1000-replicate bootstrapping was performed; an average of these replicates is shown. (B), (C) Phylogenetic analysis of internal segments amongst H7N9 strains and other closely related strains shows close identity between the ZJ12-like(H7N3, dark blue) HA donor and JS5-like(H10N9, red) NA donor. Maximum-likelihood trees using nucleotide sequences of (B) NP and (C) PB2 gene segments were generated as described before. Reassortant H7N9 strains (green), presumed BJ16-like internal segment donor (purple), previously postulated KO14-like (H7N9) NA donor (blue), newly proposed N9 relative from Lam et al. (pink) and internal gene relatives from Wu et al. (dark red) are also indicated. (D) The NA gene segment of the reassortant H7N9 virus derives from JS5-like (H10N9, red), the HA gene segment from ZJ12-like (H7N3, blue) and the internal segments derive from BJ16-like or ZJ04-like (H9N2, orange) strains.

Mentions: The outbreak of a highly pathogenic novel avian-origin influenza A (H7N9) virus with multiple human fatalities earlier this year in the eastern provinces of China was a wake-up call for the pandemic potential of animal-hosted influenza strains and new subtypes outside of the typical surveillance focus. A remarkably efficient regional and international response resulted in a rapid genomic characterization including hypotheses on the evolutionary and reassortment history of this new virus [1-3]. The consensus picture that emerged in the first publications was that while the internal segments were of BJ16-like (H9N2) origin (e.g. A/brambling/Beijing/16/2012(H9N2)), the reassortant H7N9 virus received its hemagglutinin (HA) segment from ZJ12-like (H7N3) (e.g. A/duck/Zhejiang/12/2011(H7N3)) and its neuraminidase (NA) segment from KO14-like (H7N9) (e.g. A/wild bird/Korea/A14/2011(H7N9)) viruses, respectively. While this manuscript was submitted, two related new works were published and are relevant for our discussion. Lam et al.[4] reported sequence results from 388 new isolates sampled from domestic waterfowl and poultry in the region during the outbreak and Wu et al.[5] shed further light on different H9N2 sources of the internal gene segments. Lam et al. also highlight H11N9 and H2N9 precursors for the NA segment that were more closely related to the H7N9 causing recent human infections than the initially mentioned KO14-like (H7N9) viruses. However, we would like to draw attention to a new development which is the identification of a different closest precursor strain for the NA segment by Su et al.[6] which became available only after the first analyses were published but was not mentioned by Lam et al.. Contemporary to the H7N9 outbreak, A/chicken/Jiangsu/RD5/2013(H10N9) was collected in March 2013 from a live poultry market in Jiangsu and the genome submitted to Genbank [7] in May by Su et al. who also reported a quick characterization without phylogenetic analysis [6]. We have examined the detailed phylogenetic relationship of the NA of this new strain (hereafter referred to as JS5-like (H10N9)) using a maximum-likelihood tree (employing a gamma-distributed HKY85 substitution model [8] and 1000-replicate bootstrapping [9]) using MAFFT [10], Jalview [11] and PhyML [12] (Figure 1A) and confirmed that this JS5-like N9 NA was indeed more closely related to the H7N9 outbreak sequences than the previously postulated closest KO14-like (H7N9) ancestor and the H11N9 or H2N9 strains listed by Lam et al.. Notably, like KO14-like (H7N9) also JS5-like (H10N9) did not yet have the NA stalk deletion seen in the novel avian-origin influenza A (H7N9). In order to confirm the results of the maximum likelihood analysis, the same set of sequences was also analyzed using Neighbour-joining performed in MEGA5.2 [13-15] and Bayesian Markov Chain Monte Carlo analysis performed in BEAST [16] (see Additional file 1). The results from all analyses using different phylogenetic approaches identified the same JS5-like (H10N9) virus as being the closest ancestor to the reassortant NA, and hence served to validate the initial findings.


A new piece in the puzzle of the novel avian-origin influenza A (H7N9) virus.

Lee RT, Gunalan V, Van TD, Le LT, Eisenhaber F, Maurer-Stroh S - Biol. Direct (2013)

A new JS5-like(H10N9) precursor is the closest NA segment relative to the 2013 H7N9 and its internal genes are closely related to the HA donor ZJ12-like(H7N3). (A) Maximum likelihood phylogenetic tree of NA gene segments shows the NA from the novel avian-origin H7N9 virus (green) is more closely related to JS5-like (H10N9, red) than KO14-like (H7N9, blue) and precursors proposed by Lam et al. (pink). Methods: The H7N9 outbreak sequences were downloaded from GISAID’s EpiFlu™ database on June 13th 2013 (detailed acknowledgment in additional file 3) and complemented with best BLAST hits from Genbank as well as selected older representative strains as outgroup. The sequences were aligned with MAFFT using the L-INS-I parameters, the alignment was checked in Jalview and a nonredundant subset with less than 100% identity was retained. The phylogenetic tree was generated in PhyML with a gamma-distributed HKY85 substitution model. Positions with gaps and missing data were completely deleted, and 1000-replicate bootstrapping was performed; an average of these replicates is shown. (B), (C) Phylogenetic analysis of internal segments amongst H7N9 strains and other closely related strains shows close identity between the ZJ12-like(H7N3, dark blue) HA donor and JS5-like(H10N9, red) NA donor. Maximum-likelihood trees using nucleotide sequences of (B) NP and (C) PB2 gene segments were generated as described before. Reassortant H7N9 strains (green), presumed BJ16-like internal segment donor (purple), previously postulated KO14-like (H7N9) NA donor (blue), newly proposed N9 relative from Lam et al. (pink) and internal gene relatives from Wu et al. (dark red) are also indicated. (D) The NA gene segment of the reassortant H7N9 virus derives from JS5-like (H10N9, red), the HA gene segment from ZJ12-like (H7N3, blue) and the internal segments derive from BJ16-like or ZJ04-like (H9N2, orange) strains.
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Figure 1: A new JS5-like(H10N9) precursor is the closest NA segment relative to the 2013 H7N9 and its internal genes are closely related to the HA donor ZJ12-like(H7N3). (A) Maximum likelihood phylogenetic tree of NA gene segments shows the NA from the novel avian-origin H7N9 virus (green) is more closely related to JS5-like (H10N9, red) than KO14-like (H7N9, blue) and precursors proposed by Lam et al. (pink). Methods: The H7N9 outbreak sequences were downloaded from GISAID’s EpiFlu™ database on June 13th 2013 (detailed acknowledgment in additional file 3) and complemented with best BLAST hits from Genbank as well as selected older representative strains as outgroup. The sequences were aligned with MAFFT using the L-INS-I parameters, the alignment was checked in Jalview and a nonredundant subset with less than 100% identity was retained. The phylogenetic tree was generated in PhyML with a gamma-distributed HKY85 substitution model. Positions with gaps and missing data were completely deleted, and 1000-replicate bootstrapping was performed; an average of these replicates is shown. (B), (C) Phylogenetic analysis of internal segments amongst H7N9 strains and other closely related strains shows close identity between the ZJ12-like(H7N3, dark blue) HA donor and JS5-like(H10N9, red) NA donor. Maximum-likelihood trees using nucleotide sequences of (B) NP and (C) PB2 gene segments were generated as described before. Reassortant H7N9 strains (green), presumed BJ16-like internal segment donor (purple), previously postulated KO14-like (H7N9) NA donor (blue), newly proposed N9 relative from Lam et al. (pink) and internal gene relatives from Wu et al. (dark red) are also indicated. (D) The NA gene segment of the reassortant H7N9 virus derives from JS5-like (H10N9, red), the HA gene segment from ZJ12-like (H7N3, blue) and the internal segments derive from BJ16-like or ZJ04-like (H9N2, orange) strains.
Mentions: The outbreak of a highly pathogenic novel avian-origin influenza A (H7N9) virus with multiple human fatalities earlier this year in the eastern provinces of China was a wake-up call for the pandemic potential of animal-hosted influenza strains and new subtypes outside of the typical surveillance focus. A remarkably efficient regional and international response resulted in a rapid genomic characterization including hypotheses on the evolutionary and reassortment history of this new virus [1-3]. The consensus picture that emerged in the first publications was that while the internal segments were of BJ16-like (H9N2) origin (e.g. A/brambling/Beijing/16/2012(H9N2)), the reassortant H7N9 virus received its hemagglutinin (HA) segment from ZJ12-like (H7N3) (e.g. A/duck/Zhejiang/12/2011(H7N3)) and its neuraminidase (NA) segment from KO14-like (H7N9) (e.g. A/wild bird/Korea/A14/2011(H7N9)) viruses, respectively. While this manuscript was submitted, two related new works were published and are relevant for our discussion. Lam et al.[4] reported sequence results from 388 new isolates sampled from domestic waterfowl and poultry in the region during the outbreak and Wu et al.[5] shed further light on different H9N2 sources of the internal gene segments. Lam et al. also highlight H11N9 and H2N9 precursors for the NA segment that were more closely related to the H7N9 causing recent human infections than the initially mentioned KO14-like (H7N9) viruses. However, we would like to draw attention to a new development which is the identification of a different closest precursor strain for the NA segment by Su et al.[6] which became available only after the first analyses were published but was not mentioned by Lam et al.. Contemporary to the H7N9 outbreak, A/chicken/Jiangsu/RD5/2013(H10N9) was collected in March 2013 from a live poultry market in Jiangsu and the genome submitted to Genbank [7] in May by Su et al. who also reported a quick characterization without phylogenetic analysis [6]. We have examined the detailed phylogenetic relationship of the NA of this new strain (hereafter referred to as JS5-like (H10N9)) using a maximum-likelihood tree (employing a gamma-distributed HKY85 substitution model [8] and 1000-replicate bootstrapping [9]) using MAFFT [10], Jalview [11] and PhyML [12] (Figure 1A) and confirmed that this JS5-like N9 NA was indeed more closely related to the H7N9 outbreak sequences than the previously postulated closest KO14-like (H7N9) ancestor and the H11N9 or H2N9 strains listed by Lam et al.. Notably, like KO14-like (H7N9) also JS5-like (H10N9) did not yet have the NA stalk deletion seen in the novel avian-origin influenza A (H7N9). In order to confirm the results of the maximum likelihood analysis, the same set of sequences was also analyzed using Neighbour-joining performed in MEGA5.2 [13-15] and Bayesian Markov Chain Monte Carlo analysis performed in BEAST [16] (see Additional file 1). The results from all analyses using different phylogenetic approaches identified the same JS5-like (H10N9) virus as being the closest ancestor to the reassortant NA, and hence served to validate the initial findings.

Bottom Line: Using phylogenetic analysis on newly available sequences, we characterize A/chicken/Jiangsu/RD5/2013(H10N9) as currently closest precursor strain for the NA segment in the novel avian-origin H7N9 virus responsible for an outbreak in China.We also show that the internal segments of this precursor strain are closely related to those of the presumed precursor for the HA segment, A/duck/Zhejiang/12/2011(H7N3), which indicates that the sources of both HA and NA donors for the reassortant virus are of regional and not migratory-bird origin and highlights the role of chicken already in the early reassortment events.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Institute (BII), Agency for Science Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix Building, 138671 Singapore, Singapore. sebastianms@bii.a-star.edu.sg.

ABSTRACT
Using phylogenetic analysis on newly available sequences, we characterize A/chicken/Jiangsu/RD5/2013(H10N9) as currently closest precursor strain for the NA segment in the novel avian-origin H7N9 virus responsible for an outbreak in China. We also show that the internal segments of this precursor strain are closely related to those of the presumed precursor for the HA segment, A/duck/Zhejiang/12/2011(H7N3), which indicates that the sources of both HA and NA donors for the reassortant virus are of regional and not migratory-bird origin and highlights the role of chicken already in the early reassortment events.

Show MeSH
Related in: MedlinePlus