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Local-scale diversity and between-year "frozen evolution" of avian influenza A viruses in nature.

Nagy A, Cerníková L, Jiřincová H, Havlíčková M, Horníčková J - PLoS ONE (2014)

Bottom Line: Moreover, the H6, H11, and N2 segments belonged to two distinguishable sub-lineages.Interestingly the IAV, with the H6N9 subtype, was re-detected a year later in a genetically unchanged form in the close proximity of the original sampling locality.The persistence of the H6N9 IAV in various abiotic and biotic environmental components was also discussed.

View Article: PubMed Central - PubMed

Affiliation: State Veterinary Institute Prague, National Reference Laboratory for Avian Influenza and Newcastle Disease, Laboratory of Molecular Methods, Prague, Czech Republic; National Institute of Public Health, Centre for Epidemiology and Microbiology, National Reference Laboratory for Influenza, Prague, Czech Republic.

ABSTRACT
Influenza A virus (IAV) in wild bird reservoir hosts is characterized by the perpetuation in a plethora of subtype and genotype constellations. Multiyear monitoring studies carried out during the last two decades worldwide have provided a large body of knowledge regarding the ecology of IAV in wild birds. Nevertheless, other issues of avian IAV evolution have not been fully elucidated, such as the complexity and dynamics of genetic interactions between the co-circulating IAV genomes taking place at a local-scale level or the phenomenon of frozen evolution. We investigated the IAV diversity in a mallard population residing in a single pond in the Czech Republic. Despite the relative small number of samples collected, remarkable heterogeneity was revealed with four different IAV subtype combinations, H6N2, H6N9, H11N2, and H11N9, and six genomic constellations in co-circulation. Moreover, the H6, H11, and N2 segments belonged to two distinguishable sub-lineages. A reconstruction of the pattern of genetic reassortment revealed direct parent-progeny relationships between the H6N2, H11N9 and H6N9 viruses. Interestingly the IAV, with the H6N9 subtype, was re-detected a year later in a genetically unchanged form in the close proximity of the original sampling locality. The almost absolute nucleotide sequence identity of all the respective genomic segments between the two H6N9 viruses indicates frozen evolution as a result of prolonged conservation in the environment. The persistence of the H6N9 IAV in various abiotic and biotic environmental components was also discussed.

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Segment identity matrix (SIM).The SIM was generated by plotting the influenza A virus (IAV) genomes against each other, with the relationships between the segments derived from the phylogenetic trees (Figure 1a–j) highlighted with colored pixels. The virus nomenclature corresponds to that in Table 1. The deduced genome constellations in the SIM were represented by columns 1–13 and the pixels within the columns were aligned according to the conventional listing of the IAV genome segments (from left to right: PB2, PB1, PA, HA, NP, NA, MP, and NS). The color scheme for the segments is given at the bottom of the figure and corresponds to the tables S3 in File S1. Empty pixels mean unknown or undetermined. Figures: 2a, the entire SIM; 2b overview of the genomic diversity of locality P IAV. For information regarding the Figures 2c-f please refer to the text.
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pone-0103053-g002: Segment identity matrix (SIM).The SIM was generated by plotting the influenza A virus (IAV) genomes against each other, with the relationships between the segments derived from the phylogenetic trees (Figure 1a–j) highlighted with colored pixels. The virus nomenclature corresponds to that in Table 1. The deduced genome constellations in the SIM were represented by columns 1–13 and the pixels within the columns were aligned according to the conventional listing of the IAV genome segments (from left to right: PB2, PB1, PA, HA, NP, NA, MP, and NS). The color scheme for the segments is given at the bottom of the figure and corresponds to the tables S3 in File S1. Empty pixels mean unknown or undetermined. Figures: 2a, the entire SIM; 2b overview of the genomic diversity of locality P IAV. For information regarding the Figures 2c-f please refer to the text.

Mentions: The number assigned for each strain corresponds to Figure 2.


Local-scale diversity and between-year "frozen evolution" of avian influenza A viruses in nature.

Nagy A, Cerníková L, Jiřincová H, Havlíčková M, Horníčková J - PLoS ONE (2014)

Segment identity matrix (SIM).The SIM was generated by plotting the influenza A virus (IAV) genomes against each other, with the relationships between the segments derived from the phylogenetic trees (Figure 1a–j) highlighted with colored pixels. The virus nomenclature corresponds to that in Table 1. The deduced genome constellations in the SIM were represented by columns 1–13 and the pixels within the columns were aligned according to the conventional listing of the IAV genome segments (from left to right: PB2, PB1, PA, HA, NP, NA, MP, and NS). The color scheme for the segments is given at the bottom of the figure and corresponds to the tables S3 in File S1. Empty pixels mean unknown or undetermined. Figures: 2a, the entire SIM; 2b overview of the genomic diversity of locality P IAV. For information regarding the Figures 2c-f please refer to the text.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4116140&req=5

pone-0103053-g002: Segment identity matrix (SIM).The SIM was generated by plotting the influenza A virus (IAV) genomes against each other, with the relationships between the segments derived from the phylogenetic trees (Figure 1a–j) highlighted with colored pixels. The virus nomenclature corresponds to that in Table 1. The deduced genome constellations in the SIM were represented by columns 1–13 and the pixels within the columns were aligned according to the conventional listing of the IAV genome segments (from left to right: PB2, PB1, PA, HA, NP, NA, MP, and NS). The color scheme for the segments is given at the bottom of the figure and corresponds to the tables S3 in File S1. Empty pixels mean unknown or undetermined. Figures: 2a, the entire SIM; 2b overview of the genomic diversity of locality P IAV. For information regarding the Figures 2c-f please refer to the text.
Mentions: The number assigned for each strain corresponds to Figure 2.

Bottom Line: Moreover, the H6, H11, and N2 segments belonged to two distinguishable sub-lineages.Interestingly the IAV, with the H6N9 subtype, was re-detected a year later in a genetically unchanged form in the close proximity of the original sampling locality.The persistence of the H6N9 IAV in various abiotic and biotic environmental components was also discussed.

View Article: PubMed Central - PubMed

Affiliation: State Veterinary Institute Prague, National Reference Laboratory for Avian Influenza and Newcastle Disease, Laboratory of Molecular Methods, Prague, Czech Republic; National Institute of Public Health, Centre for Epidemiology and Microbiology, National Reference Laboratory for Influenza, Prague, Czech Republic.

ABSTRACT
Influenza A virus (IAV) in wild bird reservoir hosts is characterized by the perpetuation in a plethora of subtype and genotype constellations. Multiyear monitoring studies carried out during the last two decades worldwide have provided a large body of knowledge regarding the ecology of IAV in wild birds. Nevertheless, other issues of avian IAV evolution have not been fully elucidated, such as the complexity and dynamics of genetic interactions between the co-circulating IAV genomes taking place at a local-scale level or the phenomenon of frozen evolution. We investigated the IAV diversity in a mallard population residing in a single pond in the Czech Republic. Despite the relative small number of samples collected, remarkable heterogeneity was revealed with four different IAV subtype combinations, H6N2, H6N9, H11N2, and H11N9, and six genomic constellations in co-circulation. Moreover, the H6, H11, and N2 segments belonged to two distinguishable sub-lineages. A reconstruction of the pattern of genetic reassortment revealed direct parent-progeny relationships between the H6N2, H11N9 and H6N9 viruses. Interestingly the IAV, with the H6N9 subtype, was re-detected a year later in a genetically unchanged form in the close proximity of the original sampling locality. The almost absolute nucleotide sequence identity of all the respective genomic segments between the two H6N9 viruses indicates frozen evolution as a result of prolonged conservation in the environment. The persistence of the H6N9 IAV in various abiotic and biotic environmental components was also discussed.

Show MeSH
Related in: MedlinePlus