One hundred years of influenza A evolution
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
Standard
One hundred years of influenza A evolution. / Nielsen, Bjarke Frost; Berrig, Christian; Grenfell, Bryan T.; Andreasen, Viggo.
I: Theoretical Population Biology, Bind 159, 31.07.2024, s. 25-34.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
Harvard
APA
Vancouver
Author
Bibtex
}
RIS
TY - JOUR
T1 - One hundred years of influenza A evolution
AU - Nielsen, Bjarke Frost
AU - Berrig, Christian
AU - Grenfell, Bryan T.
AU - Andreasen, Viggo
N1 - Publisher Copyright: © 2024
PY - 2024/7/31
Y1 - 2024/7/31
N2 - Leveraging the simplicity of nucleotide mismatch distributions, we provide an intuitive window into the evolution of the human influenza A ‘nonstructural’ (NS) gene segment. In an analysis suggested by the eminent Danish biologist Freddy B. Christiansen, we illustrate the existence of a continuous genetic “backbone” of influenza A NS sequences, steadily increasing in nucleotide distance to the 1918 root over more than a century. The 2009 influenza A/H1N1 pandemic represents a clear departure from this enduring genetic backbone. Utilizing nucleotide distance maps and phylogenetic analyses, we illustrate remaining uncertainties regarding the origin of the 2009 pandemic, highlighting the complexity of influenza evolution. The NS segment is interesting precisely because it experiences less pervasive positive selection, and departs less strongly from neutral evolution than e.g. the HA antigen. Consequently, sudden deviations from neutral diversification can indicate changes in other genes via the hitchhiking effect. Our approach employs two measures based on nucleotide mismatch counts to analyze the evolutionary dynamics of the NS gene segment. The rooted Hamming map of distances between a reference sequence and all other sequences over time, and the unrooted temporal Hamming distribution which captures the distribution of genotypic distances between simultaneously circulating viruses, thereby revealing patterns of nucleotide diversity and epi-evolutionary dynamics.
AB - Leveraging the simplicity of nucleotide mismatch distributions, we provide an intuitive window into the evolution of the human influenza A ‘nonstructural’ (NS) gene segment. In an analysis suggested by the eminent Danish biologist Freddy B. Christiansen, we illustrate the existence of a continuous genetic “backbone” of influenza A NS sequences, steadily increasing in nucleotide distance to the 1918 root over more than a century. The 2009 influenza A/H1N1 pandemic represents a clear departure from this enduring genetic backbone. Utilizing nucleotide distance maps and phylogenetic analyses, we illustrate remaining uncertainties regarding the origin of the 2009 pandemic, highlighting the complexity of influenza evolution. The NS segment is interesting precisely because it experiences less pervasive positive selection, and departs less strongly from neutral evolution than e.g. the HA antigen. Consequently, sudden deviations from neutral diversification can indicate changes in other genes via the hitchhiking effect. Our approach employs two measures based on nucleotide mismatch counts to analyze the evolutionary dynamics of the NS gene segment. The rooted Hamming map of distances between a reference sequence and all other sequences over time, and the unrooted temporal Hamming distribution which captures the distribution of genotypic distances between simultaneously circulating viruses, thereby revealing patterns of nucleotide diversity and epi-evolutionary dynamics.
KW - Hamming distance
KW - Influenza evolution
KW - Nonstructural gene
KW - NS gene
KW - Nucleotide distance
KW - Viral diversity
KW - Viral evolution
U2 - 10.1016/j.tpb.2024.07.005
DO - 10.1016/j.tpb.2024.07.005
M3 - Journal article
C2 - 39094981
AN - SCOPUS:85200597103
VL - 159
SP - 25
EP - 34
JO - Theoretical Population Biology
JF - Theoretical Population Biology
SN - 0040-5809
ER -
ID: 402399404